From ac8307a7112b0c6d763c9470213ad95fcb722ce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Apr 2023 21:21:28 +0200 Subject: [PATCH 01/41] add page with overview of changes in EasyBuild v5.0 (WIP) --- docs/easybuild-v5/overview-of-changes.md | 93 ++++++++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 docs/easybuild-v5/overview-of-changes.md diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md new file mode 100644 index 000000000..62077eaa7 --- /dev/null +++ b/docs/easybuild-v5/overview-of-changes.md @@ -0,0 +1,93 @@ +# Overview of changes in EasyBuild version 5.0 {: #overview } + +This page provides a concise overview of the most prominent changes in EasyBuild version 5.0, +which can be categorized as: + +* [Significant enhancements][significant_enhancements] +* [Backward-incompatible changes][backwards_incompatible] +* [Deprecated functionality][deprecated] + +For in-depth details on a particular change, see the pull requests that are linked from each of the subsections below. + +!!! warning + + EasyBuild 5.0 is currently still under development, via the `5.0.x` branches in the EasyBuild GitHub repositories. + + We intend to update this page regularly as the planned changes are being implemented. + + +--- + +## Significant enhancements in EasyBuild v5.0 {: #significant_enhancements } + +Various significant enhancements are included in EasyBuild v5.0, including: + +* *(no significant enhancements implemented so far in the `5.0.x` branches)* + +--- + +## Backwards-incompatible changes in EasyBuild v4.0 {: #backwards_incompatible } + +A number of *backwards-incompatible* changes are being made in EasyBuild v5.0: + +* [Support for Python 2.7 is removed -- Python 3.6+ is required][py36] +* [Deprecated EasyBuild bootstrap script is removed][bootstrap_script] +* [Experimental support for the .yeb easyconfig format is removed][yeb] + +--- + +### Support for Python 2.7 is removed -- Python 3.6+ is required {: #py36 } + +EasyBuild 5.0 requires Python >= 3.6 to run. + +Running EasyBuild with Python 2.7 or a Python 3 version older than Python 3.6 is no longer supported. + +Trying to run EasyBuild with a Python version that is too old will result in an error: +``` +ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 3.6+) +``` + +Python 2.7 has been [end-of-life since 1 Jan 2020](https://www.python.org/doc/sunset-python-2), +and dropping compatibility with Python 2.7 and Python 3.5 enabled some significant code cleanup +(see [easybuild-framework PR #4229](https://github.com/easybuilders/easybuild-framework/pull/4229)). + +The [results of the 6th EasyBuild User Survey (2022)](https://easybuild.io/user_survey) show that the impact of +this breaking change on the EasyBuild community should be very limited, since: + +* Only ~13% of survey participants were still running EasyBuild on top of Python 2.7; +* No survey participants reported using Python 3.5; +* Over 85% of survey participants reported using Python 3.6, or a more recent version of Python 3; +* Only 3 out of 118 survey participants (~2.5%) reported that dropping support for running EasyBuild + on top of Python 2 would be *problematic* for them; + +Along with actively removing code that was only required to retain compatibility with Python 2.7 or 3.5, +the `easybuild.tools.py2vs3` module that was introduced to facilitate supporting both Python 2.7 and Python 3 +has been deprecated ([see also below][py2vs3]). + +--- + +### Deprecated EasyBuild bootstrap script is removed {: #bootstrap_script } + +[easybuild-framework PR #4233](https://github.com/easybuilders/easybuild-framework/pull/4233) + +--- + +### Experimental support for the .yeb easyconfig format is removed {: #yeb } + +[easybuild-framework PR #4237](https://github.com/easybuilders/easybuild-framework/pull/4237) + +--- + +## Deprecated functionality in EasyBuild v5.0 {: #deprecated } + +Some functionality is being deprecated in EasyBuild v5.0, and will no longer be supported in EasyBuild v6.0: + +* [`easybuild.tools.py2vs3` module][py2vs3] + +If you trigger any deprecated functionality, a warning message will be printed. + +--- + +### `easybuild.tools.py2vs3` module {: #py2vs3 } + +[easybuild-framework PR #4229](https://github.com/easybuilders/easybuild-framework/pull/4229) From 0b7c61c88c9a459cfb7b02dd1fd0986bc2488c74 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 14 May 2023 11:27:14 +0100 Subject: [PATCH 02/41] planned and proposed changes, and py2vs3 info --- docs/easybuild-v5/overview-of-changes.md | 71 ++++++++++++++++++++++-- 1 file changed, 66 insertions(+), 5 deletions(-) diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md index 62077eaa7..a634ec200 100644 --- a/docs/easybuild-v5/overview-of-changes.md +++ b/docs/easybuild-v5/overview-of-changes.md @@ -1,5 +1,11 @@ # Overview of changes in EasyBuild version 5.0 {: #overview } +!!! warning + EasyBuild 5.0 is currently still under development, via the `5.0.x` branches in the EasyBuild GitHub repositories. + + We intend to update this page regularly as the [planned changes][eb5_plans] are being implemented and when there + are [proposed changes][eb5_proposals] where we are requesting community feedback. + This page provides a concise overview of the most prominent changes in EasyBuild version 5.0, which can be categorized as: @@ -9,12 +15,32 @@ which can be categorized as: For in-depth details on a particular change, see the pull requests that are linked from each of the subsections below. -!!! warning +--- - EasyBuild 5.0 is currently still under development, via the `5.0.x` branches in the EasyBuild GitHub repositories. +## Planned and proposed changes for EasyBuild v5.0 {: #eb5_changes } + +At the [EasyBuild User Meetin](https://easybuild.io/eum23), Simon Branford set out the +[roadmap for EasyBuild v5.0](https://easybuild.io/eum23/#easybuild5). + +### Proposed changes for EasyBuild v5.0 {: #eb5_proposals } - We intend to update this page regularly as the planned changes are being implemented. +There are several proposed changes where the EasyBuild maintainers are seeking community feedback. If you wish to provide +feedback then please comment in the GitHub issue for the proposal. +* Minimum supported Lmod Version: _proposal forthcoming_ +* Toolchain Support Policy: _proposal forthcoming_ + +### Planned changes for EasyBuild v5.0 {: #eb5_plans } + +* [enable `--trace` by default](https://github.com/easybuilders/easybuild-framework/pull/4250) + +!!! note + This list is the major planned changes. It is not intended to be a complete list of all changes that are + planned for EasyBuild v5.0. + +### Tracking development of EasyBuild v5.0 + +* [GitHub Project board for EasyBuild v5.0](https://github.com/orgs/easybuilders/projects/18) --- @@ -43,6 +69,7 @@ EasyBuild 5.0 requires Python >= 3.6 to run. Running EasyBuild with Python 2.7 or a Python 3 version older than Python 3.6 is no longer supported. Trying to run EasyBuild with a Python version that is too old will result in an error: + ``` ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 3.6+) ``` @@ -68,13 +95,16 @@ has been deprecated ([see also below][py2vs3]). ### Deprecated EasyBuild bootstrap script is removed {: #bootstrap_script } -[easybuild-framework PR #4233](https://github.com/easybuilders/easybuild-framework/pull/4233) +The EasyBuild bootstrap script has been removed (see [easybuild-framework PR #4233](https://github.com/easybuilders/easybuild-framework/pull/4233)). +Please see the [installation page][installation] for the suggested methods for installing EasyBuild. --- ### Experimental support for the .yeb easyconfig format is removed {: #yeb } -[easybuild-framework PR #4237](https://github.com/easybuilders/easybuild-framework/pull/4237) +Support for the experimental `.yeb` easyconfig format has been removed (see [easybuild-framework PR #4237](https://github.com/easybuilders/easybuild-framework/pull/4237)). +This format allowed easyconfigs to be specified in YAML. However, there has been no recent development of this +format and little suggestion that anyone was using it. --- @@ -91,3 +121,34 @@ If you trigger any deprecated functionality, a warning message will be printed. ### `easybuild.tools.py2vs3` module {: #py2vs3 } [easybuild-framework PR #4229](https://github.com/easybuilders/easybuild-framework/pull/4229) + +The following table lists the changes required to replace imports from the the `py2vs3` module. + +| `from easybuild.tools.py2vs3 import ...` | Replacement | +|--|--| +| `ascii_letters` | `from string import ascii_letters` | +| `ascii_lowercase` | `from string import ascii_lowercase` | +| `build_opener` | `from urllib.request import build_opener` | +| `ConfigParser` | `from configparser import ConfigParser` | +| `configparser` | `import configparser` | +| `create_base_metaclass` | `from easybuild.base.wrapper import create_base_metaclass` | +| `extract_method_name` | No import required. Replace `extract_method_name(method)` with `'_'.join(method.__code__.co_names)` | +| `HTMLParser` | `from html.parser import HTMLParser` | +| `HTTPError` | `from urllib.request import HTTPError` | +| `HTTPSHandler` | `from urllib.request import HTTPSHandler` | +| `json_loads` | `from json import loads` and rename `json_loads` to `loads` | +| `Mapping` | `from collections.abc import Mapping` | +| `mk_wrapper_baseclass` | `from easybuild.base.wrapper import mk_wrapper_baseclass` | +| `OrderedDict` | `from collections import OrderedDict` | +| `raise_with_traceback` | No import required. Replace `raise_with_traceback(exception, message, tb)` with `raise exception(message).with_traceback(tb)` | +| `reload` | `from importlib import reload` | +| `Request` | `from urllib.request import Request` | +| `string_type` | No import required. Use `str` directly. | +| `StringIO` | `from io import StringIO` | +| `std_urllib` | `import urllib.request as std_urllib` | +| `subprocess_popen_text` | `from easybuild.tools.run import subprocess_popen_text` | +| `subprocess_terminate` | `from easybuild.tools.run import subprocess_terminate` | +| `urlencode` | `from urllib.parse import urlencode` | +| `URLError` | `from urllib.request import URLError` | +| `urlopen` | `from urllib.request import urlopen` | + From cc2e9da8e9784a83fef9d81fff6d094b28b008ca Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 14 May 2023 12:20:47 +0100 Subject: [PATCH 03/41] fix ci failure --- docs/easybuild-v5/overview-of-changes.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md index a634ec200..0967968ee 100644 --- a/docs/easybuild-v5/overview-of-changes.md +++ b/docs/easybuild-v5/overview-of-changes.md @@ -11,7 +11,7 @@ which can be categorized as: * [Significant enhancements][significant_enhancements] * [Backward-incompatible changes][backwards_incompatible] -* [Deprecated functionality][deprecated] +* [Deprecated functionality][deprecated_v5] For in-depth details on a particular change, see the pull requests that are linked from each of the subsections below. @@ -70,7 +70,7 @@ Running EasyBuild with Python 2.7 or a Python 3 version older than Python 3.6 is Trying to run EasyBuild with a Python version that is too old will result in an error: -``` +```log ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 3.6+) ``` @@ -108,7 +108,7 @@ format and little suggestion that anyone was using it. --- -## Deprecated functionality in EasyBuild v5.0 {: #deprecated } +## Deprecated functionality in EasyBuild v5.0 {: #deprecated_v5 } Some functionality is being deprecated in EasyBuild v5.0, and will no longer be supported in EasyBuild v6.0: From caa4e30d7fddb16d7741dfb083f37f5a90b62737 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 15 May 2023 09:09:56 +0100 Subject: [PATCH 04/41] deprecation warning on .yeb page --- docs/writing-yeb-easyconfig-files.md | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/docs/writing-yeb-easyconfig-files.md b/docs/writing-yeb-easyconfig-files.md index 752773ab0..6b299cf67 100644 --- a/docs/writing-yeb-easyconfig-files.md +++ b/docs/writing-yeb-easyconfig-files.md @@ -1,12 +1,7 @@ -# Writing easyconfig files in YAML syntax (`.yeb` format) **[IN DEVELOPMENT]** {: #easyconfig_yeb_format } +# Writing easyconfig files in YAML syntax (`.yeb` format) **Deprecated** {: #easyconfig_yeb_format } -!!! note - Because support for easyconfig files in YAML syntax (a.k.a. `.yeb` files) is still *in development*, - using them currently requires enabling the use of experimental features (`--experimental`), - see also [Experimental features][experimental_features]. - - An up-to-date overview of current progress on support for `.yeb` easyconfigs is available at - . +!!! warning + Use of `.yeb` easyconfigs is deprecated and [will be removed in EasyBuild v5.0][yeb]. Useful links: From 6201f8cfea320a24e09ef7d035d1d28bb35bd391 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 07:57:10 +0200 Subject: [PATCH 05/41] rank down release notes page in search results --- docs/release-notes.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/release-notes.md b/docs/release-notes.md index 63bb95ac4..1ff6e1b1b 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.5 +--- + # EasyBuild release notes {: #release_notes } The latest version of EasyBuild provides support for building and From 37e6f95f1288edfaf3a60cce2e7a11991aa36c90 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 08:05:56 +0200 Subject: [PATCH 06/41] configure markdownlint to ignore front matter --- .mdlrc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.mdlrc b/.mdlrc index 06bdeb92f..77bdf7d2c 100644 --- a/.mdlrc +++ b/.mdlrc @@ -1 +1,3 @@ style "#{File.dirname(__FILE__)}/.mdl.rb" + +ignore_front_matter true From eaba089b9a086881ff9ea7e5b5c0f0f44d79c399 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 24 May 2023 10:14:09 +0100 Subject: [PATCH 07/41] redorder --- .mdlrc | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.mdlrc b/.mdlrc index 77bdf7d2c..85d2755f1 100644 --- a/.mdlrc +++ b/.mdlrc @@ -1,3 +1,2 @@ -style "#{File.dirname(__FILE__)}/.mdl.rb" - ignore_front_matter true +style "#{File.dirname(__FILE__)}/.mdl.rb" From 719b194ebc46ee8d61edb70076936895fcdff506 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 17:37:22 +0200 Subject: [PATCH 08/41] fix typo (Meetin -> Meeting) --- docs/easybuild-v5/overview-of-changes.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md index 0967968ee..267f6d7c1 100644 --- a/docs/easybuild-v5/overview-of-changes.md +++ b/docs/easybuild-v5/overview-of-changes.md @@ -19,7 +19,7 @@ For in-depth details on a particular change, see the pull requests that are link ## Planned and proposed changes for EasyBuild v5.0 {: #eb5_changes } -At the [EasyBuild User Meetin](https://easybuild.io/eum23), Simon Branford set out the +At the [EasyBuild User Meeting](https://easybuild.io/eum23), Simon Branford set out the [roadmap for EasyBuild v5.0](https://easybuild.io/eum23/#easybuild5). ### Proposed changes for EasyBuild v5.0 {: #eb5_proposals } From 8f9a53b72695b01076baf460a663b6a3962416e9 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 31 May 2023 21:39:12 +0200 Subject: [PATCH 09/41] Updated outputs --- docs/log-files.md | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/log-files.md b/docs/log-files.md index 3566fba62..f943aff00 100644 --- a/docs/log-files.md +++ b/docs/log-files.md @@ -17,7 +17,7 @@ file is copied to the install directory for future reference. By default, the application log file is copied to a subdirectory of the installation prefix named `easybuild`, and has a filename like -`easybuild-HPL-2.0-20141103.104412.log` for example, which corresponds +`easybuild-WRF-4.4.1-20230426.143346.log` for example, which corresponds to the filename template `easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log`. This aspect can be tweaked via the `--logfile-format` configuration option. @@ -25,16 +25,16 @@ be tweaked via the `--logfile-format` configuration option. Example: ``` console -$ eb HPL-2.0-goolf-1.4.10.eb -== temporary log file in case of crash /tmp/easybuild-rHHgBu/easybuild-XD0Ae_.log +$ eb WRF-4.4.1-foss-2022b-dmpar.eb +== Temporary log file in case of crash /tmp/eb-1zbqix6e/easybuild-1ixy86r2.log [...] -== building and installing HPL/2.0-goolf-1.4.10... +== building and installing WRF/4.4.1-foss-2022b-dmpar... [...] == COMPLETED: Installation ended successfully -== Results of the build can be found in the log file /home/example/.local/easybuild/software/HPL/2.0-goolf-1.4.10/easybuild/easybuild-HPL-2.0-20141103.104412.log +== Results of the build can be found in the log file(s) /home/example/.local/easybuild/software/WRF/4.4.1-foss-2022b-dmpar/easybuild/easybuild-WRF-4.4.1-20230531.181321.log == Build succeeded for 1 out of 1 -== temporary log file /tmp/easybuild-rHHgBu/easybuild-XD0Ae_.log has been removed. -== temporary directory /tmp/easybuild-rHHgBu has been removed. +== temporary log file /tmp/eb-1zbqix6e/easybuild-1ixy86r2.log* has been removed. +== temporary directory /tmp/eb-1zbqix6e has been removed. ``` !!! note @@ -63,16 +63,16 @@ Each log message as emitted by EasyBuild follows a well-defined format. Example: ``` console -== 2014-11-03 13:34:31,906 main.EB_HPL INFO This is EasyBuild 1.15.2 (framework: 1.15.2, easyblocks: 1.15.2) on host example. +== 2023-05-31 16:11:21,044 easyblock.py:313 INFO This is EasyBuild 4.7.3 (framework: 4.7.3, easyblocks: 4.7.3) on host example. ``` Each log line consists of the following parts: - a prefix label `==`, which is useful to discriminate between EasyBuild log messages and the output of executed shell commands; -- date and time information (e.g., `2014-11-03 13:34:31,906`); +- date and time information (e.g., `2023-05-31 16:11:21,044`); - the Python module/class/function that is responsible for the log - message (e.g., `main.EB_HPL`); + message (e.g., `easyblock.py:313`); - the log level (e.g., `INFO`); - and a string with the actual log message at the end @@ -88,10 +88,10 @@ For each step performed in the build and installation process, corresponding log messages is emitted. For example: ``` console -== 2014-11-03 13:34:48,816 main.EB_HPL INFO configuring... -== 2014-11-03 13:34:48,817 main.EB_HPL INFO Starting configure step +== 2023-05-31 16:11:44,977 build_log.py:267 INFO configuring... +== 2023-05-31 16:11:44,981 easyblock.py:3926 INFO Starting configure step [...] -== 2014-11-03 13:34:48,823 main.EB_HPL INFO Running method configure_step part of step configure +== 2023-05-31 16:11:44,982 easyblock.py:3934 INFO Running method configure_step part of step configure ``` This allows you to navigate a log file step by step, for example using @@ -104,9 +104,10 @@ command line, the location where the command was executed and the command's output and exit code. For example: ``` console -== 2014-11-03 13:34:48,823 main.run DEBUG run_cmd: running cmd /bin/bash make_generic (in /tmp/user/easybuild_build/HPL/2.0/goolf-1.4.10/hpl-2.0/setup) -== 2014-11-03 13:34:48,823 main.run DEBUG run_cmd: Command output will be logged to /tmp/easybuild-W85p4r/easybuild-run_cmd-XoJwMY.log -== 2014-11-03 13:34:48,849 main.run INFO cmd "/bin/bash make_generic" exited with exitcode 0 and output: +== 2023-05-31 18:59:24,222 run.py:176 DEBUG run_cmd: Output of "/home/example/.local/easybuild/software/WRF/4.4.1-foss-2022b-dmpar/WRF-4.4.1/compile -j 8 wrf" will be logged to /tmp/eb-1zbqix6e/easybuild-run_cmd-ueqo5bn0.log +== 2023-05-31 18:59:24,225 run.py:217 DEBUG run_cmd: running cmd /home/example/.local/easybuild/software//WRF/4.4.1-foss-2022b-dmpar/WRF-4.4.1/compile -j 8 wrf (in /home/example/.local/easybuild/software//WRF/4.4.1-foss-2022b-dmpar/WRF-4.4.1) +[...] +== 2023-05-31 20:06:35,979 run.py:650 DEBUG cmd "/home/example/.local/easybuild/software/WRF/4.4.1-foss-2022b-dmpar/WRF-4.4.1/compile -j 8 wrf" exited with exit code 0 and output: ``` If you are primarily interested in the different commands as they were From 523e8611e79b96549f51dec8651c27da7592222c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 7 Jun 2023 15:41:39 +0100 Subject: [PATCH 10/41] proposed changes --- docs/easybuild-v5/overview-of-changes.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md index 267f6d7c1..570181d7e 100644 --- a/docs/easybuild-v5/overview-of-changes.md +++ b/docs/easybuild-v5/overview-of-changes.md @@ -27,8 +27,8 @@ At the [EasyBuild User Meeting](https://easybuild.io/eum23), Simon Branford set There are several proposed changes where the EasyBuild maintainers are seeking community feedback. If you wish to provide feedback then please comment in the GitHub issue for the proposal. -* Minimum supported Lmod Version: _proposal forthcoming_ -* Toolchain Support Policy: _proposal forthcoming_ +* [Minimum supported Lmod Version](https://github.com/easybuilders/easybuild/issues/871) +* [Toolchain Support Policy](https://github.com/easybuilders/easybuild/issues/872) ### Planned changes for EasyBuild v5.0 {: #eb5_plans } From 282b1f26f64c1484263530840e1971731188beef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Jun 2023 20:53:55 +0200 Subject: [PATCH 11/41] add link to EasyBuild 5.0 docs on landing page --- docs/easybuild-v5/index.md | 5 +++++ docs/index.md | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 docs/easybuild-v5/index.md diff --git a/docs/easybuild-v5/index.md b/docs/easybuild-v5/index.md new file mode 100644 index 000000000..2146257cf --- /dev/null +++ b/docs/easybuild-v5/index.md @@ -0,0 +1,5 @@ +# EasyBuild v5.0 + +* [Overview of changes](overview-of-changes.md) +* [GitHub Project board](https://github.com/orgs/easybuilders/projects/18) +* [Talk on EasyBuild 5.0 at EUM'23](https://easybuild.io/eum23/#easybuild5) diff --git a/docs/index.md b/docs/index.md index 3fac0173f..98b025fa6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -24,7 +24,7 @@ To contribute to this documentation, [open a pull request](https://github.com/ea - [Generic easyblocks](version-specific/generic-easyblocks.md) - List of [common toolchains](common-toolchains.md) and [supported software](version-specific/supported-software) - [Contributing to EasyBuild](contributing.md) - [GitHub integration features](integration-with-github.md) -- [EasyBuild release notes](release-notes.md) +- [EasyBuild release notes](release-notes.md) - [EasyBuild v5.0](easybuild-v5/index.md) - [Getting help](getting-help.md): [mailing list](https://lists.ugent.be/wws/info/easybuild) - [Slack](https://easybuild.io/join-slack) - [conference calls](https://github.com/easybuilders/easybuild/wiki/Conference-calls) - [GitHub](https://github.com/easybuilders) --- From ddd1286f57527414e3e45a9dcd37596a98cf9db7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 7 Jun 2023 20:25:52 +0100 Subject: [PATCH 12/41] down rank API pages --- docs/gen_ref_pages.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/gen_ref_pages.py b/docs/gen_ref_pages.py index 8ed4bfd67..25bd62271 100644 --- a/docs/gen_ref_pages.py +++ b/docs/gen_ref_pages.py @@ -9,6 +9,11 @@ EB_FRAMEWORK = "src/easybuild-framework" +MKDOCS_SEARCH_PRIORITY = """--- +search: + boost: 0.5 +--- +""" if not Path(f"{EB_FRAMEWORK}/easybuild").is_dir(): print("WARNING - EasyBuild Framework is not available. API documentation will not be generated.") @@ -53,6 +58,7 @@ navs[nav_tuple][parts] = doc_path_relative_to_nav with mkdocs_gen_files.open(full_doc_path, "w") as fd: + fd.write(MKDOCS_SEARCH_PRIORITY) identifier = ".".join(parts) fd.write(f"::: {identifier}\n") @@ -60,10 +66,17 @@ # Generate the menu navigation file with mkdocs_gen_files.open("api/summary.md", "w") as nav_file: + nav_file.write(MKDOCS_SEARCH_PRIORITY) nav_file.writelines(menu_nav.build_literate_nav()) # Generate the section navigation files, appending to any existing API content for key, nav in navs.items(): fp = '/'.join(key) - with mkdocs_gen_files.open(f"api/{fp}/index.md", "a") as nav_file: + filename = f"api/{fp}/index.md" + + if not Path(filename).is_file(): + with mkdocs_gen_files.open(filename, "w") as nav_file: + nav_file.write(MKDOCS_SEARCH_PRIORITY) + + with mkdocs_gen_files.open(filename, "a") as nav_file: nav_file.writelines(nav.build_literate_nav()) From 3f56b4582c52254fafbd26c8e720169849fa07b7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 8 Jun 2023 12:36:47 +0100 Subject: [PATCH 13/41] down rank docs changlog page --- docs/changelog-docs.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/changelog-docs.md b/docs/changelog-docs.md index a611cdc6b..3c9cee310 100644 --- a/docs/changelog-docs.md +++ b/docs/changelog-docs.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.5 +--- + # Changelog for EasyBuild documentation {: #changelog } (for EasyBuild release notes, see [EasyBuild release notes][release_notes]) From f5a9f5c3a5cb20cb667d6bf939f8aa866fabd013 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 13 Jun 2023 09:26:53 +0200 Subject: [PATCH 14/41] updated easyconfigs in examples --- docs/partial-installations.md | 76 +++++++++++++++++------------------ 1 file changed, 38 insertions(+), 38 deletions(-) diff --git a/docs/partial-installations.md b/docs/partial-installations.md index e786983c3..45d65cfda 100644 --- a/docs/partial-installations.md +++ b/docs/partial-installations.md @@ -17,10 +17,10 @@ The following step names are recognized (listed in execution order): `fetch`, `r Example usage: ``` console -$ eb GCC-4.9.2.eb --stop configure +$ eb GCC-11.3.0.eb --stop configure == temporary log file in case of crash /tmp/eb-X2Z0b7/easybuild-mGxmNb.log -== processing EasyBuild easyconfig /home/example/GCC-4.9.2.eb -== building and installing GCC/4.9.2... +== processing EasyBuild easyconfig /home/example/GCC-11.3.0.eb +== building and installing GCC/11.3.0... == fetching files... == creating build dir, resetting environment... == unpacking... @@ -28,7 +28,7 @@ $ eb GCC-4.9.2.eb --stop configure == preparing... == configuring... == COMPLETED: Installation STOPPED successfully -== Results of the build can be found in the log file /dev/shm/example/GCC/4.9.2/dummy-dummy/easybuild/easybuild-GCC-4.9.2-20150430.091644.log +== Results of the build can be found in the log file /dev/shm/example/GCC/11.3.0/dummy-dummy/easybuild/easybuild-GCC-11.3.0-20230613.091644.log == Build succeeded for 1 out of 1 == temporary log file(s) /tmp/eb-X2Z0b7/easybuild-mGxmNb.log* have been removed. == temporary directory /tmp/eb-X2Z0b7 has been removed. @@ -44,15 +44,15 @@ Example usage: ``` console $ eb GCCcore-6.2.0.eb --fetch -== temporary log file in case of crash /tmp/eb-1ZZX2b/easybuild-NSmm5P.log -== processing EasyBuild easyconfig /home/example/GCCcore-6.2.0.eb -== building and installing GCCcore/6.2.0... +== Temporary log file in case of crash /tmp/eb-23iu2fpm/easybuild-ss0wcidi.log +== processing EasyBuild easyconfig /home/example/GCCcore-11.3.0.eb +== building and installing GCCcore/11.3.0... == fetching files... -== COMPLETED: Installation STOPPED successfully -== Results of the build can be found in the log file(s) /dev/shm/example/GCC/4.9.2/dummy-dummy/easybuild/easybuild-GCCcore-6.2.0-20180330.170523.log +== COMPLETED: Installation STOPPED successfully (took 1 secs) +== Results of the build can be found in the log file(s) /tmp/example/easybuild/build/GCCcore/11.3.0/system-system/easybuild/easybuild-GCCcore-11.3.0-20230613.090338.log == Build succeeded for 1 out of 1 -== Temporary log file(s) /tmp/eb-1ZZX2b/easybuild-NSmm5P.log* have been removed. -== Temporary directory /tmp/eb-1ZZX2b has been removed. +== Temporary log file(s) /tmp/example/eb-23iu2fpm/easybuild-ss0wcidi.log* have been removed. +== Temporary directory /tmp/example/eb-23iu2fpm has been removed. ``` !!! note @@ -87,17 +87,17 @@ vi) regenerate the module file (since it contains a list of installed extensions Example usage: ``` console -$ eb Python-2.7.9-intel-2015a.eb --skip +$ eb Python-3.10.4-GCCcore-11.3.0.eb --skip ... -== Python/2.7.9-intel-2015a is already installed (module found), skipping +== Python/3.10.4-GCCcore-11.3.0 is already installed (module found), skipping == No easyconfigs left to be built. == Build succeeded for 0 out of 0 ``` ``` console -$ eb Python-2.7.9-intel-2015a.eb --skip --rebuild +$ eb Python-3.10.4-GCCcore-11.3.0.eb --skip --rebuild ... -== building and installing Python/2.7.9-intel-2015a... +== building and installing Python/3.10.4-GCCcore-11.3.0... ... == configuring [skipped] == building [skipped] @@ -168,11 +168,11 @@ Example usage: ``` console $ module avail GCC ---------------------------- /home/example/.local/modules/all ---------------------------- - GCC/4.8.2 + GCC/11.2.0 - $ eb GCC-5.1.0.eb --module-only --rebuild + $ eb GCC-11.3.0.eb --module-only --rebuild ... - == building and installing GCC/5.1.0... + == building and installing GCC/11.3.0... == fetching files [skipped] ... == configuring [skipped] @@ -189,31 +189,31 @@ Example usage: $ module avail GCC ---------------------------- /home/example/.local/modules/all ---------------------------- - GCC/4.8.2 GCC/5.1.0 + GCC/11.2.0 GCC/11.3.0 ``` * regenerate existing module file: ``` console - $ module avail GCC/4.8.2 + $ module avail GCC/11.3.0 ---------------------------- /home/example/.local/modules/all ---------------------------- - GCC/4.8.2 + GCC/11.3.0 - $ ls -l /home/example/.local/modules/all/GCC/4.8.2 - -rw-rw-r-- 1 example example 1002 Jan 11 17:19 /home/example/.local/modules/all/GCC/4.8.2 + $ ls -l /home/example/.local/modules/all/GCC/11.3.0 + -rw-rw-r-- 1 example example 1002 Jun 13 08:35 /home/example/.local/modules/all/GCC/11.3.0 - $ eb GCC-4.8.2.eb --module-only --rebuild + $ eb GCC-11.3.0.eb --module-only --rebuild ... - == building and installing GCC/4.8.2... + == building and installing GCC/11.3.0... ... == sanity checking [skipped] == creating module... == COMPLETED: Installation ended successfully ... - $ ls -l /home/example/.local/modules/all/GCC/4.8.2 - -rw-rw-r-- 1 example example 1064 Apr 30 10:54 /home/example/.local/modules/all/GCC/4.8.2 + $ ls -l /home/example/.local/modules/all/GCC/11.3.0 + -rw-rw-r-- 1 example example 1064 Jun 13 10:54 /home/example/.local/modules/all/GCC/11.3.0 ``` @@ -228,26 +228,26 @@ Examples: `--module-only --module-syntax=Lua` can be used: ``` console - $ module avail GCC/4.8.2 + $ module avail GCC/11.3.0 ---------------------------- /home/example/.local/modules/all ---------------------------- - GCC/4.8.2 + GCC/11.3.0 - $ ls -l /home/example/.local/modules/all/GCC/4.8.2* - -rw-rw-r-- 1 example example 1064 Apr 30 10:54 /home/example/.local/modules/all/GCC/4.8.2 + $ ls -l /home/example/.local/modules/all/GCC/11.3.0* + -rw-rw-r-- 1 example example 1064 Jun 13 08:54 /home/example/.local/modules/all/GCC/11.3.0 - $ eb GCC-4.8.2.eb --modules-tool=Lmod --module-only --module-syntax=Lua --rebuild + $ eb GCC-11.3.0.eb --modules-tool=Lmod --module-only --module-syntax=Lua --rebuild ... - == building and installing GCC/4.8.2... + == building and installing GCC/11.3.0... ... == sanity checking [skipped] == creating module... == COMPLETED: Installation ended successfully ... - $ ls -l /home/example/.local/modules/all/GCC/4.8.2* - -rw-rw-r-- 1 example example 1064 Apr 30 10:54 /home/example/.local/modules/all/GCC/4.8.2 - -rw-rw-r-- 1 example example 1249 Apr 30 11:56 /home/example/.local/modules/all/GCC/4.8.2.lua + $ ls -l /home/example/.local/modules/all/GCC/11.3.0* + -rw-rw-r-- 1 example example 1064 Jun 13 08:54 /home/example/.local/modules/all/GCC/11.3.0 + -rw-rw-r-- 1 example example 1249 Jun 13 08:56 /home/example/.local/modules/all/GCC/11.3.0.lua ``` !!! note @@ -263,7 +263,7 @@ Examples: ``` console $ eb --installpath-modules=$HOME/test/modules --module-only --module-naming-scheme=HierarchicalMNS --rebuild ... - == building and installing Core/GCC/4.8.2... + == building and installing Core/GCC/11.3.0... ... == sanity checking [skipped] == creating module... @@ -274,7 +274,7 @@ Examples: $ module avail ---------------------------- /home/example/test/modules/all ---------------------------- - Core/GCC/4.8.2 + Core/GCC/11.3.0 ``` !!! note From 39b1b4f542704a4cc776fad6559760e6fc88c004 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2023 14:35:49 +0200 Subject: [PATCH 15/41] add warning to highlight deprecation of `--wait-on-lock` configuration option --- docs/locks.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/locks.md b/docs/locks.md index 2f425a1da..545b62ca0 100644 --- a/docs/locks.md +++ b/docs/locks.md @@ -75,6 +75,9 @@ Using the `--wait-on-lock` configuration option, you can change how EasyBuild de how frequently EasyBuild should check whether an existing lock was removed. By specifying a non-zero value `secs`, you can indicate how many seconds EasyBuild should wait before checking again whether the lock is still in place. +!!! warning + The `--wait-on-lock` configuration option is deprecated, please use `--wait-on-lock-interval` and `--wait-on-lock-limit` instead! + !!! note If the lock is never removed, the EasyBuild session will never terminate; it will keep checking every `S` seconds whether the lock is still in place. From b7e166bed44e08c915357715548c7d384cbedf03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2023 21:58:22 +0200 Subject: [PATCH 16/41] auto-update docs for EasyBuild v4.8.0 --- docs/version-specific/easyblocks.md | 2 + docs/version-specific/eb-help.md | 4 +- docs/version-specific/generic-easyblocks.md | 29 +- docs/version-specific/supported-software.md | 1570 +++++++++++++++---- 4 files changed, 1286 insertions(+), 319 deletions(-) diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index 529619756..bfa627766 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -51,6 +51,7 @@ - EB_Clang_minus_AOMP - EB_OpenSSL_wrapper - JuliaBundle + - PerlBundle - PythonBundle - SystemCompiler - SystemMPI @@ -167,6 +168,7 @@ - EB_QuantumESPRESSO - EB_R - EB_Ruby + - EB_Rust - EB_SAMtools - EB_Scalasca1 - EB_Score_minus_P diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index 5871d65f0..b89d065f9 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -31,8 +31,8 @@ Option flag |Option description ## Configfile options Option flag |Option description ------------------------------------------|---------------------------------------------------------- -``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list) +-----------------------------------------|---------------------------------------------------------------------------------------------------------------- +``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list; default: /home/example/.config/easybuild/config.cfg) ``--ignoreconfigfiles=IGNORECONFIGFILES``|Ignore configfiles (type comma-separated list) ## Basic options diff --git a/docs/version-specific/generic-easyblocks.md b/docs/version-specific/generic-easyblocks.md index c4e7c1e87..ffd79de33 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -6,7 +6,7 @@ # Overview of generic easyblocks {: #generic_easyblocks } -[BinariesTarball](#binariestarball) - [Binary](#binary) - [BuildEnv](#buildenv) - [Bundle](#bundle) - [CMakeMake](#cmakemake) - [CMakeMakeCp](#cmakemakecp) - [CMakeNinja](#cmakeninja) - [CMakePythonPackage](#cmakepythonpackage) - [Cargo](#cargo) - [CargoPythonPackage](#cargopythonpackage) - [CmdCp](#cmdcp) - [Conda](#conda) - [ConfigureMake](#configuremake) - [ConfigureMakePythonPackage](#configuremakepythonpackage) - [CrayToolchain](#craytoolchain) - [FortranPythonPackage](#fortranpythonpackage) - [GoPackage](#gopackage) - [IntelBase](#intelbase) - [JAR](#jar) - [JuliaBundle](#juliabundle) - [JuliaPackage](#juliapackage) - [MakeCp](#makecp) - [MesonNinja](#mesonninja) - [ModuleRC](#modulerc) - [OCamlPackage](#ocamlpackage) - [OctavePackage](#octavepackage) - [PackedBinary](#packedbinary) - [PerlModule](#perlmodule) - [PythonBundle](#pythonbundle) - [PythonPackage](#pythonpackage) - [RPackage](#rpackage) - [Rpm](#rpm) - [RubyGem](#rubygem) - [SCons](#scons) - [SystemCompiler](#systemcompiler) - [SystemMPI](#systemmpi) - [Tarball](#tarball) - [Toolchain](#toolchain) - [VSCPythonPackage](#vscpythonpackage) - [VersionIndependentPythonPackage](#versionindependentpythonpackage) - [Waf](#waf) +[BinariesTarball](#binariestarball) - [Binary](#binary) - [BuildEnv](#buildenv) - [Bundle](#bundle) - [CMakeMake](#cmakemake) - [CMakeMakeCp](#cmakemakecp) - [CMakeNinja](#cmakeninja) - [CMakePythonPackage](#cmakepythonpackage) - [Cargo](#cargo) - [CargoPythonPackage](#cargopythonpackage) - [CmdCp](#cmdcp) - [Conda](#conda) - [ConfigureMake](#configuremake) - [ConfigureMakePythonPackage](#configuremakepythonpackage) - [CrayToolchain](#craytoolchain) - [FortranPythonPackage](#fortranpythonpackage) - [GoPackage](#gopackage) - [IntelBase](#intelbase) - [JAR](#jar) - [JuliaBundle](#juliabundle) - [JuliaPackage](#juliapackage) - [MakeCp](#makecp) - [MesonNinja](#mesonninja) - [ModuleRC](#modulerc) - [OCamlPackage](#ocamlpackage) - [OctavePackage](#octavepackage) - [PackedBinary](#packedbinary) - [PerlBundle](#perlbundle) - [PerlModule](#perlmodule) - [PythonBundle](#pythonbundle) - [PythonPackage](#pythonpackage) - [RPackage](#rpackage) - [Rpm](#rpm) - [RubyGem](#rubygem) - [SCons](#scons) - [SystemCompiler](#systemcompiler) - [SystemMPI](#systemmpi) - [Tarball](#tarball) - [Toolchain](#toolchain) - [VSCPythonPackage](#vscpythonpackage) - [VersionIndependentPythonPackage](#versionindependentpythonpackage) - [Waf](#waf) ## ``BinariesTarball`` @@ -44,6 +44,7 @@ easyconfig parameter|description --------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|------------- ``extract_sources`` |Whether or not to extract sources |``False`` ``install_cmd`` |Install command to be used. |``None`` +``install_cmds`` |List of install commands to be used. |``None`` ``prepend_to_path`` |Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself.|``['']`` ``staged_install`` |Perform staged installation via subdirectory of build directory |``False`` @@ -488,6 +489,7 @@ easyconfig parameter |description ``environment_file`` |Conda environment.yml file to use with 'conda env create' |``None`` ``extract_sources`` |Whether or not to extract sources |``False`` ``install_cmd`` |Install command to be used. |``None`` +``install_cmds`` |List of install commands to be used. |``None`` ``prepend_to_path`` |Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself.|``['']`` ``remote_environment``|Remote conda environment to use with 'conda env create' |``None`` ``requirements`` |Requirements specification to pass to 'conda install' |``None`` @@ -790,6 +792,7 @@ easyconfig parameter|description --------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|------------- ``extract_sources`` |Whether or not to extract sources |``False`` ``install_cmd`` |Install command to be used. |``None`` +``install_cmds`` |List of install commands to be used. |``None`` ``prepend_to_path`` |Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself.|``['']`` ``staged_install`` |Perform staged installation via subdirectory of build directory |``False`` @@ -964,6 +967,7 @@ easyconfig parameter|description --------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|------------- ``extract_sources`` |Whether or not to extract sources |``False`` ``install_cmd`` |Install command to be used. |``None`` +``install_cmds`` |List of install commands to be used. |``None`` ``prepend_to_path`` |Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself.|``['']`` ``staged_install`` |Perform staged installation via subdirectory of build directory |``False`` @@ -972,6 +976,28 @@ easyconfig parameter|description * ``install_step`` - Copy all unpacked source directories to install directory, one-by-one. +## ``PerlBundle`` + +(derives from [``Bundle``](#bundle)) + + +Bundle of perl modules + + +### Extra easyconfig parameters specific to ``PerlBundle`` easyblock + +easyconfig parameter |description |default value +-------------------------------|---------------------------------------------------------------------------|------------- +``altroot`` |Software name of dependency to use to define $EBROOT for this bundle |``None`` +``altversion`` |Software name of dependency to use to define $EBVERSION for this bundle |``None`` +``components`` |List of components to install: tuples w/ name, version and easyblock to use|``()`` +``default_component_specs`` |Default specs to use for every component |``{}`` +``default_easyblock`` |Default easyblock to use for components |``None`` +``options`` |Dictionary with extension options. |``{}`` +``runtest`` |Run unit tests. |``"test"`` +``sanity_check_all_components``|Enable sanity checks for all components |``False`` +``sanity_check_components`` |List of components for which to run sanity checks |``[]`` + ## ``PerlModule`` (derives from ``ExtensionEasyBlock``, [``ConfigureMake``](#configuremake)) @@ -1122,6 +1148,7 @@ easyconfig parameter|description ``extract_sources`` |Whether or not to extract sources |``False`` ``force`` |Use force |``False`` ``install_cmd`` |Install command to be used. |``None`` +``install_cmds`` |List of install commands to be used. |``None`` ``makesymlinks`` |Create symlinks for listed paths |``[]`` ``postinstall`` |Enable post install |``False`` ``preinstall`` |Enable pre install |``False`` diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index 8c16bfbf3..2a08950d1 100644 --- a/docs/version-specific/supported-software.md +++ b/docs/version-specific/supported-software.md @@ -5,7 +5,7 @@ This page contains a lot of information, it may take a while to load. -EasyBuild supports 3085 different software packages (incl. toolchains, bundles): +EasyBuild supports 3161 different software packages (incl. toolchains, bundles): [a](#a) - [b](#b) - [c](#c) - [d](#d) - [e](#e) - [f](#f) - [g](#g) - [h](#h) - [i](#i) - [j](#j) - [k](#k) - [l](#l) - [m](#m) - [n](#n) - [o](#o) - [p](#p) - [q](#q) - [r](#r) - [s](#s) - [t](#t) - [u](#u) - [v](#v) - [w](#w) - [x](#x) - [y](#y) - [z](#z) @@ -13,9 +13,19 @@ EasyBuild supports 3085 different software packages (incl. toolchains, bundles): ## 3 -[3to2](#3to2) +[3d-dna](#3d-dna) - [3to2](#3to2) +### 3d-dna + +3D de novo assembly (3D DNA) pipeline + +*homepage*: + +version |versionsuffix |toolchain +----------|------------------|----------------- +``180922``|``-Python-2.7.15``|``GCCcore/8.2.0`` + ### 3to2 lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x. @@ -46,7 +56,7 @@ version |toolchain ## A -[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASE](#ase) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) +[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [axel](#axel) ### ABAQUS @@ -88,7 +98,7 @@ version |versionsuffix |toolchain ``8.6.3`` | |``intel/2018a`` ``8.10.2``| |``intel/2018b`` ``8.10.3``| |``intel/2018b`` -``9.2.1`` | |``intel/2020a`` +``9.2.1`` | |``foss/2019b``, ``intel/2019b``, ``intel/2020a`` ``9.4.1`` | |``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``9.4.2`` | |``foss/2021a``, ``intel/2021a`` ``9.6.2`` | |``foss/2022a``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` @@ -123,9 +133,9 @@ Abseil is an open-source collection of C++ library code designed to augment the *homepage*: version |toolchain ---------------|------------------ +--------------|-------------------------------------- ``20210324.2``|``GCCcore/11.2.0`` -``20230125.2``|``GCCcore/12.2.0`` +``20230125.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``20230125.3``|``GCCcore/12.3.0`` ### abTEM @@ -298,6 +308,16 @@ version |toolchain ``2021.4.0`` |``system`` ``2022.1.0`` |``system`` +### affinity + +A small C++ wrapper for managing Linux CPU sets and CPU affinity. It also includes a tool to report binding, which is useful for testing different binding options + +*homepage*: + +version |toolchain +------------|------------------------------- +``20230524``|``foss/2022a``, ``intel/2022a`` + ### AFNI AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. @@ -320,6 +340,7 @@ AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotation version |toolchain ---------|-------------- ``0.9.2``|``GCC/11.2.0`` +``1.1.0``|``GCC/12.2.0`` ### AGeNT @@ -341,6 +362,16 @@ version|versionsuffix |toolchain -------|-----------------|-------------- ``1.2``|``-Python-3.7.2``|``foss/2019a`` +### AIMAll + +AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data. + +*homepage*: + +version |versionsuffix |toolchain +------------|----------------|--------------- +``19.10.12``|``-linux_64bit``|``intel/2020b`` + ### aiohttp Asynchronous HTTP client/server framework for asyncio and Python. @@ -426,6 +457,17 @@ The alleleCount package primarily exists to prevent code duplication between som version |toolchain ---------|----------------- ``4.0.0``|``GCCcore/6.4.0`` +``4.2.1``|``GCC/11.3.0`` + +### alleleIntegrator + +R package to generate allele specific counts for scRNA data and use it to identify cancer cells + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.8.8``|``-R-4.2.1`` |``foss/2022a`` ### Allinea @@ -493,6 +535,16 @@ version |versionsuffix |toolchain ``2.3.4``|``-CUDA-11.7.0-ColabFold``|``foss/2022a`` ``2.3.4``|``-ColabFold`` |``foss/2022a`` +### AlphaPulldown + +AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer + +*homepage*: + +version |toolchain +----------|---------------------------------- +``0.30.4``|``foss/2020b``, ``fosscuda/2020b`` + ### ALPS The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code. @@ -708,6 +760,7 @@ version |versionsuffix|toolchain ------------|-------------|--------------- ``2020.102``|``-intelmpi``|``iimpi/2020b`` ``2022.102``|``-intelmpi``|``iimpi/2021b`` +``2023.101``|``-intelmpi``|``iimpi/2022a`` ### Anaconda2 @@ -734,25 +787,26 @@ Built to complement the rich, open source Python community, the Anaconda platfor *homepage*: -version |toolchain ------------|---------- -``4.0.0`` |``system`` -``4.2.0`` |``system`` -``4.4.0`` |``system`` -``5.0.1`` |``system`` -``5.1.0`` |``system`` -``5.3.0`` |``system`` -``2018.12``|``system`` -``2019.03``|``system`` -``2019.07``|``system`` -``2019.10``|``system`` -``2020.02``|``system`` -``2020.07``|``system`` -``2020.11``|``system`` -``2021.05``|``system`` -``2021.11``|``system`` -``2022.05``|``system`` -``2022.10``|``system`` +version |toolchain +-------------|---------- +``4.0.0`` |``system`` +``4.2.0`` |``system`` +``4.4.0`` |``system`` +``5.0.1`` |``system`` +``5.1.0`` |``system`` +``5.3.0`` |``system`` +``2018.12`` |``system`` +``2019.03`` |``system`` +``2019.07`` |``system`` +``2019.10`` |``system`` +``2020.02`` |``system`` +``2020.07`` |``system`` +``2020.11`` |``system`` +``2021.05`` |``system`` +``2021.11`` |``system`` +``2022.05`` |``system`` +``2022.10`` |``system`` +``2023.03-1``|``system`` ### aNCI @@ -861,6 +915,7 @@ version |toolchain ----------|---------- ``15.0`` |``system`` ``2022R2``|``system`` +``2023R1``|``system`` ### ANSYS_CFD @@ -1377,6 +1432,16 @@ version |versionsuffix |toolchain ``3.12.2`` |``-ASE-3.21.1`` |``foss/2020b``, ``intel/2020b`` ``3.12.7`` |``-ASE-3.21.1`` |``foss/2020b``, ``intel/2020b`` +### ASCAT + +ASCAT is a method to derive copy number profiles of tumor cells, accounting for normal cell admixture and tumor aneuploidy. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``3.1.2``|``-R-4.2.1`` |``foss/2022a`` + ### ASE ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. @@ -1412,6 +1477,16 @@ version |versionsuffix |toolchain ``3.22.0`` | |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` ``3.22.1`` | |``foss/2021b``, ``foss/2022a``, ``gfbf/2022b``, ``gomkl/2021a``, ``intel/2021b``, ``intel/2022a`` +### ASF-SearchAPI + +asf_search is a Python module for performing searches of the ASF catalog. In addition, it offers baseline functionality and download support. + +*homepage*: + +version |toolchain +---------|-------------- +``6.5.0``|``foss/2022a`` + ### ASHS Automatic Segmentation of Hippocampal Subfields (ASHS) @@ -1535,6 +1610,16 @@ version |toolchain ``2.44.1``|``GCCcore/11.3.0`` ``2.46.0``|``GCCcore/12.2.0`` +### ATAT + +The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools + +*homepage*: + +version |toolchain +--------|----------------- +``3.36``|``GCCcore/9.3.0`` + ### ATK ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. @@ -1628,10 +1713,10 @@ Commands for Manipulating Filesystem Extended Attributes *homepage*: version |toolchain -----------|-------------------------------------- +----------|---------------------------------------------------------- ``2.4.47``|``GCCcore/8.2.0`` ``2.4.48``|``GCCcore/9.3.0`` -``2.5.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.5.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### attrdict @@ -1679,7 +1764,7 @@ version |versionsuffix |toolchain ``3.3.2``|``-Python-2.7.15``|``intel/2018b`` ``3.3.3``| |``foss/2019b``, ``intel/2019b`` ``3.4.0``| |``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` -``3.5.0``| |``foss/2022a`` +``3.5.0``| |``foss/2022a``, ``foss/2022b`` ### Austin @@ -1711,7 +1796,7 @@ version |toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.68``|``foss/2016b`` ``2.69``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### Autoconf-archive @@ -1744,6 +1829,7 @@ OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly version |versionsuffix |toolchain ---------|----------------|-------------- ``1.5.3``|``-CUDA-11.3.1``|``GCC/10.3.0`` +``1.5.3``|``-CUDA-11.7.0``|``GCC/11.3.0`` ### AutoDock-Vina @@ -1756,6 +1842,16 @@ version |versionsuffix |toolchain ``1.1.2``|``-linux_x86``|``system`` ``1.2.3``| |``foss/2021a``, ``foss/2021b`` +### AutoDockSuite + +AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. + +*homepage*: + +version |toolchain +---------|----------------- +``4.2.6``|``GCCcore/8.3.0`` + ### AutoGeneS AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples. @@ -1793,7 +1889,7 @@ version |toolchain ``1.16.2``|``GCCcore/10.2.0`` ``1.16.3``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``1.16.4``|``GCCcore/11.2.0`` -``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### AutoMap @@ -1830,7 +1926,7 @@ version |toolchain ``20200321``|``GCCcore/10.2.0`` ``20210128``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``20210726``|``GCCcore/11.2.0`` -``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### Avogadro2 @@ -1868,10 +1964,20 @@ version |versionsuffix |toolchain ``2.0.55`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``2.11.21`` | |``GCCcore/11.3.0`` +### axel + +Lightweight CLI download accelerator + +*homepage*: + +version |toolchain +----------|------------------------------------ +``2.17.9``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` + ## B -[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) +[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) ### BA3-SNPS-autotune @@ -2028,10 +2134,10 @@ Bandage is a program for visualising de novo assembly graphs *homepage*: version |versionsuffix|toolchain ----------|-------------|------------------ +---------|-------------|-------------------------------------- ``0.8.1``|``_Centos`` |``system`` ``0.8.1``|``_Ubuntu`` |``system`` -``0.9.0``| |``GCCcore/11.2.0`` +``0.9.0``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### barrnap @@ -2040,8 +2146,8 @@ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal *homepage*: version|toolchain --------|---------------------------------------------------------------------- -``0.9``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b``, ``gompi/2021b`` +-------|--------------------------------------------------------------------------------------- +``0.9``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b``, ``gompi/2021b``, ``gompi/2022a`` ### basemap @@ -2148,16 +2254,27 @@ version|toolchain -------|------------------------------------------------------ ``1.1``|``GCC/8.3.0``, ``foss/2016a``, ``iccifort/2019.5.281`` +### BayesPrism + +Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression + +*homepage*: + +version|versionsuffix|toolchain +-------|-------------|-------------- +``2.0``|``-R-4.2.1`` |``foss/2022a`` + ### BayesTraits BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------------|-----------------|---------- ``1.0-linux32``| |``system`` ``2.0`` |``-Beta-Linux64``|``system`` +``3.0.2`` |``-Linux`` |``system`` ### Bazel @@ -2227,7 +2344,7 @@ version |versionsuffix |toolchain ``38.90`` | |``GCC/10.2.0``, ``GCC/9.3.0`` ``38.96`` | |``GCC/10.3.0`` ``38.98`` | |``GCC/11.2.0`` -``39.01`` | |``GCC/11.3.0`` +``39.01`` | |``GCC/11.3.0``, ``GCC/12.2.0`` ### bc @@ -2502,6 +2619,16 @@ version|toolchain -------|-------------- ``1`` |``foss/2018a`` +### BGC-Bayesian-genomic-clines + +Collection of code for Bayesian genomic cline analyses. + +*homepage*: + +version |toolchain +--------|--------------- +``1.03``|``gompi/2021a`` + ### bgen A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. @@ -2587,7 +2714,7 @@ version |toolchain ``2.37`` |``GCCcore/11.2.0``, ``system`` ``2.38`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ``2.39`` |``GCCcore/12.2.0``, ``system`` -``2.40`` |``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.40`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### Bio-DB-HTS @@ -2692,10 +2819,10 @@ version |versionsuffix |toolchain Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. -*homepage*: +*homepage*: version |versionsuffix |toolchain ------------|----------------|------------------------------------------------------------------------------ +-----------|----------------|-------------------------------------------------------------------------------------------------- ``1.6.924``|``-Perl-5.20.3``|``intel/2016a`` ``1.6.924``|``-Perl-5.22.1``|``foss/2016a`` ``1.7.0`` |``-Perl-5.24.0``|``foss/2016b`` @@ -2707,7 +2834,7 @@ version |versionsuffix |toolchain ``1.7.2`` |``-Perl-5.28.0``|``foss/2018b``, ``intel/2018b`` ``1.7.2`` |``-Perl-5.28.1``|``GCCcore/8.2.0`` ``1.7.7`` | |``GCCcore/9.3.0`` -``1.7.8`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.7.8`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### BioPP @@ -2791,6 +2918,7 @@ version |toolchain ``0.20.1``|``foss/2018b``, ``intel/2018b`` ``0.23.1``|``foss/2021b`` ``0.24.0``|``GCC/11.3.0`` +``0.24.1``|``GCC/12.2.0`` ### Bison @@ -2812,7 +2940,7 @@ version |toolchain ``3.6.1``|``GCCcore/10.1.0`` ``3.7.1``|``GCCcore/10.2.0``, ``system`` ``3.7.6``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.5.0``, ``system`` +``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.5.0``, ``system`` ### bitarray @@ -2894,6 +3022,7 @@ version |versionsuffix |toolchain ``2.11.0``| |``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` ``2.12.0``| |``gompi/2021b`` ``2.13.0``| |``gompi/2022a`` +``2.14.0``| |``gompi/2022b`` ### BLAT @@ -2904,7 +3033,7 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity version|toolchain -------|-------------------------------------------------------------------------------------------------------------------- ``3.5``|``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` -``3.7``|``GCC/11.3.0`` +``3.7``|``GCC/11.2.0``, ``GCC/11.3.0`` ### Blender @@ -2933,12 +3062,12 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: version |versionsuffix|toolchain ----------|-------------|------------------------------------------------------------ +---------|-------------|---------------------------------------------------------------------------- ``0.3.2``| |``GCC/7.3.0-2.30`` ``0.6.0``| |``GCC/8.3.0-2.32`` ``0.8.0``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``0.8.1``| |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` -``0.9.0``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.1.0`` +``0.9.0``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2022.1.0`` ``1.2`` |``-amd`` |``GCC/7.3.0-2.30`` ``2.2`` |``-amd`` |``GCCcore/9.3.0`` ``3.0`` |``-amd`` |``GCCcore/10.3.0`` @@ -3233,10 +3362,11 @@ Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python *homepage*: -version |toolchain ------------|-------------------------------------- -``1.20.13``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.26.37``|``GCCcore/11.3.0`` +version |toolchain +------------|-------------------------------------- +``1.20.13`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.26.37`` |``GCCcore/11.3.0`` +``1.26.163``|``GCCcore/12.2.0`` ### Bottleneck @@ -3287,6 +3417,7 @@ version |toolchain ``2.4.2`` |``GCC/10.2.0``, ``GCC/9.3.0`` ``2.4.4`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``2.4.5`` |``GCC/11.3.0`` +``2.5.1`` |``GCC/12.2.0`` ### Bpipe @@ -3478,8 +3609,8 @@ A simple, correct Python build frontend. *homepage*: version |toolchain -----------|-------------- -``0.10.0``|``foss/2022a`` +----------|------------------------------ +``0.10.0``|``foss/2022a``, ``foss/2022b`` ### buildenv @@ -3533,6 +3664,7 @@ version |versionsuffix |toolchain ``5.4.2``| |``foss/2021a`` ``5.4.3``| |``foss/2021b`` ``5.4.5``| |``foss/2022a`` +``5.4.7``| |``foss/2022b`` ### BUStools @@ -3666,7 +3798,7 @@ version |toolchain ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) +[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) ### c-ares @@ -3770,6 +3902,16 @@ version |versionsuffix |toolchain ``2.1.0``|``-Python-2.7.14``|``intel/2018a`` ``2.1.0``|``-Python-3.6.4`` |``intel/2018a`` +### CalculiX-CrunchiX + +A Free Software Three-Dimensional Structural Finite Element Program + +*homepage*: + +version |toolchain +--------|-------------- +``2.20``|``foss/2021a`` + ### Calendrical Calendrical module is for calendrical calculations. @@ -3824,7 +3966,7 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: version |versionsuffix |toolchain ----------|----------------|---------------------------------------------------------- +---------|----------------|------------------------------------------------------------------------------ ``1.4`` | |``foss/2016b`` ``1.7`` | |``intel/2018a`` ``1.8`` |``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` @@ -3833,7 +3975,7 @@ version |versionsuffix |toolchain ``1.9`` |``-Java-11`` |``GCCcore/8.3.0`` ``2.1.1``| |``GCCcore/10.2.0`` ``2.1.1``|``-Java-11`` |``GCCcore/9.3.0`` -``2.2`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``2.2`` |``-Java-11`` |``GCCcore/10.3.0`` ### Canvas @@ -3929,6 +4071,16 @@ version |versionsuffix |toolchain ``0.20.0`` | |``foss/2021a`` ``0.20.3`` | |``foss/2021b``, ``foss/2022a`` +### CASA + +CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama Large Millimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also for other radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, and one of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA Sky Survey (VLASS). + +*homepage*: + +version |versionsuffix|toolchain +------------|-------------|---------- +``6.5.5-21``|``-py3.8`` |``system`` + ### casacore A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them. @@ -4115,7 +4267,7 @@ Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by cach *homepage*: version |versionsuffix|toolchain -----------|-------------|------------------ +----------|-------------|------------------------------ ``3.2.5`` | |``system`` ``3.3.1`` | |``system`` ``3.3.3`` | |``system`` @@ -4123,7 +4275,7 @@ version |versionsuffix|toolchain ``3.7.11``| |``system`` ``4.2.1`` | |``system`` ``4.6.1`` | |``GCCcore/11.2.0`` -``4.6.3`` | |``system`` +``4.6.3`` | |``GCCcore/11.3.0``, ``system`` ### CCfits @@ -4159,6 +4311,16 @@ version |versionsuffix |toolchain ``1.6.3``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` ``1.7.2``| |``foss/2021b`` +### cctbx-base + +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications. + +*homepage*: + +version |toolchain +----------|---------------------------------- +``2020.8``|``foss/2020b``, ``fosscuda/2020b`` + ### cctools The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once. @@ -4176,11 +4338,11 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: version |versionsuffix |toolchain ----------|--------------|------------------------------------------------------------------------------------------------------------------------------------- +---------|--------------|----------------------------------------------------------------------------------------------------------------------------------------------------- ``4.6.4``|``-2015-0603``|``GNU/4.9.3-2.25`` ``4.6.6``| |``foss/2016b`` ``4.6.8``| |``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +``4.8.1``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` ### CDAT @@ -4331,11 +4493,13 @@ version |toolchain a generalist algorithm for cellular segmentation -*homepage*: +*homepage*: -version |toolchain ----------|---------------------------------- -``0.6.5``|``foss/2020b``, ``fosscuda/2020b`` +version |versionsuffix |toolchain +---------|----------------|---------------------------------- +``0.6.5``| |``foss/2020b``, ``fosscuda/2020b`` +``2.2.2``| |``foss/2022a`` +``2.2.2``|``-CUDA-11.7.0``|``foss/2022a`` ### CellRanger @@ -4665,6 +4829,7 @@ version |versionsuffix |toolchain ---------|-----------------|------------------------------- ``1.2.0``|``-Python-3.6.6``|``intel/2018b`` ``1.3.0``| |``foss/2020b``, ``intel/2020b`` +``1.4.0``| |``foss/2020b``, ``intel/2020b`` ### chewBBACA @@ -4783,6 +4948,16 @@ version |versionsuffix |toolchain ``0.69-6``|``-Perl-5.28.0``|``GCCcore/7.3.0`` ``0.69-9``| |``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +### Circuitscape + +Algorithms from circuit theory to predict connectivity in heterogeneous landscapes + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|---------- +``5.12.3``|``-Julia-1.7.2``|``system`` + ### CIRI CircRNA Identifier. A de novo circular RNA identification tool @@ -4923,6 +5098,8 @@ version |toolchain ``2.4.1.3``|``foss/2019b``, ``foss/2020a`` ``2.4.4.0``|``GCC/10.2.0``, ``GCC/11.2.0`` ``2.4.5.1``|``GCC/11.2.0`` +``2.4.5.3``|``GCC/11.3.0`` +``2.4.6.2``|``GCC/11.3.0`` ``2.4.6.4``|``GCC/12.2.0`` ### CliMetLab @@ -5107,6 +5284,7 @@ CmdStanR is a lightweight interface to Stan for R users version |versionsuffix|toolchain ---------|-------------|-------------- ``0.5.0``|``-R-4.1.2`` |``foss/2021b`` +``0.5.2``|``-R-4.2.1`` |``foss/2022a`` ### cmocean @@ -5145,12 +5323,13 @@ A command-line toolkit and Python library for detecting copy number variants an *homepage*: -version |versionsuffix |toolchain ----------|-------------------------|--------------- -``0.9.2``|``-Python-2.7.14`` |``intel/2017b`` -``0.9.3``|``-Python-3.6.4`` |``intel/2018a`` -``0.9.6``|``-Python-3.7.2-R-3.6.0``|``foss/2019a`` -``0.9.8``|``-R-4.0.3`` |``foss/2020b`` +version |versionsuffix |toolchain +----------|-------------------------|--------------- +``0.9.2`` |``-Python-2.7.14`` |``intel/2017b`` +``0.9.3`` |``-Python-3.6.4`` |``intel/2018a`` +``0.9.6`` |``-Python-3.7.2-R-3.6.0``|``foss/2019a`` +``0.9.8`` |``-R-4.0.3`` |``foss/2020b`` +``0.9.10``|``-R-4.2.2`` |``foss/2022b`` ### CNVnator @@ -5498,6 +5677,7 @@ version |versionsuffix |toolchain ---------|------------------|-------------- ``2.0.1``|``-Python-2.7.15``|``foss/2019a`` ``2.0.1``|``-Python-3.7.2`` |``foss/2019a`` +``2.2.2``| |``foss/2021b`` ### CoSymLib @@ -5594,6 +5774,16 @@ version |toolchain ---------|-------------- ``0.3.1``|``GCC/11.3.0`` +### CppHeaderParser + +CppHeaderParser is a pure python module that will parse C++ header files and generate a data structure representing the class. + +*homepage*: + +version |toolchain +---------|------------------ +``2.7.4``|``GCCcore/11.3.0`` + ### CppUnit CppUnit is the C++ port of the famous JUnit framework for unit testing. @@ -5984,6 +6174,16 @@ version |toolchain ``4.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``4.8`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +### CuCLARK + +Metagenomic classifier for CUDA-enabled GPUs + +*homepage*: + +version|toolchain +-------|------------------ +``1.1``|``fosscuda/2019b`` + ### CUDA CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. @@ -6022,6 +6222,8 @@ version |toolchain ``11.8.0`` |``system`` ``12.0.0`` |``system`` ``12.1.0`` |``system`` +``12.1.1`` |``system`` +``12.2.0`` |``system`` ### CUDA-Samples @@ -6105,6 +6307,7 @@ version |versionsuffix |toolchain ``8.6.0.163``|``-CUDA-11.8.0`` |``system`` ``8.7.0.84`` |``-CUDA-11.8.0`` |``system`` ``8.8.0.121``|``-CUDA-12.0.0`` |``system`` +``8.9.2.26`` |``-CUDA-12.1.1`` |``system`` ### Cufflinks @@ -6215,11 +6418,13 @@ version |versionsuffix |toolchain ``2.1`` |``-Python-3.6.6`` |``foss/2018b`` ``2.7`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` ``2.8`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` +``2.10`` | |``GCCcore/10.2.0`` ``2.10`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` ``2.10`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``3.4`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.5`` | |``GCCcore/11.2.0`` ``4.2`` | |``GCCcore/11.3.0`` +``4.4`` | |``GCCcore/12.2.0`` ### cuTENSOR @@ -6234,6 +6439,17 @@ version |versionsuffix |toolchain ``1.6.0.3``|``-CUDA-11.3.1``|``system`` ``1.6.1.5``|``-CUDA-11.4.1``|``system`` ``1.6.1.5``|``-CUDA-11.7.0``|``system`` +``1.7.0.1``|``-CUDA-12.0.0``|``system`` + +### cuteSV + +cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. + +*homepage*: + +version |toolchain +---------|-------------- +``2.0.3``|``foss/2022a`` ### CVS @@ -6259,6 +6475,7 @@ version |versionsuffix |toolchain ``1.2.3``|``-Python-3.6.6`` |``intel/2018b`` ``1.2.4``|``-Python-3.7.4`` |``intel/2019b`` ``1.2.6``| |``foss/2020b``, ``foss/2021a`` +``1.3.1``| |``foss/2022a`` ### CVXPY @@ -6387,7 +6604,7 @@ version |versionsuffix |toolchain ## D -[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dxpy](#dxpy) - [DyMat](#dymat) +[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) ### dadi @@ -6420,6 +6637,26 @@ version |toolchain ----------|-------------- ``6.16.0``|``foss/2021b`` +### DALI + +R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``2.1.2``|``-R-4.2.2`` |``foss/2022b`` + +### DaliLite + +DaliLite is a light version of the software run by the Dali server. The web server has search and data visualization options which are not included in this package. DaliLite supports data import (import.pl) to convert PDB entries to Dali's internal data format and pairwise comparison (dali.pl) to structurally align a list of query structures to a list of target structures. + +*homepage*: + +version|toolchain +-------|--------------- +``4.1``|``gompi/2021a`` + ### Dalton The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html. @@ -6430,6 +6667,7 @@ version |versionsuffix|toolchain ----------|-------------|--------------- ``2016`` |``-i8`` |``intel/2017b`` ``2020.0``| |``foss/2021a`` +``2020.1``| |``foss/2022b`` ### damageproto @@ -6524,6 +6762,7 @@ version|toolchain -------|-------------------------------------------------------- ``1.3``|``foss/2018a`` ``1.5``|``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.8``|``GCCcore/11.3.0`` ### davix @@ -6809,6 +7048,17 @@ version |versionsuffix |toolchain ``3.3.1``|``-Python-3.8.2``|``foss/2020a`` ``3.5.0``| |``foss/2021a`` ``3.5.1``| |``foss/2021b`` +``3.5.2``| |``foss/2022a`` + +### DEICODE + +DEICODE is a form of Aitchison Distance that is robust to high levels of sparsity. DEICODE utilizes a natural solution to the zero problem formulated in recommendation systems called matrix completion. A simple way to interpret the method is, as a robust compositional PCA (via SVD) where zero values do not influence the resulting ordination. + +*homepage*: + +version |toolchain +---------|-------------- +``0.2.4``|``foss/2022a`` ### Delly @@ -6839,10 +7089,10 @@ A Python library for phylogenetics and phylogenetic computing: reading, writing *homepage*: version |versionsuffix |toolchain ----------|------------------|------------------------------------------------------------------------------ +---------|------------------|-------------------------------------------------------------------------------------------------- ``4.4.0``| |``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` ``4.4.0``|``-Python-2.7.15``|``intel/2018b`` -``4.5.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.5.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``4.5.2``|``-Python-2.7.18``|``GCCcore/10.2.0`` ### DensPart @@ -7010,6 +7260,7 @@ version |toolchain ``2.0.11``|``GCC/10.3.0`` ``2.0.13``|``GCC/10.3.0``, ``GCC/11.2.0`` ``2.1.0`` |``GCC/11.3.0`` +``2.1.8`` |``GCC/10.3.0`` ### Dice @@ -7038,9 +7289,9 @@ Python library for converting dicom files to nifti *homepage*: version |versionsuffix |toolchain -----------|-----------------|-------------- +----------|-----------------|---------------------------------- ``2.2.12``|``-Python-3.8.2``|``foss/2020a`` -``2.3.0`` | |``foss/2020b`` +``2.3.0`` | |``foss/2020b``, ``fosscuda/2020b`` ### DicomBrowser @@ -7092,12 +7343,12 @@ DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electr *homepage*: version |versionsuffix |toolchain ---------|----------------------------|------------------------------- +--------|----------------------------|---------------------------------------------------------------- ``19.0``|``-Python-2.7.18-int64`` |``intel/2020a`` ``19.0``|``-Python-2.7.18-mpi-int64``|``intel/2020a`` ``22.0``| |``foss/2021a``, ``intel/2021a`` ``22.0``|``-int64`` |``intel/2021a`` -``23.0``| |``foss/2022b``, ``intel/2022b`` +``23.0``| |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` ``23.0``|``-int64`` |``intel/2022b`` ### distributed @@ -7176,6 +7427,16 @@ version|toolchain -------|-------------- ``0.3``|``GCC/10.3.0`` +### dm-haiku + +Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural network library for TensorFlow. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.0.9``|``-CUDA-11.3.1``|``foss/2021a`` + ### dm-reverb Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues. @@ -7233,6 +7494,7 @@ version |toolchain ``2.5.1``|``system`` ``2.5.2``|``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b`` ``2.6.0``|``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``3.0.0``|``GCCcore/11.3.0`` ### DOLFIN @@ -7245,6 +7507,16 @@ version |versionsuffix |toolchain ``2018.1.0.post1``|``-Python-3.6.4``|``foss/2018a`` ``2019.1.0.post0``|``-Python-3.7.4``|``foss/2019b`` +### dominate + +Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API. It allows you to write HTML pages in pure Python very concisely, which eliminates the need to learn another template language, and lets you take advantage of the more powerful features of Python. + +*homepage*: + +version |toolchain +---------|------------------ +``2.8.0``|``GCCcore/11.3.0`` + ### dorado Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. @@ -7254,6 +7526,8 @@ Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nan version |versionsuffix |toolchain ---------|----------------|-------------- ``0.1.1``|``-CUDA-11.7.0``|``foss/2022a`` +``0.3.0``|``-CUDA-11.7.0``|``foss/2022a`` +``0.3.1``|``-CUDA-11.7.0``|``foss/2022a`` ### Doris @@ -7452,6 +7726,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.1.0``|``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` ``1.1.2``|``gompi/2020b`` +``1.1.4``|``gompi/2022a`` ### dtcwt @@ -7514,6 +7789,17 @@ Duplex Tools contains a set of utilities for dealing with Duplex sequencing data version |toolchain ---------|-------------- ``0.3.1``|``foss/2022a`` +``0.3.3``|``foss/2022a`` + +### dx-toolkit + +The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; and Python, Java, C++ and R bindings for working on the DNAnexus Platform. + +*homepage*: + +version |toolchain +-----------|------------------ +``0.350.1``|``GCCcore/12.2.0`` ### dxpy @@ -7538,7 +7824,7 @@ version|versionsuffix |toolchain ## E -[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ED2](#ed2) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) +[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) ### E-ANTIC @@ -7572,6 +7858,16 @@ version |versionsuffix |toolchain -----------|------------------|--------------- ``0.1.143``|``-Python-2.7.14``|``intel/2018a`` +### easel + +Easel supports computational analysis of biological sequences using probabilistic models. + +*homepage*: + +version |toolchain +--------|-------------- +``0.48``|``GCC/12.2.0`` + ### EasyBuild EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. @@ -7675,6 +7971,7 @@ version |toolchain ``4.6.2`` |``system`` ``4.7.0`` |``system`` ``4.7.1`` |``system`` +``4.7.2`` |``system`` ### EasyQC @@ -7729,6 +8026,16 @@ version |versionsuffix |toolchain ``1.0.0``|``-Python-3.8.2``|``foss/2020a`` ``1.1.0``| |``foss/2020b`` +### ecFlow + +ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms. + +*homepage*: + +version |toolchain +---------|-------------- +``5.7.0``|``GCC/10.2.0`` + ### ED2 The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry @@ -7740,6 +8047,16 @@ version |versionsuffix|toolchain ``20170201``| |``intel/2017a`` ``20170201``|``-serial`` |``intel/2017a`` +### EDirect + +Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. + +*homepage*: + +version |toolchain +-----------------|------------------ +``19.7.20230531``|``GCCcore/10.3.0`` + ### edlib Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. @@ -7747,11 +8064,11 @@ Lightweight, super fast library for sequence alignment using edit (Levenshtein) *homepage*: version |versionsuffix |toolchain ----------------|-----------------|-------------------------------------------------------------- +---------------|-----------------|------------------------------------------------------------------------------ ``1.3.8.post1``|``-Python-3.7.4``|``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.3.8.post1``|``-Python-3.8.2``|``GCC/9.3.0`` ``1.3.8.post2``|``-Python-3.8.2``|``iccifort/2020.1.217`` -``1.3.9`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.3.9`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### EggLib @@ -7774,6 +8091,7 @@ version |versionsuffix |toolchain ``1.0.3`` |``-Python-2.7.14``|``intel/2018a`` ``2.1.4`` | |``foss/2020b`` ``2.1.7`` | |``foss/2021b`` +``2.1.9`` | |``foss/2022a`` ``2.1.10``| |``foss/2020b`` ### EGTtools @@ -7838,11 +8156,11 @@ The EIGENSOFT package combines functionality from our population genetics method *homepage*: version |toolchain ----------|------------------------------------------------------------------------------- +---------|----------------------------------------------------------------------------------------------- ``6.0.1``|``foss/2016a`` ``6.1.1``|``foss/2016a`` ``6.1.4``|``foss/2016b`` -``7.2.1``|``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2021a``, ``intel/2019a`` +``7.2.1``|``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019a`` ### einops @@ -7861,9 +8179,10 @@ elastix: a toolbox for rigid and nonrigid registration of images. *homepage*: -version |toolchain ----------|-------------- -``4.9.0``|``foss/2018a`` +version |versionsuffix |toolchain +---------|-----------------|-------------- +``4.9.0``| |``foss/2018a`` +``5.0.0``|``-Python-3.7.4``|``foss/2019b`` ### elbencho @@ -7933,7 +8252,7 @@ version |versionsuffix |toolchain ``2020.11.001`` | |``foss/2020b``, ``intel/2020b`` ``2021.05.001`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` ``2021.05.002`` | |``intel/2020b`` -``2021.11.001`` | |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``2021.11.001`` | |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b`` ``2022.05.001`` | |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` ``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ``2022.05.001`` |``-CUDA-12.0.0``|``foss/2022b`` @@ -7999,6 +8318,7 @@ version |versionsuffix|toolchain ``27.1``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``27.2``| |``GCCcore/11.2.0`` ``28.1``| |``GCCcore/10.2.0`` +``28.2``| |``GCCcore/12.2.0`` ### EMAN2 @@ -8040,13 +8360,14 @@ version |toolchain Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet! -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|------------------|------------------------------- ``2.2.1``| |``foss/2019a`` ``2.2.1``|``-Python-2.7.15``|``foss/2018b``, ``intel/2018b`` ``2.2.1``|``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` +``3.1.4``| |``foss/2021b`` ### EMU @@ -8266,6 +8587,7 @@ version |versionsuffix |toolchain ``3.0.0b36``|``-Python-2.7.12``|``intel/2016b`` ``3.1.1`` |``-Python-3.6.6`` |``foss/2018b`` ``3.1.2`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``3.1.2`` |``-Python-3.7.4`` |``foss/2019b`` ``3.1.2`` |``-Python-3.8.2`` |``foss/2020a`` ### ETSF_IO @@ -8379,8 +8701,8 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.4.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``2.4.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` ### expat @@ -8445,6 +8767,7 @@ version |toolchain ``3.7.1``|``intel/2019a`` ``3.8.0``|``gompi/2020b`` ``3.8.3``|``gompi/2021a`` +``4.0.4``|``gompi/2022a`` ### EZC3D @@ -8459,7 +8782,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) +[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) ### f90cache @@ -8549,12 +8872,12 @@ version |toolchain The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. -*homepage*: +*homepage*: version |toolchain ------------|-------------- +-----------|------------------------------ ``36.3.5e``|``foss/2016b`` -``36.3.8i``|``GCC/11.2.0`` +``36.3.8i``|``GCC/11.2.0``, ``GCC/12.2.0`` ### fastahack @@ -8662,7 +8985,9 @@ version |toolchain ----------|------------------------------------------------------------ ``0.19.7``|``foss/2018b`` ``0.20.0``|``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.20.1``|``iccifort/2020.1.217`` ``0.23.2``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``0.23.4``|``GCC/12.2.0`` ### fastparquet @@ -9101,7 +9426,7 @@ version |versionsuffix|toolchain ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` -``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a`` +``3.3.10``| |``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2022b`` ### FFTW.MPI @@ -9110,8 +9435,8 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------------ -``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``nvompi/2022.07`` +----------|----------------------------------------------------------------------------------------------------------- +``3.3.10``|``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023a``, ``nvompi/2022.07`` ### fgbio @@ -9433,9 +9758,9 @@ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate softwa *homepage*: version |toolchain -----------|------------------------------------------------------------- +----------|------------------------------------------------------------------ ``1.2.11``|``GCC/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` -``2.2.00``|``GCC/11.2.0``, ``foss/2018b``, ``foss/2020b`` +``2.2.00``|``GCC/11.2.0``, ``GCCcore/12.2.0``, ``foss/2018b``, ``foss/2020b`` ### Flask @@ -9496,14 +9821,14 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.5.35``|``system`` ``2.5.38``|``GCC/4.8.2`` ``2.5.39``|``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` ``2.6.0`` |``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` |``intel/2016b`` ``2.6.3`` |``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` +``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` ### Flexbar @@ -9527,6 +9852,7 @@ version |toolchain ``3.1.3``|``GCC/11.2.0`` ``3.2.0``|``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``3.2.1``|``GCC/12.2.0`` +``3.3.1``|``GCC/12.3.0`` ### FlexiDot @@ -9611,6 +9937,7 @@ version |toolchain ``18.0`` |``system`` ``18.1`` |``system`` ``18.2`` |``system`` +``2019R3``|``system`` ``2021R1``|``system`` ``2021R2``|``system`` @@ -9743,6 +10070,7 @@ version |versionsuffix |toolchain ``2.13.94``| |``GCCcore/11.2.0`` ``2.14.0`` | |``GCCcore/11.3.0`` ``2.14.1`` | |``GCCcore/12.2.0`` +``2.14.2`` | |``GCCcore/12.3.0`` ### fontsproto @@ -9795,6 +10123,7 @@ version |toolchain ``2022.10``|``system`` ``2022a`` |``system`` ``2022b`` |``system`` +``2023a`` |``system`` ### fosscuda @@ -9883,6 +10212,16 @@ version |toolchain --------|--------------------------------------------------------------------------------------------- ``1.31``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +### FragPipe + +FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. + +*homepage*: + +version |versionsuffix|toolchain +--------|-------------|---------- +``20.0``|``-Java-11`` |``system`` + ### FRANz A fast and flexible parentage inference program for natural populations. @@ -9992,6 +10331,9 @@ version |versionsuffix |toolchain ``7.2.0``|``-ubuntu18_amd64``|``system`` ``7.3.2``|``-centos7_x86_64``|``system`` ``7.3.2``|``-centos8_x86_64``|``system`` +``7.4.0``|``-centos8_x86_64``|``system`` +``7.4.0``|``-ubuntu20_amd64``|``system`` +``7.4.0``|``-ubuntu22_amd64``|``system`` ### FreeTDS @@ -10026,6 +10368,7 @@ version |versionsuffix |toolchain ``2.10.4``| |``GCCcore/10.3.0`` ``2.11.0``| |``GCCcore/11.2.0`` ``2.12.1``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.13.0``| |``GCCcore/12.3.0`` ### freetype-py @@ -10300,7 +10643,7 @@ version|toolchain ## G -[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM-library](#gem-library) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) +[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -10471,7 +10814,7 @@ version |versionsuffix |toolchain ``8.2`` |``-Python-2.7.15`` |``foss/2018b`` ``9.0`` |``-Python-3.7.4`` |``foss/2019b`` ``9.1`` | |``foss/2021b`` -``9.2`` | |``foss/2021b`` +``9.2`` | |``foss/2021b``, ``foss/2022a`` ### GATK @@ -10520,6 +10863,7 @@ version |versionsuffix |toolchain ``4.2.5.0`` |``-Java-11`` |``GCCcore/11.2.0`` ``4.2.6.1`` |``-Java-11`` |``GCCcore/11.2.0`` ``4.3.0.0`` |``-Java-11`` |``GCCcore/11.3.0`` +``4.4.0.0`` |``-Java-17`` |``GCCcore/12.2.0`` ### Gaussian @@ -10569,9 +10913,10 @@ GBprocesS allows for the extraction of genomic inserts from NGS data for GBS exp *homepage*: -version|versionsuffix |toolchain --------|-----------------|--------------- -``2.3``|``-Python-3.8.2``|``intel/2020a`` +version |versionsuffix |toolchain +---------------|-----------------|--------------- +``2.3`` |``-Python-3.8.2``|``intel/2020a`` +``4.0.0.post1``| |``foss/2022a`` ### gbs2ploidy @@ -10679,6 +11024,7 @@ version |versionsuffix |toolchain ``11.1.0``| |``system`` ``11.2.0``| |``system`` ``11.3.0``| |``system`` +``11.4.0``| |``system`` ``12.1.0``| |``system`` ``12.2.0``| |``system`` ``12.3.0``| |``system`` @@ -10724,6 +11070,7 @@ version |toolchain ``11.1.0``|``system`` ``11.2.0``|``system`` ``11.3.0``|``system`` +``11.4.0``|``system`` ``12.1.0``|``system`` ``12.2.0``|``system`` ``12.3.0``|``system`` @@ -10776,6 +11123,7 @@ GCTA (Genome-wide Complex Trait Analysis) is a software package, which was init version |toolchain --------------|------------------------------ ``1.94.0beta``|``foss/2021b``, ``gfbf/2022a`` +``1.94.1`` |``gfbf/2022a`` ### Gctf @@ -10974,13 +11322,14 @@ A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. *homepage*: -version|versionsuffix |toolchain --------|----------------|---------------------------------------------------------- -``2.1``|``-CUDA-11.0.2``|``GCCcore/9.3.0`` -``2.1``|``-CUDA-11.1.1``|``GCCcore/10.2.0`` -``2.1``|``-CUDA-11.2.1``|``GCCcore/10.2.0`` -``2.2``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +version |versionsuffix |toolchain +---------|----------------|---------------------------------------------------------- +``2.1`` |``-CUDA-11.0.2``|``GCCcore/9.3.0`` +``2.1`` |``-CUDA-11.1.1``|``GCCcore/10.2.0`` +``2.1`` |``-CUDA-11.2.1``|``GCCcore/10.2.0`` +``2.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.3`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.3.1``| |``GCCcore/12.3.0`` ### Geant4 @@ -11002,7 +11351,8 @@ version |toolchain ``10.7.1`` |``GCC/10.2.0``, ``GCC/11.2.0`` ``11.0.0`` |``GCC/11.2.0`` ``11.0.1`` |``GCC/11.2.0`` -``11.0.2`` |``GCC/11.2.0`` +``11.0.2`` |``GCC/11.2.0``, ``GCC/11.3.0`` +``11.1.2`` |``GCC/11.3.0`` ### Geant4-data @@ -11012,6 +11362,7 @@ Datasets for Geant4. version |toolchain ------------|---------- +``11.1`` |``system`` ``20201103``|``system`` ``20210510``|``system`` @@ -11035,6 +11386,16 @@ version |toolchain ----------|------------------ ``0.4.30``|``GCCcore/10.3.0`` +### GEM + +GEM (Gene-Environment interaction analysis for Millions of samples) is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference. + +*homepage*: + +version |toolchain +---------|------------------------------ +``1.5.1``|``foss/2022a``, ``foss/2022b`` + ### GEM-library Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true "next-generation" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it. @@ -11045,6 +11406,16 @@ version |versionsuffix |toolchain -------------------|-------------------------------|---------- ``20130406-045632``|``_pre-release-3_Linux-x86_64``|``system`` +### gemelli + +Gemelli is a tool box for running both Robust Aitchison PCA (RPCA) and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets. + +*homepage*: + +version |toolchain +---------|-------------- +``0.0.9``|``foss/2022a`` + ### GEMMA Genome-wide Efficient Mixed Model Association @@ -11055,7 +11426,7 @@ version |toolchain ----------|------------------------------ ``0.97`` |``foss/2016b``, ``foss/2017a`` ``0.98.1``|``foss/2018b`` -``0.98.5``|``foss/2021b`` +``0.98.5``|``foss/2021b``, ``foss/2022b`` ### gemmi @@ -11097,8 +11468,8 @@ Gengetopt is a tool to write command line option parsing code for C programs. *homepage*: version |toolchain ---------|--------------------------------------------------------- -``2.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +--------|----------------------------------------------------------------------------- +``2.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### GenMap @@ -11168,12 +11539,12 @@ A comprehensive software library for efficient processing of structured genome a *homepage*: version |versionsuffix |toolchain -----------|------------------|-------------------------------------------- +----------|------------------|---------------------------------------------- ``1.5.10``| |``foss/2018b`` ``1.5.10``|``-Python-2.7.15``|``foss/2018b`` ``1.6.1`` | |``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0`` ``1.6.1`` |``-Python-2.7.16``|``GCC/8.3.0`` -``1.6.2`` | |``GCC/10.3.0``, ``GCC/11.3.0`` +``1.6.2`` | |``GCC/10.3.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### GenomeWorks @@ -11325,6 +11696,7 @@ version |versionsuffix |toolchain ``1.7.4-pre2``| |``foss/2020b`` ``1.7.5.3`` | |``foss/2021b`` ``1.7.6.1`` | |``foss/2021b`` +``1.7.7.0`` | |``foss/2022a`` ### gettext @@ -11365,6 +11737,7 @@ version |toolchain ---------|---------- ``2022a``|``system`` ``2022b``|``system`` +``2023a``|``system`` ### GffCompare @@ -11387,11 +11760,11 @@ GFF/GTF parsing utility providing format conversions, region filtering, FASTA se *homepage*: version |toolchain -----------|-------------------------------------- +----------|---------------------------------------------------------- ``0.9.12``|``foss/2016b`` ``0.10.6``|``GCCcore/7.3.0`` ``0.11.6``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.12.7``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.12.7``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.2.0`` ### gflags @@ -11627,6 +12000,7 @@ version |versionsuffix|toolchain ``2.33.1`` |``-nodocs`` |``GCCcore/11.2.0`` ``2.36.0`` |``-nodocs`` |``GCCcore/11.3.0`` ``2.38.1`` |``-nodocs`` |``GCCcore/12.2.0`` +``2.41.0`` |``-nodocs`` |``GCCcore/12.3.0`` ### git-extras @@ -11737,7 +12111,7 @@ version |versionsuffix|toolchain ``2.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` ``2.2.0``|``-egl`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``2.2.0``|``-glx`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``2.2.0``|``-osmesa`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``2.2.0``|``-osmesa`` |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### GLFW @@ -11844,6 +12218,16 @@ version |toolchain ``3.0.4`` |``foss/2016b``, ``foss/2018b`` ``3.0.4c``|``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/8.3.0`` +### GLIMPSE + +GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets + +*homepage*: + +version |toolchain +---------|---------------------------------------------- +``2.0.0``|``GCC/10.3.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` + ### GLM OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. @@ -11968,8 +12352,9 @@ version |toolchain ``2019-03-15``|``foss/2018b`` ``2019-09-12``|``GCC/8.3.0`` ``2020-12-17``|``GCC/9.3.0`` -``2021-21-17``|``GCC/11.2.0`` +``2021-12-17``|``GCC/11.2.0`` ``2023-02-17``|``GCC/11.3.0`` +``2023-04-20``|``GCC/12.2.0`` ### GMP @@ -11987,7 +12372,7 @@ version |toolchain ``6.1.1`` |``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` |``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``6.2.1`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### gmpich @@ -12314,6 +12699,7 @@ version |versionsuffix|toolchain ``2022.10``| |``system`` ``2022a`` | |``system`` ``2022b`` | |``system`` +``2023a`` | |``system`` ``system`` |``-2.29`` |``system`` ### gompic @@ -12416,9 +12802,9 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.0.4``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gperftools @@ -12569,8 +12955,8 @@ Graphite is a "smart font" system developed specifically to handle the complexi *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------------------------- -``1.3.14``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` +----------|----------------------------------------------------------------------------------------------------------------------------------------- +``1.3.14``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` ### GraPhlAn @@ -12714,6 +13100,16 @@ version |toolchain ------------|--------------- ``20220610``|``intel/2022a`` +### GRIDSS + +GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``2.13.2``|``-Java-11`` |``foss/2021b`` + ### GRIT GRIT - A tool for the integrative analysis of RNA-seq type assays @@ -12783,7 +13179,8 @@ version |versionsuffix |toolchain ``2019`` | |``foss/2018b``, ``fosscuda/2018b`` ``2019.2``| |``fosscuda/2019a`` ``2019.3``| |``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``2019.4``| |``foss/2019b`` +``2019.4``| |``foss/2019b``, ``fosscuda/2019b`` +``2019.4``|``-PLUMED-2.5.4`` |``foss/2019b``, ``fosscuda/2019b`` ``2019.6``| |``fosscuda/2019b`` ``2020`` | |``foss/2019b``, ``fosscuda/2019b`` ``2020.1``|``-Python-3.8.2`` |``foss/2020a`` @@ -12800,6 +13197,8 @@ version |versionsuffix |toolchain ``2021.5``|``-CUDA-11.4.1`` |``foss/2021b`` ``2021.5``|``-CUDA-11.4.1-PLUMED-2.8.0``|``foss/2021b`` ``2021.5``|``-PLUMED-2.8.0`` |``foss/2021b`` +``2023.1``| |``foss/2022a`` +``2023.1``|``-CUDA-11.7.0`` |``foss/2022a`` ### GromacsWrapper @@ -12859,7 +13258,7 @@ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmer *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``1.16`` |``foss/2016a``, ``intel/2016a`` ``2.1`` |``GCC/5.4.0-2.26``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.2.1``|``intel/2016a``, ``intel/2016b`` @@ -12867,7 +13266,7 @@ version |toolchain ``2.4`` |``GCCcore/6.4.0`` ``2.5`` |``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` |``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCCcore/12.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### gSOAP @@ -13131,7 +13530,7 @@ version |versionsuffix |toolchain ``9.1.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` ``9.5.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``9.5.2`` | |``GCCcore/11.3.0`` -``10.0.1``| |``GCCcore/12.2.0`` +``10.0.1``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### GUSHR @@ -13159,7 +13558,7 @@ version |toolchain ## H -[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HD-BET](#hd-bet) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [HTSplotter](#htsplotter) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) +[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HD-BET](#hd-bet) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [HOOMD-blue](#hoomd-blue) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [HTSplotter](#htsplotter) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) ### h4toh5 @@ -13461,8 +13860,8 @@ version |versionsuffix|toolchain ``1.10.8`` | |``gompi/2021b``, ``gompi/2022a`` ``1.12.0`` | |``gompi/2020a``, ``iimpi/2020a`` ``1.12.1`` | |``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` -``1.12.2`` | |``gompi/2022a``, ``iimpi/2022a`` -``1.12.2`` |``-serial`` |``GCC/11.3.0`` +``1.12.2`` | |``gompi/2022a``, ``iimpi/2022a``, ``nvompi/2022.07`` +``1.12.2`` |``-serial`` |``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``1.13.1`` | |``gompi/2022a``, ``iimpi/2022a`` ``1.13.1`` |``-serial`` |``GCC/11.3.0`` ``1.14.0`` | |``gompi/2022b``, ``iimpi/2022b`` @@ -13568,7 +13967,7 @@ version |toolchain ``1.47.16``|``GCCcore/10.2.0`` ``1.48.3`` |``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` ``1.49.2`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` -``1.49.3`` |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0`` ### HepMC3 @@ -13644,6 +14043,7 @@ version |toolchain ----------|------------------------------------- ``0.15.2``|``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.16.1``|``GCCcore/10.3.0`` +``0.19.5``|``GCCcore/11.2.0`` ### HighFive @@ -13665,7 +14065,7 @@ version |toolchain ----------|-------------------------------------- ``0.12.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.0.3`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``1.0.4`` |``GCCcore/12.3.0`` +``1.0.4`` |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### HIP @@ -13779,11 +14179,11 @@ HMMER is used for searching sequence databases for homologs of protein sequence *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.1b2``|``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1``|``gompi/2020a``, ``iimpi/2020a`` -``3.3.2``|``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` +``3.3.2``|``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` ### HMMER2 @@ -13816,6 +14216,16 @@ version|versionsuffix |toolchain -------|------------------|-------------- ``0.9``|``-Python-2.7.13``|``foss/2017a`` +### HOOMD-blue + +HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs. + +*homepage*: + +version |toolchain +---------|-------------- +``4.0.1``|``foss/2022a`` + ### Horovod Horovod is a distributed training framework for TensorFlow. @@ -13843,6 +14253,7 @@ version |versionsuffix |toolchain ``0.22.1``|``-TensorFlow-2.5.0-Python-3.7.4`` |``fosscuda/2019b`` ``0.23.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` ``0.23.0``|``-TensorFlow-2.5.0`` |``fosscuda/2020b`` +``0.25.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` ### horton @@ -13904,10 +14315,10 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: version|toolchain --------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1``|``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2``|``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022b``, ``intel/2023.03``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` +``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -14045,6 +14456,7 @@ version |toolchain ``2.5.0`` |``GCCcore/11.2.0`` ``2.7.1`` |``GCCcore/11.3.0`` ``2.8.0`` |``GCCcore/12.2.0`` +``2.9.1`` |``GCCcore/12.3.0`` ### Hydra @@ -14563,6 +14975,7 @@ version |versionsuffix |toolchain ``2022a`` | |``system`` ``2022b`` | |``system`` ``2023.03`` | |``system`` +``2023a`` | |``system`` ``system`` |``-GCC-system-2.29``|``system`` ### iimpic @@ -14629,9 +15042,9 @@ Imagecodecs is a Python library that provides block-oriented, in-memory buffer t *homepage*: version |toolchain --------------|-------------- +-------------|------------------------------ ``2021.8.26``|``foss/2020b`` -``2022.9.26``|``foss/2021a`` +``2022.9.26``|``foss/2021a``, ``foss/2022a`` ### imageio @@ -14818,7 +15231,7 @@ version |toolchain ``2022.2.0``|``iimpi/2022.09`` ``2022.2.1``|``iimpi/2022.11``, ``iimpi/2022b`` ``2023.0.0``|``iimpi/2022.12`` -``2023.1.0``|``iimpi/2023.03`` +``2023.1.0``|``iimpi/2023.03``, ``iimpi/2023a`` ### Imlib2 @@ -14989,9 +15402,9 @@ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases *homepage*: version |toolchain ----------|---------------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``1.1.2``|``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` -``1.1.4``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022b`` +``1.1.4``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b`` ### Infomap @@ -15136,6 +15549,7 @@ version |versionsuffix|toolchain ``2022a`` | |``system`` ``2022b`` | |``system`` ``2023.03`` | |``system`` +``2023a`` | |``system`` ### intel-compilers @@ -15217,6 +15631,7 @@ version |toolchain ``5.28-67.0``|``intel/2018a`` ``5.52-86.0``|``GCCcore/10.3.0`` ``5.55-88.0``|``foss/2021a`` +``5.62-94.0``|``foss/2022b`` ### InterProScan_data @@ -15256,8 +15671,8 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: version |versionsuffix |toolchain -----------|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.51.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +----------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.51.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.51.0``|``-Perl-5.20.3``|``intel/2016a`` ``0.51.0``|``-Perl-5.22.1``|``foss/2016a``, ``intel/2016a`` ``0.51.0``|``-Perl-5.24.0``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` @@ -15489,6 +15904,7 @@ version |versionsuffix|toolchain ``2.1.3`` | |``gompi/2021a`` ``2.2.1`` | |``gompi/2021b`` ``2.2.2.3``| |``gompi/2022a`` +``2.2.2.6``| |``gompi/2022a``, ``gompi/2022b`` ### Iris @@ -15545,8 +15961,8 @@ Intelligent Storage Acceleration Library *homepage*: version |toolchain -----------|------------------------------------------------------------------------------ -``2.30.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +----------|-------------------------------------------------------------------------------------------------- +``2.30.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### ISL @@ -15633,7 +16049,7 @@ Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite *homepage*: version |versionsuffix |toolchain -----------|------------------|-------------------------------------------------------------- +----------|------------------|---------------------------------------------------------------------------------- ``4.12.2``|``-Python-2.7.12``|``foss/2016b`` ``4.13.0``|``-Python-2.7.14``|``foss/2018a`` ``4.13.0``|``-Python-3.6.4`` |``foss/2018a`` @@ -15647,7 +16063,7 @@ version |versionsuffix |toolchain ``5.0b01``|``-Python-3.6.6`` |``foss/2018b`` ``5.1.2`` | |``foss/2020a``, ``fosscuda/2020a`` ``5.1.2`` |``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a`` -``5.2.1`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``5.2.1`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``fosscuda/2020b`` ### itpp @@ -15666,10 +16082,11 @@ ITS Tool allows you to translate your XML documents with PO files *homepage*: version |versionsuffix |toolchain ----------|------------------|----------------- +---------|------------------|------------------ ``2.0.5``|``-Python-2.7.14``|``intel/2018a`` ``2.0.5``|``-Python-2.7.15``|``foss/2018b`` ``2.0.6``|``-Python-3.7.2`` |``GCCcore/8.2.0`` +``2.0.7``| |``GCCcore/11.3.0`` ### ITSx @@ -15710,6 +16127,7 @@ version |toolchain ``4.2.0``|``foss/2016a``, ``intel/2016a``, ``intel/2017a`` ``4.3.0``|``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2017b`` ``4.3.1``|``foss/2022a`` +``4.3.2``|``foss/2022b`` ### Jansson @@ -15970,7 +16388,7 @@ jq is a lightweight and flexible command-line JSON processor. version|toolchain -------|---------------------------------------------------------- -``1.5``|``GCCcore/6.4.0`` +``1.5``|``GCCcore/10.2.0``, ``GCCcore/6.4.0`` ``1.6``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### json-c @@ -16071,6 +16489,7 @@ version |versionsuffix |toolchain ``1.8.0``|``-linux-x86_64``|``system`` ``1.8.2``|``-linux-x86_64``|``system`` ``1.8.5``|``-linux-x86_64``|``system`` +``1.9.0``|``-linux-x86_64``|``system`` ### JUnit @@ -16220,13 +16639,13 @@ Open source implementation of jpegxr *homepage*: version|toolchain --------|-------------------------------------- -``1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +-------|---------------------------------------------------------- +``1.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ## K -[KaHIP](#kahip) - [Kaiju](#kaiju) - [Kaleido](#kaleido) - [Kalign](#kalign) - [kallisto](#kallisto) - [KAT](#kat) - [kb-python](#kb-python) - [kbproto](#kbproto) - [kedro](#kedro) - [Kent_tools](#kent_tools) - [Keras](#keras) - [khmer](#khmer) - [kim-api](#kim-api) - [kineto](#kineto) - [king](#king) - [KITE](#kite) - [kma](#kma) - [KMC](#kmc) - [KMCP](#kmcp) - [KmerGenie](#kmergenie) - [KNIME](#knime) - [kpcalg](#kpcalg) - [Kraken](#kraken) - [Kraken2](#kraken2) - [KrakenUniq](#krakenuniq) - [Kratos](#kratos) - [krbalancing](#krbalancing) - [KronaTools](#kronatools) - [kwant](#kwant) - [KWIML](#kwiml) - [kWIP](#kwip) - [KyotoCabinet](#kyotocabinet) +[KaHIP](#kahip) - [Kaiju](#kaiju) - [Kaleido](#kaleido) - [Kalign](#kalign) - [kallisto](#kallisto) - [KAT](#kat) - [kb-python](#kb-python) - [kbproto](#kbproto) - [kedro](#kedro) - [Kent_tools](#kent_tools) - [Keras](#keras) - [KerasTuner](#kerastuner) - [khmer](#khmer) - [kim-api](#kim-api) - [kineto](#kineto) - [king](#king) - [KITE](#kite) - [kma](#kma) - [KMC](#kmc) - [KMCP](#kmcp) - [KmerGenie](#kmergenie) - [KNIME](#knime) - [kpcalg](#kpcalg) - [Kraken](#kraken) - [Kraken2](#kraken2) - [KrakenUniq](#krakenuniq) - [Kratos](#kratos) - [krbalancing](#krbalancing) - [KronaTools](#kronatools) - [kwant](#kwant) - [KWIML](#kwiml) - [kWIP](#kwip) - [KyotoCabinet](#kyotocabinet) ### KaHIP @@ -16384,6 +16803,16 @@ version |versionsuffix |toolchain ``2.4.3``| |``foss/2020b``, ``fosscuda/2020b`` ``2.4.3``|``-TensorFlow-2.5.0``|``fosscuda/2020b`` +### KerasTuner + +KerasTuner is an easy-to-use, scalable hyperparameter optimization framework that solves the pain points of hyperparameter search. + +*homepage*: + +version |toolchain +---------|-------------- +``1.3.5``|``foss/2022a`` + ### khmer In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more @@ -16406,7 +16835,7 @@ version |toolchain ``2.1.2``|``foss/2019a``, ``intel/2019a`` ``2.1.3``|``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3.0``|``GCCcore/11.2.0`` +``2.3.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### kineto @@ -16620,7 +17049,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) +[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) ### L_RNA_scaffolder @@ -16682,12 +17111,12 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At *homepage*: version |versionsuffix |toolchain --------------|-----------------------------|------------------------------- +-------------|-----------------------------|---------------------------------------------- ``3Mar2020`` |``-Python-3.7.4-kokkos`` |``foss/2019b``, ``intel/2019b`` ``3Mar2020`` |``-Python-3.8.2-kokkos`` |``foss/2020a``, ``intel/2020a`` ``7Aug2019`` |``-Python-3.7.4-kokkos`` |``foss/2019b``, ``intel/2019b`` ``7Aug2019`` |``-Python-3.7.4-kokkos-OCTP``|``intel/2019b`` -``23Jun2022``|``-kokkos`` |``foss/2021a``, ``foss/2021b`` +``23Jun2022``|``-kokkos`` |``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ``23Jun2022``|``-kokkos-CUDA-11.3.1`` |``foss/2021a`` ``23Jun2022``|``-kokkos-CUDA-11.4.1`` |``foss/2021b`` @@ -16743,8 +17172,8 @@ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally de *homepage*: version |toolchain ------------|-------------- -``1.02.00``|``foss/2016a`` +-----------|--------------------------------- +``1.02.00``|``GCCcore/8.2.0``, ``foss/2016a`` ``1.04.03``|``foss/2019b`` ### lavaan @@ -16759,6 +17188,17 @@ version |versionsuffix|toolchain ``0.6-4.1433``|``-R-3.6.0`` |``foss/2019a`` ``0.6-9`` |``-R-4.1.0`` |``foss/2021a`` +### LayoutParser + +A Unified Toolkit for Deep Learning Based Document Image Analysis + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.3.4``| |``foss/2022a`` +``0.3.4``|``-CUDA-11.7.0``|``foss/2022a`` + ### LBFGS++ A header-only C++ library for L-BFGS and L-BFGS-B algorithms @@ -16859,7 +17299,7 @@ LERC is an open-source image or raster format which supports rapid encoding and version |toolchain ---------|-------------------------------------- ``3.0`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``4.0.0``|``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### less @@ -16969,9 +17409,9 @@ This library aims to be a friendly, portable C implementation of the AV1 Image F *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``0.9.0`` |``foss/2020b`` -``0.11.1``|``foss/2021a`` +``0.11.1``|``foss/2021a``, ``foss/2022a`` ### libBigWig @@ -17041,9 +17481,9 @@ An API to provide an efficient distributed queue on a cluster. libcircle is an *homepage*: version |toolchain ---------------|------------------------------------------------- +--------------|------------------------------------------------------------------ ``0.2.1-rc.1``|``gompi/2019a``, ``iimpi/2019a`` -``0.3`` |``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` +``0.3`` |``gompi/2020a``, ``gompi/2020b``, ``gompi/2022a``, ``iimpi/2020a`` ### libcmaes @@ -17126,9 +17566,10 @@ libde265 is an open source implementation of the h.265 video codec *homepage*: -version |toolchain ----------|------------------------------ -``1.0.8``|``GCC/10.3.0``, ``GCC/11.2.0`` +version |toolchain +----------|------------------------------ +``1.0.8`` |``GCC/10.3.0``, ``GCC/11.2.0`` +``1.0.11``|``GCC/11.3.0`` ### libdeflate @@ -17271,7 +17712,7 @@ The libevent API provides a mechanism to execute a callback function when a spec version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------- ``2.0.22``|``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` -``2.1.8`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``2.1.8`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``2.1.11``|``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.1.12``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` @@ -17302,6 +17743,7 @@ version |toolchain ``1.13.2``|``GCCcore/11.2.0`` ``1.15.1``|``GCCcore/11.3.0`` ``1.16.1``|``GCCcore/12.2.0`` +``1.18.0``|``GCCcore/12.3.0`` ### libfdf @@ -17548,6 +17990,7 @@ libheif is an HEIF and AVIF file format decoder and encoder version |toolchain ----------|------------------------------ ``1.12.0``|``GCC/10.3.0``, ``GCC/11.2.0`` +``1.16.2``|``GCC/11.3.0`` ### libibmad @@ -17678,6 +18121,7 @@ version |toolchain ---------|------------------ ``0.5`` |``GCCcore/10.3.0`` ``0.6.1``|``GCCcore/10.2.0`` +``0.8.1``|``foss/2022a`` ### LibLZF @@ -17686,9 +18130,9 @@ LibLZF is a very small data compression library. It consists of only two .c and *homepage*: version|toolchain --------|------------------ +-------|-------------------------------------- ``3.4``|``GCCcore/10.2.0`` -``3.6``|``GCCcore/10.3.0`` +``3.6``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### libmad @@ -17848,7 +18292,7 @@ version |toolchain ``0.13.4``|``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.16`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``0.17`` |``GCCcore/12.2.0`` +``0.17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libplinkio @@ -17924,11 +18368,11 @@ version|toolchain libpspio is a library to read and write pseudopotentials in multiple formats. -*homepage*: +*homepage*: version |toolchain ----------|------------------------------------------------------- -``0.2.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` +---------|----------------------------------------------------------------------------------------------------------------------------------- +``0.2.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### libpthread-stubs @@ -18050,8 +18494,8 @@ libSBML (Systems Biology Markup Language library) is a free, open-source program *homepage*: version |toolchain -----------|-------------- -``5.19.0``|``GCC/10.3.0`` +----------|------------------------------ +``5.19.0``|``GCC/10.2.0``, ``GCC/10.3.0`` ### libsigc++ @@ -18109,7 +18553,7 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------------------------- ``1.0.6`` |``intel/2016a`` ``1.0.8`` |``foss/2016a`` ``1.0.11``|``foss/2016b``, ``intel/2016b`` @@ -18117,7 +18561,7 @@ version |toolchain ``1.0.13``|``GCCcore/6.4.0``, ``foss/2017a`` ``1.0.16``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17``|``GCCcore/8.2.0`` -``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### LibSoup @@ -18273,7 +18717,7 @@ version |toolchain ``2.4.2``|``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5``|``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6``|``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### libtree @@ -18852,6 +19296,17 @@ version|toolchain -------|------------- ``bcp``|``GCC/9.3.0`` +### LISFLOOD-FP + +The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by the University of Bristol. It has undergone extensive development since conception and includes a collection of numerical schemes implemented to solve a variety of mathematical approximations of the 2D shallow water equations of different complexity. The local inertia solver, known as the ACC solver, is widely used to simulate floods with gradually-varying, subcritical flow over sufficiently rough surfaces with Manning’s coefficient of at least 0.03. It has a version with CPU-specific optimisations and enhanced with a subgrid channel model. LISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and first-order finite volume (FV1) solvers of the full shallow water equations for modelling a wide range of flows, including rapidly-propagating, supercritical flows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are parallelised for the multi-core CPU architecture, but do not integrate with the subgrid channel model nor with the CPU-specific optimisations. + +*homepage*: + +version|versionsuffix |toolchain +-------|----------------|--------------- +``8.1``| |``gompi/2022a`` +``8.1``|``-CUDA-11.7.0``|``gompi/2022a`` + ### LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. @@ -18916,14 +19371,14 @@ LMDB is a fast, memory-efficient database. With memory-mapped files, it has the *homepage*: version |toolchain -----------|-------------------------------------------------------- +----------|---------------------------------------------------------- ``0.9.18``|``foss/2016a`` ``0.9.21``|``GCCcore/6.4.0``, ``intel/2017a`` ``0.9.22``|``GCCcore/7.3.0`` ``0.9.23``|``GCCcore/8.2.0`` ``0.9.24``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.9.28``|``GCCcore/10.3.0`` -``0.9.29``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.9.29``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### LMfit @@ -18939,6 +19394,7 @@ version |versionsuffix |toolchain ``1.0.1`` |``-Python-3.8.2`` |``foss/2020a`` ``1.0.2`` | |``foss/2020b``, ``intel/2020b`` ``1.0.3`` | |``foss/2021a``, ``foss/2022a``, ``intel/2022a`` +``1.2.1`` | |``foss/2021b`` ### Lmod @@ -19129,7 +19585,7 @@ Mixed Integer Linear Programming (MILP) solver version |toolchain ------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``5.5.2.5`` |``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/9.3.0`` +``5.5.2.11``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/9.3.0`` ### lrslib @@ -19167,6 +19623,7 @@ version |toolchain ``1.9.7``|``GCCcore/9.3.0`` ``2.2`` |``GCCcore/10.2.0`` ``2.3`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.4.1``|``GCCcore/12.2.0`` ### LSMS @@ -19220,11 +19677,12 @@ version |toolchain LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language. -*homepage*: +*homepage*: -version |toolchain ----------|------------- -``2.0.2``|``GCC/4.9.2`` +version |toolchain +------------------------|-------------- +``2.0.2`` |``GCC/4.9.2`` +``2.1.0-beta3_20230602``|``GCC/11.3.0`` ### LuaJIT2-OpenResty @@ -19236,6 +19694,16 @@ version |toolchain ----------------|------------- ``2.1-20220411``|``GCC/9.3.0`` +### LuaRocks + +LuaRocks is the package manager for Lua modules. It allows you to create and install Lua modules as self-contained packages called rocks. + +*homepage*: + +version |toolchain +---------|------------------ +``3.9.2``|``GCCcore/11.3.0`` + ### Lucene-Geo-Gazetteer A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library to create a searchable gazetteer. @@ -19277,6 +19745,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.0.2``|``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` ``1.0.3``|``gompi/2020b`` +``1.0.5``|``gompi/2022a`` ### lxml @@ -19301,7 +19770,7 @@ version |versionsuffix |toolchain ``4.6.2``| |``GCCcore/10.2.0`` ``4.6.3``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.9.1``| |``GCCcore/11.3.0`` -``4.9.2``| |``GCCcore/12.2.0`` +``4.9.2``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### lynx @@ -19342,7 +19811,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) +[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) ### M1QN3 @@ -19376,7 +19845,7 @@ version |toolchain ``1.4.16``|``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` +``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ### MACH @@ -19441,7 +19910,7 @@ version |versionsuffix |toolchain ``7.475``|``-with-extensions``|``GCC/10.2.0``, ``gompi/2020b`` ``7.487``|``-with-extensions``|``gompi/2021a`` ``7.490``|``-with-extensions``|``GCC/10.3.0``, ``GCC/11.2.0``, ``gompi/2021b`` -``7.505``|``-with-extensions``|``GCC/11.3.0`` +``7.505``|``-with-extensions``|``GCC/11.3.0``, ``GCC/12.2.0`` ### MAGeCK @@ -19452,6 +19921,7 @@ Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computati version |toolchain -----------|------------------------------ ``0.5.9.4``|``foss/2021a``, ``foss/2022a`` +``0.5.9.5``|``gfbf/2022b`` ### magick @@ -19634,6 +20104,16 @@ version |toolchain ---------|-------------- ``1.2.2``|``foss/2022a`` +### mannkendall + +A python package for non parametric Mann Kendall family of trend tests. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.1``|``foss/2022a`` + ### manta Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. @@ -19839,6 +20319,7 @@ version |versionsuffix|toolchain ``2022a``|``-r3`` |``system`` ``2022b``| |``system`` ``2022b``|``-r5`` |``system`` +``2023a``| |``system`` ### MATLAB-Engine @@ -20006,6 +20487,7 @@ version |toolchain ``1.6.10.43``|``foss/2018b`` ``2.0.3.0`` |``GCCcore/11.2.0`` ``2.2.0.0`` |``GCCcore/11.2.0`` +``2.4.2.0`` |``system`` ### mayavi @@ -20114,6 +20596,7 @@ version |versionsuffix|toolchain ``R2021b``|``.2`` |``system`` ``R2022a``| |``system`` ``R2022a``|``.1`` |``system`` +``R2022a``|``.5`` |``system`` ### mctc-lib @@ -20253,8 +20736,8 @@ MedPy is a library and script collection for medical image processing in Python, *homepage*: version |versionsuffix |toolchain ----------|-----------------|-------------- -``0.4.0``| |``foss/2020b`` +---------|-----------------|---------------------------------- +``0.4.0``| |``foss/2020b``, ``fosscuda/2020b`` ``0.4.0``|``-Python-3.7.4``|``foss/2019b`` ### Meep @@ -20500,6 +20983,7 @@ version |versionsuffix |toolchain ``1.7.1``|``-Python-2.7.12``|``intel/2016b`` ``2.0.2``|``-Python-2.7.14``|``intel/2018a`` ``2.0.2``|``-Python-3.6.4`` |``intel/2018a`` +``5.3.4``| |``foss/2022b`` ### meshtool @@ -20534,6 +21018,7 @@ version |versionsuffix |toolchain ``0.59.1``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``0.62.1``| |``GCCcore/11.3.0`` ``0.64.0``| |``GCCcore/12.2.0`` +``1.1.1`` | |``GCCcore/12.3.0`` ### meson-python @@ -20552,8 +21037,8 @@ Mesh-Quality Improvement Library *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------- -``2.3.0``|``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` +---------|------------------------------------------------------------------------------------------------------------ +``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` ### MESS @@ -20605,10 +21090,10 @@ MetaEuk is a modular toolkit designed for large-scale gene discovery and annotat *homepage*: version|toolchain --------|------------------------------ +-------|---------------------------------------------- ``4`` |``GCC/10.2.0`` ``5`` |``GCC/10.3.0`` -``6`` |``GCC/11.2.0``, ``GCC/11.3.0`` +``6`` |``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### MetaGeneAnnotator @@ -20969,6 +21454,7 @@ version |toolchain ``2.20`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.22`` |``GCCcore/11.2.0`` ``2.24`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.26`` |``GCCcore/12.2.0`` ### Minipolish @@ -21084,8 +21570,8 @@ The MITObim procedure (mitochondrial baiting and iterative mapping) represents *homepage*: version |toolchain ----------|------------------------------- -``1.9.1``|``foss/2018b``, ``gompi/2019b`` +---------|----------------------------------------------- +``1.9.1``|``foss/2018b``, ``foss/2020b``, ``gompi/2019b`` ### MitoZ @@ -21223,6 +21709,7 @@ version |toolchain ``13-45111`` |``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` ``13-45111-20211006``|``gompi/2020b`` ``13-45111-20211019``|``gompi/2020b`` +``14-7e284`` |``gompi/2022a`` ### mmtf-cpp @@ -21264,6 +21751,16 @@ version |toolchain -----------|--------------- ``1.3.9.6``|``gompi/2019b`` +### MOB-suite + +Software tools for clustering, reconstruction and typing of plasmids from draft assemblies + +*homepage*: + +version |versionsuffix |toolchain +---------|-----------------|-------------- +``3.1.0``|``-Python-3.7.4``|``foss/2019b`` + ### ModelTest-NG ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. @@ -21326,6 +21823,16 @@ version|toolchain ``6.8``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``7.1``|``GCCcore/11.3.0`` +### molecularGSM + +Code for single-ended and double-ended molecular GSM. The growing string method is a reaction path and transition state finding method developed in c++. + +*homepage*: + +version |toolchain +------------|--------------- +``20190826``|``intel/2020b`` + ### Molekel Molekel is an open-source multi-platform molecular visualization program. @@ -21392,6 +21899,17 @@ version |versionsuffix |toolchain ``1.0.1``| |``foss/2022a`` ``1.0.1``|``-CUDA-11.7.0``|``foss/2022a`` +### MONAI-Label + +MONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server. + +*homepage*: + +version |versionsuffix |toolchain +---------|-------------------------------|-------------- +``0.5.2``|``-PyTorch-1.12.0`` |``foss/2022a`` +``0.5.2``|``-PyTorch-1.12.0-CUDA-11.7.0``|``foss/2022a`` + ### mongolite High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: . @@ -21585,7 +22103,7 @@ version |toolchain ``4.0.1``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.0.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``4.2.0``|``GCCcore/12.2.0`` +``4.2.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### mpi4py @@ -21640,6 +22158,7 @@ version |toolchain ``0.9.1`` |``gompi/2019a``, ``iimpi/2019a`` ``0.10`` |``gompi/2020a``, ``iimpi/2020a`` ``0.10.1``|``gompi/2020a`` +``0.11.1``|``gompi/2022a`` ### mpiP @@ -21828,6 +22347,7 @@ MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose phy version |toolchain ---------|------------------ ``2.1.1``|``GCCcore/11.2.0`` +``2.2.2``|``GCCcore/11.3.0`` ### mujoco-py @@ -21891,7 +22411,7 @@ version |versionsuffix |toolchain ``1.10.1``| |``foss/2020b`` ``1.11`` | |``foss/2021a`` ``1.12`` | |``foss/2021b`` -``1.14`` | |``foss/2022a`` +``1.14`` | |``foss/2022a``, ``foss/2022b`` ### Multiwfn @@ -21924,7 +22444,7 @@ version |toolchain --------------|------------------------------------------------------------------------- ``3.23`` |``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` ``4.0.0beta2``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``4.0.0rc1`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.0.0rc1`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### MUMPS @@ -21989,7 +22509,7 @@ version |versionsuffix |toolchain ``3.8.1551``| |``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ``5.0.1428``| |``GCCcore/10.3.0`` ``5.1`` | |``GCCcore/11.2.0`` -``5.1.0`` | |``GCCcore/11.3.0`` +``5.1.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### MuSiC @@ -22011,6 +22531,7 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``1.6`` |``-Python-3.6.6``|``foss/2018b`` ``1.6`` |``-Python-3.7.4``|``foss/2019b`` +``1.7.1``| |``foss/2020b`` ``1.7.2``| |``foss/2021a`` ### MuTect @@ -22047,6 +22568,16 @@ version |toolchain ``2.1`` |``GCC/4.9.3-2.25`` ``2.2b`` |``GCC/4.9.3-2.25`` +### MView + +MView reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup. + +*homepage*: + +version |toolchain +--------|-------------- +``1.67``|``GCC/11.3.0`` + ### mxml Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. @@ -22179,7 +22710,7 @@ version |versionsuffix |toolchain ## N -[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanoflann](#nanoflann) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [NCO](#nco) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCII](#netmhcii) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [NEXUS-CL](#nexus-cl) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [nichenetr](#nichenetr) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) +[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanoflann](#nanoflann) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [NanoStat](#nanostat) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [NCO](#nco) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCII](#netmhcii) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [NEXUS-CL](#nexus-cl) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [nichenetr](#nichenetr) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) ### n2v @@ -22222,7 +22753,7 @@ NAMD is a parallel molecular dynamics code designed for high-performance simulat *homepage*: version |versionsuffix |toolchain ---------|----------------|---------------------------------------------------------------- +--------|----------------|------------------------------------------------------------------------------- ``2.11``|``-mpi`` |``intel/2016a`` ``2.12``|``-CUDA-8.0.61``|``foss/2016b`` ``2.12``|``-mpi`` |``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` @@ -22230,7 +22761,7 @@ version |versionsuffix |toolchain ``2.13``|``-mpi`` |``foss/2018b``, ``foss/2019b``, ``intel/2018b`` ``2.14``| |``fosscuda/2019b``, ``fosscuda/2020b`` ``2.14``|``-CUDA-11.3.1``|``foss/2021a`` -``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2020a`` +``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2022a``, ``intel/2020a`` ### namedlist @@ -22306,10 +22837,10 @@ Functions to extract information from Oxford Nanopore sequencing data and alignm *homepage*: version |versionsuffix |toolchain -----------|-----------------|--------------- +----------|-----------------|------------------------------ ``1.12.1``|``-Python-3.7.4``|``intel/2019b`` ``1.15.0``| |``intel/2020b`` -``1.18.1``| |``foss/2021a`` +``1.18.1``| |``foss/2021a``, ``foss/2022a`` ### NanoLyse @@ -22332,6 +22863,7 @@ version |versionsuffix |toolchain ``0.23.1``|``-Python-3.7.4``|``intel/2019b`` ``1.2.0`` | |``intel/2020b`` ``1.2.1`` | |``foss/2021a`` +``1.3.0`` | |``foss/2022a`` ### nanomax-analysis-utils @@ -22390,6 +22922,16 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.6.11``|``-Python-3.8.2``|``foss/2020a`` +### NanoStat + +Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format. + +*homepage*: + +version |toolchain +---------|------------------------------ +``1.6.0``|``foss/2021a``, ``foss/2022a`` + ### napari napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). @@ -22469,6 +23011,7 @@ version |toolchain ``2.11.2`` |``gompi/2021b`` ``3.0.0`` |``gompi/2021b``, ``gompi/2022a`` ``3.0.2`` |``gompi/2022a`` +``3.0.5`` |``gompi/2021a``, ``gompi/2022b`` ### NCCL @@ -22492,6 +23035,7 @@ version |versionsuffix |toolchain ``2.11.4`` | |``gcccuda/2019b`` ``2.12.12``|``-CUDA-11.7.0`` |``GCCcore/11.3.0`` ``2.16.2`` |``-CUDA-12.0.0`` |``GCCcore/12.2.0`` +``2.18.3`` |``-CUDA-12.1.1`` |``GCCcore/12.3.0`` ### NCCL-tests @@ -22580,6 +23124,7 @@ version |toolchain ``4.9.7``|``foss/2020a``, ``foss/2020b`` ``5.0.1``|``foss/2021a`` ``5.0.3``|``foss/2021b``, ``intel/2021b`` +``5.0.6``|``intel/2019b`` ``5.1.0``|``foss/2022a`` ``5.1.3``|``foss/2021a``, ``foss/2022a`` @@ -22606,7 +23151,7 @@ version|toolchain ``6.1``|``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2``|``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` ``6.3``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` -``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### ncview @@ -22720,7 +23265,7 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: version |versionsuffix |toolchain ------------|----------------|-------------------------------------------------------------------------------------------------------------------------- +-----------|----------------|----------------------------------------------------------------------------------------------------------------------------------------- ``4.3.3.1``| |``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``4.4.0`` | |``foss/2016a``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``4.4.1`` | |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -22733,7 +23278,7 @@ version |versionsuffix |toolchain ``4.6.1`` | |``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` | |``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` | |``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` | |``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` +``4.7.4`` | |``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020a`` ``4.8.0`` | |``gompi/2021a``, ``iimpi/2021a`` ``4.8.1`` | |``gompi/2021b``, ``iimpi/2021b`` ``4.9.0`` | |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a``, ``iimpi/2022b`` @@ -22948,7 +23493,7 @@ version |versionsuffix |toolchain ``2.6.3``| |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ``2.8.4``| |``foss/2022a``, ``intel/2022a`` ``2.8.8``| |``gfbf/2022b`` -``3.0`` | |``foss/2022b`` +``3.0`` | |``gfbf/2022b`` ### NeuroKit @@ -22984,7 +23529,7 @@ version |toolchain ### Nextflow -Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data +Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data *homepage*: @@ -23004,6 +23549,7 @@ version |toolchain ``22.10.1``|``system`` ``22.10.5``|``system`` ``22.10.6``|``system`` +``23.04.2``|``system`` ### NextGenMap @@ -23145,13 +23691,14 @@ version |versionsuffix |toolchain ### ngspice -Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. +Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. *homepage*: version|toolchain -------|-------------- ``31`` |``foss/2019b`` +``39`` |``foss/2022a`` ### ngtcp2 @@ -23268,7 +23815,7 @@ version |toolchain ``1.10.0``|``GCCcore/9.3.0`` ``1.10.1``|``GCCcore/10.2.0`` ``1.10.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.11.1``|``GCCcore/12.2.0`` +``1.11.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Nipype @@ -23342,8 +23889,8 @@ nnU-Net is the first segmentation method that is designed to deal with the datas *homepage*: version |toolchain ----------|-------------- -``1.7.0``|``foss/2020b`` +---------|---------------------------------- +``1.7.0``|``foss/2020b``, ``fosscuda/2020b`` ### Node-RED @@ -23743,7 +24290,7 @@ version |toolchain NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------------------|----------------------------------------------|-------------------------------- @@ -23767,7 +24314,7 @@ version |toolchain ## O -[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxford_asl](#oxford_asl) +[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxDNA](#oxdna) - [oxford_asl](#oxford_asl) ### Oases @@ -23967,6 +24514,7 @@ version |versionsuffix |toolchain ``3.3.0``|``-Python-3.7.4``|``foss/2019b`` ``4.0.0``| |``foss/2021a`` ``4.0.2``| |``foss/2021a``, ``foss/2021b`` +``4.1.1``| |``foss/2022b`` ### ont-guppy @@ -24088,6 +24636,7 @@ version |versionsuffix |toolchain ``0.3.18``| |``GCC/11.2.0`` ``0.3.20``| |``GCC/11.2.0``, ``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``0.3.21``| |``GCC/12.2.0`` +``0.3.23``| |``GCC/12.3.0`` ### openCARP @@ -24243,7 +24792,7 @@ version |versionsuffix|toolchain ``v2006`` | |``foss/2020a``, ``intel/2020a`` ``v2012`` | |``foss/2020a`` ``v2106`` | |``foss/2021a`` -``v2112`` | |``foss/2021b`` +``v2112`` | |``foss/2020b``, ``foss/2021b`` ``v2206`` | |``foss/2022a`` ### OpenFOAM-Extend @@ -24342,7 +24891,7 @@ OpenMM is a toolkit for molecular simulation. version |versionsuffix |toolchain ---------|-------------------------------|--------------------------------------------------- ``7.1.1``|``-Python-3.6.3`` |``intel/2017b`` -``7.4.1``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` +``7.4.1``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``7.4.2``|``-Python-3.8.2`` |``intel/2020a`` ``7.5.0``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``7.5.0``|``-Python-3.8.2`` |``fosscuda/2020a``, ``intel/2020a`` @@ -24439,7 +24988,7 @@ version |versionsuffix |toolchain ``4.1.1`` | |``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ``4.1.2`` | |``GCC/10.2.0``, ``GCC/11.2.0`` ``4.1.4`` | |``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0`` -``4.1.5`` | |``GCC/12.2.0`` +``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -24469,8 +25018,8 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: version |toolchain ------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +-----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### OpenPIV @@ -24496,6 +25045,7 @@ version |versionsuffix |toolchain ``3.0.7`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.0.9`` | |``GCCcore/11.2.0`` ``3.0.10``| |``GCCcore/11.3.0`` +``3.1.2`` | |``GCCcore/12.2.0`` ### OpenRefine @@ -24779,6 +25329,7 @@ version |versionsuffix |toolchain ``5.9`` |``-CUDA-11.7.0``|``gompi/2022a`` ``5.9`` |``-ROCm-4.5.0`` |``gompi/2021b`` ``6.2`` | |``gompi/2022.10``, ``gompi/2022b`` +``7.1-1``| |``gompi/2023a`` ### OTF2 @@ -24815,6 +25366,16 @@ version |toolchain ``2.4.3``|``foss/2018b`` ``2.5.4``|``GCCcore/8.2.0`` +### oxDNA + +oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations of different kinds on both single CPU cores and NVIDIA GPUs. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``3.5.2``|``-CUDA-11.7.0``|``foss/2022a`` + ### oxford_asl A command line tool for quantification of perfusion from ASL data @@ -24828,7 +25389,7 @@ version |versionsuffix |toolchain ## P -[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [plc](#plc) - [PLINK](#plink) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) +[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -24909,9 +25470,9 @@ pagmo is a C++ scientific library for massively parallel optimization. *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``2.17.0``|``foss/2020b`` -``2.18.0``|``foss/2021a``, ``foss/2021b`` +``2.18.0``|``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ### pairsnp @@ -25202,6 +25763,7 @@ version |toolchain ``2.4.3``|``GCC/10.2.0``, ``GCC/10.3.0`` ``2.5`` |``GCC/11.2.0`` ``2.6`` |``GCC/11.3.0`` +``2.6.2``|``GCC/12.2.0`` ### Paraver @@ -25209,10 +25771,11 @@ A very powerful performance visualization and analysis tool based on traces tha *homepage*: -version |toolchain ----------|-------------- -``4.8.1``|``foss/2019a`` -``4.9.2``|``foss/2021a`` +version |toolchain +----------|-------------- +``4.8.1`` |``foss/2019a`` +``4.9.2`` |``foss/2021a`` +``4.11.1``|``foss/2022a`` ### ParaView @@ -25235,6 +25798,7 @@ version |versionsuffix |toolchain ``5.9.1`` |``-mpi`` |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``5.10.1``|``-mpi`` |``foss/2022a`` ``5.11.0``|``-mpi`` |``foss/2022b`` +``5.11.1``|``-mpi`` |``foss/2022a`` ### Parcels @@ -25318,6 +25882,16 @@ version |toolchain ---------|-------------- ``5.2.3``|``foss/2017b`` +### pastml + +Ancestor character reconstruction and visualisation for rooted phylogenetic trees + +*homepage*: + +version |toolchain +----------|-------------- +``1.9.34``|``foss/2021a`` + ### patch Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions. @@ -25342,6 +25916,7 @@ version |toolchain ``0.12`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.13`` |``GCCcore/11.2.0`` ``0.15.0``|``GCCcore/11.3.0`` +``0.18.0``|``GCCcore/12.3.0`` ### path.py @@ -25411,6 +25986,16 @@ version |toolchain ------------|--------------- ``20170330``|``intel/2017a`` +### pbipa + +Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly. IPA is fast, providing an easy to use local run mode or a distributed pipeline for a cluster. + +*homepage*: + +version |toolchain +---------|-------------- +``1.8.0``|``foss/2021b`` + ### pbmm2 A minimap2 frontend for PacBio native data formats @@ -25563,10 +26148,10 @@ PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------ +----------|---------------------------------------------------------------------------------------------------- ``0.9.8`` |``foss/2016b``, ``intel/2016b`` ``0.9.10``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``0.9.11``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` +``0.9.11``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` ### PennCNV @@ -25600,7 +26185,7 @@ version|toolchain ### Perl -Larry Wall's Practical Extraction and Report Language +Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. *homepage*: @@ -25635,6 +26220,7 @@ version |versionsuffix|toolchain ``5.34.1``|``-minimal`` |``GCCcore/11.3.0`` ``5.36.0``| |``GCCcore/12.1.0``, ``GCCcore/12.2.0`` ``5.36.0``|``-minimal`` |``GCCcore/12.2.0`` +``5.36.1``| |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` ### perl-app-cpanminus @@ -25646,6 +26232,16 @@ version |toolchain ----------|---------- ``1.7039``|``system`` +### Perl-bundle-CPAN + +A set of common packages from CPAN + +*homepage*: + +version |toolchain +----------|------------------ +``5.36.1``|``GCCcore/12.3.0`` + ### Perl4-CoreLibs Libraries historically supplied with Perl 4 @@ -25866,6 +26462,16 @@ version |versionsuffix|toolchain ``0.12`` |``-R-3.3.3`` |``foss/2016b``, ``intel/2016b`` ``0.99.5-2``|``-R-3.6.0`` |``foss/2019a``, ``intel/2019a`` +### PheWeb + +A tool for building PheWAS websites from association files + +*homepage*: + +version |versionsuffix |toolchain +----------|-----------------|-------------- +``1.1.20``|``-Python-3.7.4``|``foss/2019b`` + ### PhiPack The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. @@ -26082,7 +26688,7 @@ version |toolchain ``2.3.4``|``GCCcore/6.4.0`` ``2.4`` |``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` ``2.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.7`` |``GCCcore/11.3.0`` +``2.7`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### PIL @@ -26324,11 +26930,11 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``0.28`` |``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``0.29`` |``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``0.29.1``|``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` +``0.29.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` ### pkgconf @@ -26474,6 +27080,16 @@ version |toolchain ``2.00a3.6`` |``GCC/11.3.0`` ``2.00a3.7`` |``foss/2022a`` +### plinkliftover + +PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.0``|``foss/2022b`` + ### plinkQC plinkQC is a R/CRAN package for genotype quality control in genetic association studies. It makes PLINK basic statistics (e.g.missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions easily accessible from within R and allows for automatic evaluation of the results. @@ -26586,6 +27202,7 @@ version |versionsuffix |toolchain ``2.5.1``|``-PathCV`` |``intel/2018b`` ``2.5.2``|``-Python-3.7.2`` |``intel/2019a`` ``2.5.3``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` +``2.5.4``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b`` ``2.5b`` |``-Python-2.7.14``|``intel/2018a`` ``2.6.0``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``2.6.2``| |``foss/2020b``, ``intel/2020b`` @@ -26627,6 +27244,17 @@ version |toolchain ``4.1.0``|``GCCcore/11.2.0`` ``4.1.2``|``GCCcore/11.3.0`` ``4.2.2``|``GCCcore/12.2.0`` +``4.2.4``|``GCCcore/12.3.0`` + +### pmt + +PMT is a high-level software library capable of collecting power consumption measurements on various hardware. + +*homepage*: + +version |toolchain +---------|------------------ +``1.1.0``|``GCCcore/11.3.0`` ### pmx @@ -26754,9 +27382,10 @@ A suite of population scale analysis tools for single-cell genomics data includi *homepage*: -version |toolchain -------------|-------------- -``0.1-beta``|``foss/2019b`` +version |toolchain +---------------------|-------------- +``0.1-beta`` |``foss/2019b`` +``0.1-beta-20210505``|``GCC/11.3.0`` ### popt @@ -26765,9 +27394,9 @@ Popt is a C library for parsing command line parameters. *homepage*: version |toolchain ---------|------------------------- +--------|----------------------------------------- ``1.14``|``GCC/4.8.2`` -``1.16``|``GCC/4.9.2``, ``system`` +``1.16``|``GCC/10.2.0``, ``GCC/4.9.2``, ``system`` ### Porechop @@ -26855,6 +27484,7 @@ POT (Python Optimal Transport) is a Python library provide several solvers for o version |versionsuffix |toolchain ---------|-----------------|--------------- ``0.5.1``|``-Python-3.6.6``|``intel/2018b`` +``0.9.0``| |``foss/2022a`` ### POV-Ray @@ -27079,9 +27709,9 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.6.2``|``GCC/4.9.3-binutils-2.25`` -``2.6.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### ProFit @@ -27297,9 +27927,9 @@ version |versionsuffix |toolchain ### PSI4 -PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. +PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. -*homepage*: +*homepage*: version |versionsuffix |toolchain ---------|-------------------------|--------------- @@ -27309,6 +27939,7 @@ version |versionsuffix |toolchain ``1.2.1``|``-Python-2.7.15-maxam8``|``intel/2018b`` ``1.3.1``|``-Python-3.7.2`` |``foss/2019a`` ``1.3.2``|``-Python-3.7.4`` |``intel/2019b`` +``1.7`` | |``foss/2021b`` ### PsiCLASS @@ -27423,6 +28054,7 @@ version |versionsuffix |toolchain ``5.6.1``|``-Python-2.7.15``|``fosscuda/2018b`` ``5.6.3``| |``GCCcore/8.2.0`` ``5.9.3``| |``GCCcore/10.2.0``, ``GCCcore/11.3.0`` +``5.9.4``| |``GCCcore/11.2.0`` ### psycopg2 @@ -27436,6 +28068,7 @@ version |versionsuffix |toolchain ``2.8.3``|``-Python-3.7.2`` |``foss/2019a`` ``2.8.6``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``2.9.5``| |``GCCcore/11.2.0`` +``2.9.6``| |``GCCcore/11.3.0`` ### ptemcee @@ -27662,6 +28295,16 @@ version |toolchain ---------|-------------- ``0.9.5``|``foss/2022a`` +### PyBioLib + +PyBioLib is a Python package for running BioLib applications from Python scripts and the command line. BioLib is a library of biological data science applications. Applications on BioLib range from small bioinformatics utilities to state-of-the-art machine learning algorithms for predicting characteristics of biological molecules. + +*homepage*: + +version |toolchain +-----------|------------------ +``1.1.988``|``GCCcore/11.3.0`` + ### PyCairo Python bindings for the cairo library @@ -27691,6 +28334,7 @@ Python library for classifier calibration version |toolchain --------------|-------------- ``0.1.0.dev0``|``foss/2021b`` +``20230531`` |``gfbf/2022b`` ### pyccel @@ -27726,6 +28370,16 @@ version |toolchain ----------|-------------- ``1.8.12``|``foss/2022a`` +### Pychopper + +A tool to identify, orient, trim and rescue full length cDNA reads. + +*homepage*: + +version |versionsuffix |toolchain +---------|-----------------|--------------- +``2.3.1``|``-Python-3.7.4``|``intel/2019b`` + ### PyCifRW PyCIFRW provides support for reading and writing CIF (Crystallographic Information Format) files using Python. @@ -27768,6 +28422,7 @@ version |versionsuffix |toolchain ``2.0.1``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` ``2.0.2``|``-Python-3.8.2``|``foss/2020a``, ``fosscuda/2020a`` ``2.0.4``| |``foss/2021a`` +``2.0.6``| |``foss/2022a`` ### pycodestyle @@ -27875,6 +28530,16 @@ version |versionsuffix |toolchain ``2.2.2``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.3.0``| |``GCCcore/11.3.0`` +### pydicom-seg + +Reading and writing of DICOM-SEG medical image segmentation storage files using pydicom as DICOM serialization/deserialization library. + +*homepage*: + +version |toolchain +---------|-------------- +``0.4.1``|``foss/2022a`` + ### pydlpoly Pydlpoly is a molecular dynamics simulation package which is a modified version of DL-POLY with a Python language interface. @@ -27956,6 +28621,7 @@ version |versionsuffix |toolchain ``0.6.3.1``| |``GCCcore/10.3.0`` ``0.7.0`` | |``GCCcore/11.2.0`` ``0.7.1`` | |``GCCcore/11.3.0`` +``0.7.2.1``| |``GCCcore/12.2.0`` ### pyfasta @@ -28106,9 +28772,9 @@ pygmo is a scientific Python library for massively parallel optimization. *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``2.16.1``|``foss/2020b`` -``2.18.0``|``foss/2021a``, ``foss/2021b`` +``2.18.0``|``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ### PyGObject @@ -28217,6 +28883,7 @@ An integrated development environment (IDE) for computational materials science. version |versionsuffix |toolchain ---------|-----------------|--------------- ``0.2.5``|``-Python-3.7.2``|``intel/2019a`` +``0.3.0``|``-Python-3.8.2``|``intel/2020a`` ### Pyke3 @@ -28252,6 +28919,16 @@ version |versionsuffix |toolchain ``1.9.5``|``-Python-2.7.16``|``GCCcore/8.3.0`` ``2.7.4``| |``GCCcore/10.2.0`` +### pyMannKendall + +A python package for non parametric Mann Kendall family of trend tests. + +*homepage*: + +version |toolchain +---------|-------------- +``1.4.3``|``foss/2022a`` + ### pymatgen Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. @@ -28390,6 +29067,7 @@ version |versionsuffix |toolchain ``2020.2.2`` |``-Python-3.7.4``|``fosscuda/2019b`` ``2021.1.2`` | |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2021.2.13``| |``foss/2021b`` +``2021.2.13``|``-CUDA-11.4.1`` |``foss/2021b`` ### PyOpenGL @@ -28441,6 +29119,16 @@ version |versionsuffix |toolchain ``20160707``|``-Python-2.7.11``|``foss/2016a`` ``20160707``|``-Python-3.5.1`` |``foss/2016a`` +### pypmt + +PMT is a high-level software library capable of collecting power consumption measurements on various hardware. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2022a`` + ### PYPOWER PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python programming language. @@ -28540,6 +29228,7 @@ version |versionsuffix |toolchain ``0.11.0``|``-Python-3.7.4``|``foss/2019b`` ``0.11.1``| |``foss/2020b``, ``fosscuda/2020b`` ``0.12.3``| |``foss/2021a`` +``0.13.3``| |``foss/2022a`` ### pyradiomics @@ -28655,6 +29344,7 @@ version |versionsuffix |toolchain ``0.18.0`` | |``GCC/11.2.0`` ``0.19.1`` | |``GCC/11.3.0`` ``0.20.0`` | |``GCC/11.3.0`` +``0.21.0`` | |``GCC/12.2.0`` ### pysamstats @@ -28696,6 +29386,7 @@ pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Singl version |versionsuffix |toolchain ----------|-----------------|------------------------------- ``0.10.3``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` +``0.12.1``| |``foss/2022a`` ### PySCF @@ -28783,6 +29474,7 @@ version |versionsuffix |toolchain ---------|-----------------|---------------------------------------------- ``0.0.4``|``-Python-3.7.4``|``GCC/8.3.0`` ``0.0.8``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.0.9``| |``GCC/11.3.0``, ``GCC/12.2.0`` ### pysqlite @@ -29007,6 +29699,7 @@ version |versionsuffix |toolchain ``3.10.8``| |``GCCcore/12.2.0`` ``3.10.8``|``-bare`` |``GCCcore/12.2.0`` ``3.11.2``|``-bare`` |``GCCcore/12.2.0`` +``3.11.3``| |``GCCcore/12.3.0`` ### Python-bundle @@ -29074,7 +29767,7 @@ version |toolchain ----------|-------------------------------------- ``0.11.0``|``GCCcore/10.3.0`` ``0.11.1``|``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``1.1.0`` |``GCCcore/11.3.0`` +``1.1.0`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### python-Levenshtein @@ -29108,6 +29801,16 @@ version |toolchain --------|-------------- ``0.16``|``foss/2022a`` +### python-mujoco + +This package is the canonical Python bindings for the MuJoCo physics engine. The mujoco package provides direct access to raw MuJoCo C API functions, structs, constants, and enumerations. Structs are provided as Python classes, with Pythonic initialization and deletion semantics. + +*homepage*: + +version |toolchain +---------|-------------- +``2.2.2``|``foss/2022a`` + ### python-parasail Python Bindings for the Parasail C Library @@ -29123,6 +29826,7 @@ version |versionsuffix |toolchain ``1.2.3`` |``-Python-3.8.2`` |``foss/2020a`` ``1.2.4`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b`` ``1.3.3`` | |``foss/2022a`` +``1.3.4`` | |``foss/2022b`` ### python-telegram-bot @@ -29201,6 +29905,7 @@ version |versionsuffix |toolchain ``1.12.1``|``-CUDA-11.3.1`` |``foss/2021a`` ``1.12.1``|``-CUDA-11.5.2`` |``foss/2021b`` ``1.12.1``|``-CUDA-11.7.0`` |``foss/2022a`` +``1.13.1``| |``foss/2022a`` ### PyTorch-bundle @@ -29212,6 +29917,16 @@ version |versionsuffix |toolchain ----------|----------------|-------------- ``1.12.1``|``-CUDA-11.7.0``|``foss/2022a`` +### pytorch-CycleGAN-pix2pix + +PyTorch implementations for both unpaired and paired image-to-image translation. + +*homepage*: + +version |versionsuffix |toolchain +------------|----------------|-------------- +``20230314``|``-CUDA-11.7.0``|``foss/2022a`` + ### PyTorch-Geometric PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. @@ -29238,6 +29953,17 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``0.4.9``|``-CUDA-11.3.1``|``foss/2021a`` +### PyTorch-Image-Models + +PyTorch Image Models (timm) is a collection of image models, layers, utilities, optimizers, schedulers, data-loaders / augmentations, and reference training / validation scripts that aim to pull together a wide variety of SOTA models with ability to reproduce ImageNet training results. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.9.2``| |``foss/2022a`` +``0.9.2``|``-CUDA-11.7.0``|``foss/2022a`` + ### PyTorch-Lightning PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. @@ -29304,6 +30030,16 @@ version |versionsuffix |toolchain ``1.1.1``| |``intelcuda/2020b`` ``1.1.1``|``-Python-3.7.4``|``intel/2019b`` +### PyWBGT + +Cython source code for estimating wet bulb globe temperature (WBGT) from datasets of standard meterological measurements using models developed by Liljegren et al (2008) + +*homepage*: + +version |toolchain +---------|------------------------------ +``1.0.0``|``foss/2021b``, ``foss/2022a`` + ### PyYAML PyYAML is a YAML parser and emitter for the Python programming language. @@ -29329,7 +30065,7 @@ version |versionsuffix |toolchain ``5.3`` | |``GCCcore/9.3.0`` ``5.3.1``| |``GCCcore/10.2.0`` ``5.4.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``6.0`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``6.0`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PyZMQ @@ -29391,6 +30127,7 @@ qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from version |versionsuffix |toolchain ---------|-----------------|------------------------------- +``1.1.0``| |``foss/2022b`` ``1.1.0``|``-Python-3.7.4``|``foss/2019b``, ``intel/2019b`` ``1.1.0``|``-Python-3.8.2``|``intel/2020a`` @@ -29732,7 +30469,7 @@ version |versionsuffix|toolchain ``6.3`` | |``foss/2018b``, ``intel/2018b`` ``6.4.1``| |``intel/2019a`` ``6.5`` | |``intel/2019a``, ``intel/2019b`` -``6.6`` | |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` +``6.6`` | |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b``, ``intel/2020a`` ``6.7`` | |``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` ``6.8`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``7.0`` | |``foss/2021b``, ``intel/2021b`` @@ -30156,6 +30893,7 @@ version |versionsuffix |toolchain ``1.2.3`` | |``foss/2020b`` ``1.2.10``| |``foss/2021b`` ``1.3.4`` | |``foss/2022a`` +``1.3.8`` | |``foss/2022b`` ### rasterstats @@ -30502,10 +31240,11 @@ regionmask creates masks of geographical regions. It determines to which geograp *homepage*: -version |versionsuffix |toolchain ----------|-----------------|------------------------------ -``0.9.0``| |``foss/2021b``, ``foss/2022a`` -``0.9.0``|``-Python-3.8.2``|``foss/2020a`` +version |versionsuffix |toolchain +----------|-----------------|------------------------------ +``0.9.0`` | |``foss/2021b``, ``foss/2022a`` +``0.9.0`` |``-Python-3.8.2``|``foss/2020a`` +``0.10.0``| |``foss/2022b`` ### RegTools @@ -30912,6 +31651,7 @@ version |versionsuffix |toolchain ---------|-------------------|------------------------------ ``1.1.8``|``-Java-1.8`` |``foss/2018b`` ``1.1.8``|``-Java-1.8.0_121``|``foss/2016b`` +``1.1.8``|``-Java-11`` |``GCCcore/11.2.0`` ``2.4.2``| |``foss/2021a``, ``foss/2021b`` ### RNAclust @@ -31107,6 +31847,7 @@ version |versionsuffix |toolchain ``6.20.04`` |``-Python-3.7.4`` |``foss/2019b`` ``6.22.08`` | |``foss/2020b`` ``6.24.06`` | |``foss/2021b`` +``6.26.06`` | |``foss/2022a`` ``6.26.10`` | |``foss/2022b`` ``v5.34.34``|``-Python-2.7.11``|``intel/2016a`` ``v5.34.36``|``-Python-2.7.11``|``intel/2016a`` @@ -31202,7 +31943,7 @@ version |toolchain ``1.3.0`` |``foss/2016b``, ``intel/2017a`` ``1.3.1`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.3.2`` |``foss/2018b`` -``1.3.3`` |``foss/2019b``, ``foss/2022a`` +``1.3.3`` |``foss/2019b``, ``foss/2021b``, ``foss/2022a`` ### RSeQC @@ -31307,6 +32048,7 @@ version |toolchain ``3.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.0.3``|``GCCcore/11.3.0`` ``3.0.5``|``GCCcore/11.3.0`` +``3.2.2``|``GCCcore/12.2.0`` ### Ruby-Tk @@ -31352,6 +32094,7 @@ version |toolchain ``1.56.0``|``GCCcore/11.2.0`` ``1.60.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ``1.65.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.70.0``|``GCCcore/12.3.0`` ### rustworkx @@ -31366,7 +32109,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [S4](#s4) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [S4](#s4) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -31389,6 +32132,17 @@ version |toolchain ------------------|-------------- ``1.1.1-20180610``|``foss/2017b`` +### Safetensors + +Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.3.1``| |``foss/2022a`` +``0.3.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### SAGE S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data. @@ -31472,9 +32226,9 @@ samblaster is a fast and flexible program for marking duplicates in read-id gro *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``0.1.24``|``foss/2018b`` -``0.1.26``|``GCC/10.2.0``, ``GCC/10.3.0`` +``0.1.26``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.3.0`` ### Samcef @@ -31632,6 +32386,7 @@ ScaFaCoS is a library of scalable fast coulomb solvers. version |toolchain ---------|------------------------------------------------------------------------------- ``1.0.1``|``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a`` +``1.0.4``|``foss/2022a`` ### ScaLAPACK @@ -31658,7 +32413,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-bl`` |``gompi/2020b`` ``2.1.0``|``-fb`` |``gompi/2021a``, ``gompi/2021b`` ``2.2`` |``-amd`` |``gompi/2020a`` -``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``nvompi/2022.07`` +``2.2.0``|``-fb`` |``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023a``, ``nvompi/2022.07`` ### Scalasca @@ -31712,9 +32467,10 @@ Single-cell architecture surgery (scArches) is a package for reference-based ana *homepage*: -version |toolchain ----------|-------------- -``0.5.6``|``foss/2021a`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.5.6``| |``foss/2021a`` +``0.5.6``|``-CUDA-11.3.1``|``foss/2021a`` ### sceasy @@ -32332,14 +33088,14 @@ version |versionsuffix |toolchain ### segemehl -segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. +segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. -*homepage*: +*homepage*: version |toolchain ----------|----------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------ ``0.2.0``|``foss/2016b``, ``intel/2017b``, ``intel/2018a`` -``0.3.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b`` +``0.3.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2020.4.304`` ### segmentation-models @@ -32411,12 +33167,12 @@ SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic plac *homepage*: version |versionsuffix |toolchain -----------|-----------------|------------------------------ +----------|-----------------|---------------------------------------------- ``4.3.10``|``-Python-3.7.4``|``foss/2019b`` ``4.3.10``|``-Python-3.8.2``|``foss/2020a`` ``4.4.0`` | |``foss/2020b`` ``4.5.0`` | |``foss/2021a`` -``4.5.1`` | |``foss/2021b``, ``foss/2022a`` +``4.5.1`` | |``foss/2021b``, ``foss/2022a``, ``foss/2022b`` ### Seq-Gen @@ -32508,7 +33264,7 @@ version |toolchain ### seqtk -Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. +Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. *homepage*: @@ -32516,6 +33272,7 @@ version|toolchain -------|-------------------------------------------------------------------------------------------------------------------------------------------------- ``1.2``|``foss/2016b``, ``intel/2017a`` ``1.3``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +``1.4``|``GCC/12.2.0`` ### Serf @@ -32927,12 +33684,12 @@ SimpleITK is a simplified programming interface to the algorithms and data struc *homepage*: version |versionsuffix |toolchain ------------|------------------|------------------------------ +-----------|------------------|---------------------------------- ``1.1.0`` |``-Python-2.7.15``|``foss/2018b`` ``1.1.0`` |``-Python-3.6.4`` |``foss/2018a`` ``1.1.0`` |``-Python-3.6.6`` |``foss/2018b`` ``1.2.4`` |``-Python-3.7.4`` |``foss/2019b`` -``2.1.0`` | |``foss/2020b`` +``2.1.0`` | |``foss/2020b``, ``fosscuda/2020b`` ``2.1.1`` | |``foss/2021a`` ``2.1.1.2``| |``foss/2021b``, ``foss/2022a`` @@ -33398,6 +34155,16 @@ version |toolchain ``1.1.9`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.1.10``|``GCCcore/12.3.0`` +### Sniffles + +A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data. + +*homepage*: + +version |toolchain +---------|-------------- +``2.0.7``|``GCC/11.3.0`` + ### snippy Rapid haploid variant calling and core genome alignment @@ -33569,8 +34336,8 @@ SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU- *homepage*: version|toolchain --------|-------------- -``2.1``|``foss/2016a`` +-------|----------------------------- +``2.1``|``GCC/9.3.0``, ``foss/2016a`` ### SoupX @@ -33662,6 +34429,7 @@ version |versionsuffix |toolchain ``3.15.2``| |``GCC/10.2.0`` ``3.15.2``|``-Python-2.7.18``|``GCC/10.2.0`` ``3.15.3``| |``GCC/10.3.0``, ``GCC/11.2.0`` +``3.15.4``| |``GCC/12.2.0`` ``3.15.5``| |``GCC/11.3.0`` ### spaln @@ -33958,11 +34726,11 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg *homepage*: version |toolchain ----------|---------------------------------------------- +---------|------------------------------------------------------------------------------ ``3.0.1``|``GCC/7.3.0-2.30`` ``3.4.0``|``GCC/10.2.0`` ``4.0.0``|``GCC/8.3.0`` -``4.0.7``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +``4.0.7``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### SPOOLES @@ -34083,6 +34851,7 @@ version |versionsuffix |toolchain ``3.0.0`` | |``gompi/2021b`` ``3.0.0`` |``-centos_linux64``|``system`` ``3.0.3`` | |``gompi/2022a`` +``3.0.5`` | |``gompi/2021a`` ### sradownloader @@ -34269,7 +35038,7 @@ version |toolchain ``2.7.8a`` |``GCC/10.2.0`` ``2.7.9a`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``2.7.10a_alpha_220601``|``GCC/10.3.0`` -``2.7.10b`` |``GCC/11.3.0`` +``2.7.10b`` |``GCC/11.3.0``, ``GCC/12.2.0`` ### STAR-CCM+ @@ -34307,9 +35076,10 @@ Object Detection with Star-convex Shapes. *homepage*: -version |toolchain ----------|-------------- -``0.8.3``|``foss/2021b`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.8.3``| |``foss/2021b`` +``0.8.3``|``-CUDA-11.4.1``|``foss/2021b`` ### stars @@ -34364,6 +35134,7 @@ version |versionsuffix |toolchain ``0.12.1``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.12.2``| |``foss/2021a`` ``0.13.1``| |``foss/2021b``, ``foss/2022a``, ``intel/2021b`` +``0.14.0``| |``gfbf/2022b`` ### STEAK @@ -34398,6 +35169,16 @@ version |versionsuffix |toolchain ``1.7.6``|``-Python-3.7.2`` |``foss/2019a`` ``1.7.6``|``-Python-3.7.4`` |``foss/2019b`` +### strace + +strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state. + +*homepage*: + +version |toolchain +--------|------------------ +``5.14``|``GCCcore/11.2.0`` + ### Strainberry Strainberry is a method that performs strain separation in low-complexity metagenomes using error-prone long-read technologies. It exploits state-of-the-art tools for variant calling, haplotype phasing, and genome assembly, in order to achieve single-sample assembly of strains with higher quality than other state-of-the-art long-read assemblers. @@ -34480,6 +35261,16 @@ version |toolchain ---------|----------------------------------------------------------------------------------------------------- ``2.3.4``|``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` +### Structure_threader + +A program to parallelize the runs of Structure, fastStructure, MavericK and ALStructure software. + +*homepage*: + +version |toolchain +----------|-------------- +``1.3.10``|``foss/2022b`` + ### STRUMPACK STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling. @@ -34516,6 +35307,16 @@ version |toolchain ``2.0.3`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ``2.0.4`` |``GCC/11.3.0`` +### subset-bam + +subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag. + +*homepage*: + +version |toolchain +---------|------------------ +``1.1.0``|``GCCcore/10.3.0`` + ### Subversion Subversion is an open source version control system. @@ -34530,6 +35331,7 @@ version |toolchain ``1.12.0``|``GCCcore/8.2.0`` ``1.14.0``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.14.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.14.2``|``GCCcore/11.3.0`` ### suds @@ -34564,7 +35366,7 @@ version |versionsuffix |toolchain ``5.8.1`` |``-METIS-5.1.0`` |``foss/2020b``, ``intel/2020b`` ``5.10.1``|``-METIS-5.1.0`` |``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` ``5.10.1``|``-METIS-5.1.0-CUDA-11.3.1``|``foss/2021a`` -``5.13.0``|``-METIS-5.1.0`` |``foss/2022a`` +``5.13.0``|``-METIS-5.1.0`` |``foss/2022a``, ``foss/2022b`` ### SUMACLUST @@ -34603,7 +35405,7 @@ version |versionsuffix |toolchain SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers -*homepage*: +*homepage*: version |toolchain ---------|---------------------------------------------------------------------------------------------------------------------------------- @@ -34611,7 +35413,9 @@ version |toolchain ``2.7.0``|``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.1.0``|``foss/2019b``, ``intel/2019b`` ``5.7.0``|``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``6.2.0``|``foss/2020b``, ``intel/2020b`` ``6.3.0``|``foss/2021b``, ``foss/2022a`` +``6.5.1``|``foss/2022a`` ### SunPy @@ -34679,6 +35483,16 @@ version |toolchain ---------------------|-------------- ``1.0.7-19-ged1ca51``|``GCC/11.2.0`` +### SVclone + +Cluster structural variants of similar cancer cell fraction (CCF). + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.2``|``foss/2022b`` + ### SVDetect SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. @@ -34710,6 +35524,16 @@ version |versionsuffix |toolchain ``2.84``|``-Perl-5.30.0``|``foss/2019b`` ``2.87``| |``GCC/11.2.0``, ``GCC/11.3.0`` +### SVIM + +SVIM (pronounced swim) is a structural variant caller for third-generation sequencing reads. It is able to detect and classify the following six classes of structural variation: deletions, insertions, inversions, tandem duplications, interspersed duplications and translocations. + +*homepage*: + +version |toolchain +---------|-------------- +``2.0.0``|``foss/2022a`` + ### svist4get Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes. @@ -34907,7 +35731,7 @@ version |toolchain ## T -[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [TensorFlow-Datasets](#tensorflow-datasets) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [toil](#toil) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [TOPAS](#topas) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvision](#torchvision) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [typing-extensions](#typing-extensions) +[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [Tapenade](#tapenade) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [TensorFlow-Datasets](#tensorflow-datasets) - [TensorFlow-Graphics](#tensorflow-graphics) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [toil](#toil) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [TOPAS](#topas) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvision](#torchvision) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [Trinotate](#trinotate) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [typing-extensions](#typing-extensions) ### tabix @@ -35013,6 +35837,16 @@ version|toolchain -------|-------------- ``40`` |``GCC/11.2.0`` +### Tapenade + +Tool for Algorithmic Differentiation of programs. + +*homepage*: + +version |versionsuffix|toolchain +--------|-------------|---------- +``3.16``|``-Java-17`` |``system`` + ### task-spooler task spooler is a Unix batch system where the tasks spooled run one after the other. @@ -35273,6 +36107,9 @@ version |versionsuffix |toolchain ``2.7.1`` | |``foss/2021b`` ``2.7.1`` |``-CUDA-11.4.1`` |``foss/2021b`` ``2.8.4`` | |``foss/2021b`` +``2.8.4`` |``-CUDA-11.4.1`` |``foss/2021b`` +``2.9.1`` | |``foss/2022a`` +``2.9.1`` |``-CUDA-11.7.0`` |``foss/2022a`` ``2.11.0``| |``foss/2022a`` ``2.11.0``|``-CUDA-11.7.0`` |``foss/2022a`` @@ -35287,6 +36124,16 @@ version |versionsuffix |toolchain ``4.7.0``|``-CUDA-11.3.1``|``foss/2021a`` ``4.8.3``|``-CUDA-11.4.1``|``foss/2021b`` +### TensorFlow-Graphics + +Tensorflow Graphics provides a set of differentiable graphics and geometry layers (e.g. cameras, reflectance models, spatial transformations, mesh convolutions) and 3D viewer functionalities (e.g. 3D TensorBoard) that can be used to train and debug your machine learning models of choice. + +*homepage*: + +version |versionsuffix |toolchain +-------------|----------------|-------------- +``2021.12.3``|``-CUDA-11.4.1``|``foss/2021b`` + ### tensorflow-probability TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. @@ -35535,13 +36382,14 @@ version |versionsuffix|toolchain ### tidymodels -The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. +tidymodels is a 'meta-package' for modeling and statistical analysis that shares the underlying design philosophy, grammar, and data structures of the tidyverse. -*homepage*: +*homepage*: version |versionsuffix|toolchain ---------|-------------|-------------- ``0.1.0``|``-R-4.0.0`` |``foss/2020a`` +``1.1.0``| |``foss/2022b`` ### Tika @@ -35575,6 +36423,16 @@ version|toolchain ``1.7``|``system`` ``1.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +### timm + +timm is a library containing SOTA computer vision models, layers, utilities, optimizers, schedulers, data-loaders, augmentations, and training/evaluation scripts. It comes packaged with >700 pretrained models, and is designed to be flexible and easy to use. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``0.6.13``|``-CUDA-11.7.0``|``foss/2022a`` + ### TINKER The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. @@ -35695,14 +36553,14 @@ tmux is a terminal multiplexer: it enables a number of terminals to be created, *homepage*: version |toolchain ---------|-------------------------------------------------- +--------|---------------------------------------------------------------------- ``1.9a``|``GCC/4.9.2`` ``2.2`` |``GCCcore/4.9.3`` ``2.3`` |``GCC/5.4.0-2.26``, ``system`` ``3.1c``|``GCCcore/8.3.0`` ``3.2`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.2a``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` -``3.3a``|``GCCcore/11.3.0`` +``3.3a``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` ### TN93 @@ -35769,6 +36627,7 @@ Fast State-of-the-Art Tokenizers optimized for Research and Production version |toolchain ----------|------------------ ``0.12.1``|``GCCcore/10.3.0`` +``0.13.3``|``GCCcore/12.2.0`` ### Tombo @@ -35823,7 +36682,7 @@ version |versionsuffix |toolchain ``2.1.0``|``-Python-2.7.14``|``intel/2018a`` ``2.1.1``| |``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.1.2``| |``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` -``2.1.2``|``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.3.0`` +``2.1.2``|``-Python-2.7.18``|``GCC/10.2.0``, ``GCC/11.3.0``, ``gompi/2020a``, ``iimpi/2020a`` ### torchaudio @@ -35831,9 +36690,11 @@ Data manipulation and transformation for audio signal processing, powered by PyT *homepage*: -version |versionsuffix |toolchain ----------|-------------------------------|---------------------------------- -``0.5.0``|``-Python-3.7.4-PyTorch-1.4.0``|``foss/2019b``, ``fosscuda/2019b`` +version |versionsuffix |toolchain +----------|-------------------------------|---------------------------------- +``0.5.0`` |``-Python-3.7.4-PyTorch-1.4.0``|``foss/2019b``, ``fosscuda/2019b`` +``0.12.0``|``-PyTorch-1.12.0`` |``foss/2022a`` +``0.12.0``|``-PyTorch-1.12.0-CUDA-11.7.0``|``foss/2022a`` ### torchdata @@ -35976,6 +36837,7 @@ TransDecoder identifies candidate coding regions within transcript sequences, s version |versionsuffix |toolchain ---------|----------------|--------------- ``2.1.0``|``-Perl-5.24.1``|``intel/2017a`` +``5.5.0``| |``GCC/11.3.0`` ### Transformers @@ -35989,6 +36851,8 @@ version |versionsuffix |toolchain ``4.20.1``| |``foss/2021a`` ``4.21.1``| |``foss/2021b`` ``4.24.0``| |``foss/2022a`` +``4.29.2``| |``foss/2022a`` +``4.30.2``| |``foss/2022b`` ### Transrate @@ -36069,8 +36933,8 @@ Triangle generates exact Delaunay triangulations, constrained Delaunay triangula *homepage*: version|toolchain --------|---------------------------------------------------------------------------------------------------- -``1.6``|``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` +-------|----------------------------------------------------------------------------------------------------------------------- +``1.6``|``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` ### Trilinos @@ -36166,7 +37030,17 @@ version |versionsuffix |toolchain ``2.9.1`` |``-Python-2.7.16``|``foss/2019b`` ``2.9.1`` |``-Python-3.7.4`` |``foss/2019b`` ``2.10.0``|``-Python-3.7.4`` |``foss/2019b`` -``2.15.1``| |``foss/2022a`` +``2.15.1``| |``foss/2021b``, ``foss/2022a`` + +### Trinotate + +Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome. + +*homepage*: + +version |toolchain +---------|-------------- +``4.0.1``|``foss/2022a`` ### Triplexator @@ -36386,7 +37260,7 @@ version |versionsuffix |toolchain ## U -[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) +[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) ### UCC @@ -36399,6 +37273,7 @@ version |toolchain ---------|------------------ ``1.0.0``|``GCCcore/11.3.0`` ``1.1.0``|``GCCcore/12.2.0`` +``1.2.0``|``GCCcore/12.3.0`` ### UCC-CUDA @@ -36410,6 +37285,7 @@ version |versionsuffix |toolchain ---------|----------------|------------------ ``1.0.0``|``-CUDA-11.7.0``|``GCCcore/11.3.0`` ``1.1.0``|``-CUDA-12.0.0``|``GCCcore/12.2.0`` +``1.2.0``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` ### UCLUST @@ -36445,6 +37321,7 @@ version |versionsuffix |toolchain ``1.12.1`` | |``GCCcore/11.3.0`` ``1.13.1`` | |``GCCcore/12.2.0`` ``1.14.0`` | |``GCCcore/12.2.0`` +``1.14.1`` | |``GCCcore/12.3.0`` ### UCX-CUDA @@ -36460,6 +37337,7 @@ version |versionsuffix |toolchain ``1.11.2``|``-CUDA-11.5.2``|``GCCcore/11.2.0`` ``1.12.1``|``-CUDA-11.7.0``|``GCCcore/11.3.0`` ``1.13.1``|``-CUDA-12.0.0``|``GCCcore/12.2.0`` +``1.14.1``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` ### ucx-py @@ -36517,6 +37395,16 @@ version |versionsuffix |toolchain ``2018.1.0``|``-Python-3.6.4``|``foss/2018a`` ``2019.1.0``|``-Python-3.7.4``|``foss/2019b`` +### Ultralytics + +Ultralytics YOLOv8 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of previous YOLO versions and introduces new features and improvements to further boost performance and flexibility. YOLOv8 is designed to be fast, accurate, and easy to use, making it an excellent choice for a wide range of object detection and tracking, instance segmentation, image classification and pose estimation tasks. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``8.0.92``|``-CUDA-11.7.0``|``foss/2022a`` + ### umap-learn Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. @@ -36751,11 +37639,12 @@ version |toolchain ``2.37`` |``GCCcore/11.2.0`` ``2.38`` |``GCCcore/11.3.0`` ``2.38.1``|``GCCcore/12.2.0`` +``2.39`` |``GCCcore/12.3.0`` ## V -[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [vConTACT2](#vcontact2) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirSorter2](#virsorter2) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [vispr](#vispr) - [VisPy](#vispy) - [vitessce-python](#vitessce-python) - [vitessceR](#vitesscer) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) +[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [vConTACT2](#vcontact2) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirSorter2](#virsorter2) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [visdom](#visdom) - [vispr](#vispr) - [VisPy](#vispy) - [vitessce-python](#vitessce-python) - [vitessceR](#vitesscer) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) ### V8 @@ -36876,11 +37765,12 @@ version |toolchain The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. -*homepage*: +*homepage*: version |toolchain ---------|------------------------- ``5.4.1``|``intel/2016.02-GCC-4.9`` +``6.3.2``|``nvofbf/2022.07`` ### VAtools @@ -36995,7 +37885,7 @@ version |versionsuffix |toolchain Sequence assembler for very short reads -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|----------------|------------------------------------------------------------- @@ -37122,6 +38012,16 @@ version |toolchain -----------|-------------- ``7.2.6.1``|``GCC/10.3.0`` +### visdom + +A flexible tool for creating, organizing, and sharing visualizations of live, rich data. Supports Torch and Numpy. + +*homepage*: + +version |toolchain +---------|-------------- +``0.2.4``|``foss/2022a`` + ### vispr VISPR - A visualization framework for CRISPR data. @@ -37214,8 +38114,8 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ -``0.4.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.4.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` ### vsc-base @@ -37365,10 +38265,11 @@ version |versionsuffix |toolchain ``8.2.0`` |``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` ``8.2.0`` |``-Python-3.7.4`` |``foss/2019b`` ``8.2.0`` |``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``9.0.1`` | |``foss/2020b``, ``foss/2021a`` +``9.0.1`` | |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ``9.1.0`` | |``foss/2021b`` ``9.2.0.rc2``| |``foss/2022a`` ``9.2.2`` | |``foss/2022a`` +``9.2.6`` | |``foss/2022b`` ### VTune @@ -37425,7 +38326,7 @@ version |toolchain ## W -[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) +[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) ### wandb @@ -37612,6 +38513,7 @@ version|toolchain -------|------------------------------ ``1.1``|``foss/2020b``, ``foss/2021a`` ``1.4``|``foss/2021b`` +``1.7``|``foss/2022a`` ### wheel @@ -37742,6 +38644,16 @@ version |versionsuffix|toolchain ``4.3.1``|``-dmpar`` |``foss/2021a`` ``4.4`` |``-dmpar`` |``foss/2022a`` +### wrapt + +The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions. + +*homepage*: + +version |toolchain +----------|------------------------------- +``1.15.0``|``foss/2022a``, ``intel/2022a`` + ### WRF The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. @@ -37842,7 +38754,7 @@ version |toolchain ## X -[X11](#x11) - [x13as](#x13as) - [x264](#x264) - [x265](#x265) - [XALT](#xalt) - [xarray](#xarray) - [xbitmaps](#xbitmaps) - [xcb-proto](#xcb-proto) - [xcb-util](#xcb-util) - [xcb-util-image](#xcb-util-image) - [xcb-util-keysyms](#xcb-util-keysyms) - [xcb-util-renderutil](#xcb-util-renderutil) - [xcb-util-wm](#xcb-util-wm) - [xCell](#xcell) - [XCFun](#xcfun) - [XCrySDen](#xcrysden) - [Xerces-C++](#xerces-c++) - [xESMF](#xesmf) - [xextproto](#xextproto) - [xf86vidmodeproto](#xf86vidmodeproto) - [XGBoost](#xgboost) - [XGrafix](#xgrafix) - [xineramaproto](#xineramaproto) - [XKeyboardConfig](#xkeyboardconfig) - [XlsxWriter](#xlsxwriter) - [XMDS2](#xmds2) - [Xmipp](#xmipp) - [xmitgcm](#xmitgcm) - [XML-Compile](#xml-compile) - [XML-LibXML](#xml-libxml) - [XML-Parser](#xml-parser) - [xmlf90](#xmlf90) - [XMLSec](#xmlsec) - [XMLStarlet](#xmlstarlet) - [xonsh](#xonsh) - [xorg-macros](#xorg-macros) - [XPLOR-NIH](#xplor-nih) - [xprop](#xprop) - [xproto](#xproto) - [XSD](#xsd) - [XTandem](#xtandem) - [xtb](#xtb) - [xtensor](#xtensor) - [xtrans](#xtrans) - [Xvfb](#xvfb) - [xxd](#xxd) - [xxHash](#xxhash) - [XZ](#xz) +[X11](#x11) - [x13as](#x13as) - [x264](#x264) - [x265](#x265) - [XALT](#xalt) - [xarray](#xarray) - [xbitmaps](#xbitmaps) - [xcb-proto](#xcb-proto) - [xcb-util](#xcb-util) - [xcb-util-image](#xcb-util-image) - [xcb-util-keysyms](#xcb-util-keysyms) - [xcb-util-renderutil](#xcb-util-renderutil) - [xcb-util-wm](#xcb-util-wm) - [xCell](#xcell) - [XCFun](#xcfun) - [xclip](#xclip) - [XCrySDen](#xcrysden) - [xdotool](#xdotool) - [Xerces-C++](#xerces-c++) - [xESMF](#xesmf) - [xextproto](#xextproto) - [xf86vidmodeproto](#xf86vidmodeproto) - [XGBoost](#xgboost) - [XGrafix](#xgrafix) - [xineramaproto](#xineramaproto) - [XKeyboardConfig](#xkeyboardconfig) - [XlsxWriter](#xlsxwriter) - [XMDS2](#xmds2) - [Xmipp](#xmipp) - [xmitgcm](#xmitgcm) - [XML-Compile](#xml-compile) - [XML-LibXML](#xml-libxml) - [XML-Parser](#xml-parser) - [xmlf90](#xmlf90) - [XMLSec](#xmlsec) - [XMLStarlet](#xmlstarlet) - [xonsh](#xonsh) - [xorg-macros](#xorg-macros) - [XPLOR-NIH](#xplor-nih) - [xprop](#xprop) - [xproto](#xproto) - [XSD](#xsd) - [XTandem](#xtandem) - [xtb](#xtb) - [xtensor](#xtensor) - [xtrans](#xtrans) - [Xvfb](#xvfb) - [xxd](#xxd) - [xxHash](#xxhash) - [XZ](#xz) ### X11 @@ -37867,6 +38779,7 @@ version |toolchain ``20210802``|``GCCcore/11.2.0`` ``20220504``|``GCCcore/11.3.0`` ``20221110``|``GCCcore/12.2.0`` +``20230603``|``GCCcore/12.3.0`` ### x13as @@ -37958,6 +38871,7 @@ version |versionsuffix |toolchain ``0.20.1`` | |``foss/2021b``, ``intel/2021b`` ``2022.6.0``| |``foss/2022a``, ``intel/2022a`` ``2022.9.0``| |``foss/2022a`` +``2023.4.2``| |``gfbf/2022b`` ### xbitmaps @@ -38054,6 +38968,16 @@ version |versionsuffix |toolchain ``20180122``|``-Python-2.7.14``|``intel/2017b`` ``20190127``|``-Python-3.7.2`` |``foss/2019a`` +### xclip + +xclip is a command line utility that is designed to run on any system with an X11 implementation. + +*homepage*: + +version |toolchain +--------|------------------ +``0.13``|``GCCcore/11.3.0`` + ### XCrySDen XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. @@ -38065,6 +38989,16 @@ version |toolchain ``1.5.60``|``intel/2019a`` ``1.6.2`` |``foss/2019b``, ``foss/2020b``, ``foss/2022a``, ``intel/2019b``, ``intel/2022a`` +### xdotool + +xdotool lets you simulate keyboard input and mouse activity, move and resize windows, etc. It does this using X11’s XTEST extension and other Xlib functions. + +*homepage*: + +version |toolchain +----------------|------------------ +``3.20211022.1``|``GCCcore/11.3.0`` + ### Xerces-C++ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. @@ -38077,7 +39011,7 @@ version |toolchain ``3.2.0``|``GCCcore/7.3.0`` ``3.2.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.2.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``3.2.4``|``GCCcore/12.2.0`` +``3.2.4``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### xESMF @@ -38172,6 +39106,7 @@ version |toolchain ``1.4.4``|``GCCcore/10.3.0`` ``3.0.2``|``GCCcore/11.2.0`` ``3.0.8``|``GCCcore/11.3.0`` +``3.1.2``|``GCCcore/12.2.0`` ### XMDS2 @@ -38233,6 +39168,7 @@ version |versionsuffix |toolchain ``2.0205``| |``GCCcore/9.3.0`` ``2.0206``| |``GCCcore/10.2.0`` ``2.0207``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0208``| |``GCCcore/12.2.0`` ### XML-Parser @@ -38298,7 +39234,7 @@ version |toolchain X.org macros utilities. -*homepage*: +*homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------ @@ -38306,6 +39242,7 @@ version |toolchain ``1.19.1``|``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2``|``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``1.19.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.20.0``|``GCCcore/12.3.0`` ### XPLOR-NIH @@ -38519,9 +39456,9 @@ yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``0.6.3``|``GCCcore/8.3.0`` -``0.7.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.7.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### YANK @@ -38551,8 +39488,8 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``1.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``1.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### YAXT @@ -38640,7 +39577,7 @@ version |toolchain ``4.2.5``|``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3``|``GCCcore/10.2.0`` -``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### zfp @@ -38649,9 +39586,9 @@ zfp is a compressed format for representing multidimensional floating-point and *homepage*: version |toolchain ----------|------------------------------------- +---------|--------------------------------------------------------- ``0.5.5``|``GCCcore/10.2.0`` -``1.0.0``|``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.0.0``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### Zgoubi @@ -38706,7 +39643,7 @@ version |toolchain ``1.2.10``|``system`` ``1.2.11``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ``1.2.12``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` -``1.2.13``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``1.2.13``|``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` ### zlib-ng @@ -38718,6 +39655,7 @@ version |toolchain ---------|------------------ ``2.0.5``|``GCCcore/10.2.0`` ``2.0.6``|``GCCcore/10.3.0`` +``2.0.7``|``GCCcore/11.3.0`` ### zlibbioc @@ -38737,8 +39675,8 @@ Zopfli Compression Algorithm is a compression library programmed in C to perform *homepage*: version |toolchain ----------|-------------------------------------- -``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +---------|---------------------------------------------------------- +``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ### ZPAQ From 13bf2066dfa629c1bf928ffee56509a0668bd5c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2023 19:26:47 +0200 Subject: [PATCH 17/41] update release notes for EasyBuild v4.8.0 --- docs/changelog-docs.md | 3 + docs/installation.md | 6 +- docs/release-notes.md | 120 ++++++++++++++++++++++++++++++- docs/typical-workflow-example.md | 4 +- mkdocs.yml | 2 +- 5 files changed, 126 insertions(+), 9 deletions(-) diff --git a/docs/changelog-docs.md b/docs/changelog-docs.md index 3c9cee310..c1871a195 100644 --- a/docs/changelog-docs.md +++ b/docs/changelog-docs.md @@ -7,6 +7,9 @@ search: (for EasyBuild release notes, see [EasyBuild release notes][release_notes]) +- **release 20230707.01** (*7 July 2023*): update + release notes for EasyBuild v4.8.0 (see + [EasyBuild v4.8.0 (7 July 2023)][release_notes_eb480]) - **release 20230527.01** (*27 May 2023*): update release notes for EasyBuild v4.7.2 (see [EasyBuild v4.7.2 (27 May 2023)][release_notes_eb472]) diff --git a/docs/installation.md b/docs/installation.md index cd68246c6..246bd2758 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -62,10 +62,10 @@ $ module load EasyBuild $ module list Currently Loaded Modules: - 1) EasyBuild/4.7.2 + 1) EasyBuild/4.8.0 $ eb --version -This is EasyBuild 4.7.2 (framework: 4.7.2, easyblocks: 4.7.2) on host example.local +This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example.local ``` !!! tip @@ -228,7 +228,7 @@ $ EB_VERBOSE=1 eb --version >> 'python3' version: 3.6.8, which matches Python 3 version requirement (>= 3.5) >> Selected Python command: python3 (/usr/bin/python3.6) >> python3.6 -m easybuild.main --version -This is EasyBuild 4.7.2 (framework: 4.7.2, easyblocks: 4.7.2) on host example +This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example ``` diff --git a/docs/release-notes.md b/docs/release-notes.md index 094ef5d37..b507cb89a 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -6,10 +6,124 @@ search: # EasyBuild release notes {: #release_notes } The latest version of EasyBuild provides support for building and -installing [**3,085** different software packages](../version-specific/supported-software), +installing [**3,161** different software packages](../version-specific/supported-software), including 39 different (compiler) toolchains. -It contains 248 software-specific easyblocks and 41 generic easyblocks, -alongside 17,098 easyconfig files. +It contains 249 software-specific easyblocks and 42 generic easyblocks, +alongside 17,511 easyconfig files. + + +## EasyBuild v4.8.0 (7 July 2023) {: #release_notes_eb480 } + +feature release + +**framework** + +- various enhancements, including: + - use version suffixes in PR title instead of Python versions when using `--new-pr` ([#4253](https://github.com/easybuilders/easybuild-framework/pull/4253) + [#4286](https://github.com/easybuilders/easybuild-framework/pull/4286)) + - add script to find updated ECs for installed module ([#4271](https://github.com/easybuilders/easybuild-framework/pull/4271)) +- various bug fixes, including: + - fix regex for extracting glibc version from output of '`ldd --version`' in Gentoo Linux ([#4290](https://github.com/easybuilders/easybuild-framework/pull/4290)) + - allow versionsuffix to be set to None in `det_full_ec_version` ([#4292](https://github.com/easybuilders/easybuild-framework/pull/4292)) +- other changes: + - stop running tests with Python 2.7 since it is no longer supported in GitHub Action ([#4267](https://github.com/easybuilders/easybuild-framework/pull/4267)) + - replace `imp.load_source` by leveraging `importlib.util.module_from_spec` when using Python 3 ([#4280](https://github.com/easybuilders/easybuild-framework/pull/4280)) + +**easyblocks** + +- add `PerlBundle` generic easyblock for installing a bundle of Perl modules ([#2945](https://github.com/easybuilders/easybuild-easyblocks/pull/2945)) +- add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if `--rpath` is used ([#2952](https://github.com/easybuilders/easybuild-easyblocks/pull/2952)) +- minor enhancements and updates, including: + - add support for NVIDIA Hopper CC 9.0 in LAMMPS ([#2941](https://github.com/easybuilders/easybuild-easyblocks/pull/2941)) + - add support for `install_cmds` in `Binary` easyblock ([#2953](https://github.com/easybuilders/easybuild-easyblocks/pull/2953)) +- various bug fixes, including: + - patch CMake's `UnixPaths.cmake` script if `--sysroot` is set ([#2248](https://github.com/easybuilders/easybuild-easyblocks/pull/2248)) + - fix incorrect `sanity_check_step` for torchvision ([#2938](https://github.com/easybuilders/easybuild-easyblocks/pull/2938)) + - update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes ([#2944](https://github.com/easybuilders/easybuild-easyblocks/pull/2944)) + - improve handling of `optarch` in `Cargo` easyblock ([#2947](https://github.com/easybuilders/easybuild-easyblocks/pull/2947)) + - reset modules loaded by `PythonPackage` to let `ExtensionEasyBlock` handle `multi_deps` correctly ([#2951](https://github.com/easybuilders/easybuild-easyblocks/pull/2951)) +- other changes: + - stop running tests with Python 2.7 since it is no longer supported in GitHub Actions ([#2943](https://github.com/easybuilders/easybuild-easyblocks/pull/2943)) + +**easyconfigs** + +- added easyconfigs for `foss/2023a` ([#18264](https://github.com/easybuilders/easybuild-easyconfigs/pull/18264)) and `intel/2023a` ([#18275](https://github.com/easybuilders/easybuild-easyconfigs/pull/18275)) common toolchains +- added example easyconfig files for 76 new software packages: + - 3d-dna ([#9258](https://github.com/easybuilders/easybuild-easyconfigs/pull/9258)), affinity ([#18051](https://github.com/easybuilders/easybuild-easyconfigs/pull/18051)), AIMAll ([#13153](https://github.com/easybuilders/easybuild-easyconfigs/pull/13153)), alleleIntegrator ([#17923](https://github.com/easybuilders/easybuild-easyconfigs/pull/17923)), AlphaPulldown ([#17774](https://github.com/easybuilders/easybuild-easyconfigs/pull/17774)), + ASCAT ([#17923](https://github.com/easybuilders/easybuild-easyconfigs/pull/17923)), ASF-SearchAPI ([#18179](https://github.com/easybuilders/easybuild-easyconfigs/pull/18179)), ATAT ([#18213](https://github.com/easybuilders/easybuild-easyconfigs/pull/18213)), AutoDockSuite ([#9678](https://github.com/easybuilders/easybuild-easyconfigs/pull/9678)), axel ([#10961](https://github.com/easybuilders/easybuild-easyconfigs/pull/10961)), BayesPrism ([#17885](https://github.com/easybuilders/easybuild-easyconfigs/pull/17885)), + BGC-Bayesian-genomic-clines ([#18005](https://github.com/easybuilders/easybuild-easyconfigs/pull/18005)), CalculiX-CrunchiX ([#16805](https://github.com/easybuilders/easybuild-easyconfigs/pull/16805)), CASA ([#18055](https://github.com/easybuilders/easybuild-easyconfigs/pull/18055)), cctbx-base ([#17774](https://github.com/easybuilders/easybuild-easyconfigs/pull/17774)), + Circuitscape ([#16720](https://github.com/easybuilders/easybuild-easyconfigs/pull/16720)), CppHeaderParser ([#18272](https://github.com/easybuilders/easybuild-easyconfigs/pull/18272)), CuCLARK ([#9482](https://github.com/easybuilders/easybuild-easyconfigs/pull/9482)), cuteSV ([#18077](https://github.com/easybuilders/easybuild-easyconfigs/pull/18077)), DALI ([#18204](https://github.com/easybuilders/easybuild-easyconfigs/pull/18204)), DaliLite ([#17989](https://github.com/easybuilders/easybuild-easyconfigs/pull/17989)), + DEICODE ([#18181](https://github.com/easybuilders/easybuild-easyconfigs/pull/18181)), dm-haiku ([#18013](https://github.com/easybuilders/easybuild-easyconfigs/pull/18013)), dominate ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)), dx-toolkit ([#18232](https://github.com/easybuilders/easybuild-easyconfigs/pull/18232)), easel ([#18156](https://github.com/easybuilders/easybuild-easyconfigs/pull/18156)), ecFlow ([#15719](https://github.com/easybuilders/easybuild-easyconfigs/pull/15719)), + EDirect ([#17479](https://github.com/easybuilders/easybuild-easyconfigs/pull/17479)), FragPipe ([#18161](https://github.com/easybuilders/easybuild-easyconfigs/pull/18161)), GEM ([#18120](https://github.com/easybuilders/easybuild-easyconfigs/pull/18120)), gemelli ([#18120](https://github.com/easybuilders/easybuild-easyconfigs/pull/18120)), GLIMPSE ([#18163](https://github.com/easybuilders/easybuild-easyconfigs/pull/18163)), GRIDSS ([#18170](https://github.com/easybuilders/easybuild-easyconfigs/pull/18170)), + HOOMD-blue ([#18224](https://github.com/easybuilders/easybuild-easyconfigs/pull/18224)), KerasTuner ([#18197](https://github.com/easybuilders/easybuild-easyconfigs/pull/18197)), LayoutParser ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), LISFLOOD-FP ([#18194](https://github.com/easybuilders/easybuild-easyconfigs/pull/18194)), LuaRocks ([#18073](https://github.com/easybuilders/easybuild-easyconfigs/pull/18073)), + mannkendall ([#18043](https://github.com/easybuilders/easybuild-easyconfigs/pull/18043)), MOB-suite ([#16798](https://github.com/easybuilders/easybuild-easyconfigs/pull/16798)), molecularGSM ([#13150](https://github.com/easybuilders/easybuild-easyconfigs/pull/13150)), MONAI-Label ([#18180](https://github.com/easybuilders/easybuild-easyconfigs/pull/18180)), MView ([#18198](https://github.com/easybuilders/easybuild-easyconfigs/pull/18198)), + NanoStat ([#18201](https://github.com/easybuilders/easybuild-easyconfigs/pull/18201)), oxDNA ([#18175](https://github.com/easybuilders/easybuild-easyconfigs/pull/18175) + [#18214](https://github.com/easybuilders/easybuild-easyconfigs/pull/18214)), pastml ([#15336](https://github.com/easybuilders/easybuild-easyconfigs/pull/15336)), pbipa ([#18229](https://github.com/easybuilders/easybuild-easyconfigs/pull/18229)), Perl-bundle-CPAN ([#17970](https://github.com/easybuilders/easybuild-easyconfigs/pull/17970)), PheWeb ([#10951](https://github.com/easybuilders/easybuild-easyconfigs/pull/10951)), + plinkliftover ([#18136](https://github.com/easybuilders/easybuild-easyconfigs/pull/18136)), pmt ([#18052](https://github.com/easybuilders/easybuild-easyconfigs/pull/18052)), PyBioLib ([#18124](https://github.com/easybuilders/easybuild-easyconfigs/pull/18124)), Pychopper ([#10344](https://github.com/easybuilders/easybuild-easyconfigs/pull/10344)), pydicom-seg ([#18180](https://github.com/easybuilders/easybuild-easyconfigs/pull/18180)), + pyMannKendall ([#18044](https://github.com/easybuilders/easybuild-easyconfigs/pull/18044)), pypmt ([#18045](https://github.com/easybuilders/easybuild-easyconfigs/pull/18045)), python-mujoco ([#18253](https://github.com/easybuilders/easybuild-easyconfigs/pull/18253)), pytorch-CycleGAN-pix2pix ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)), + PyTorch-Image-Models ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), PyWBGT ([#17980](https://github.com/easybuilders/easybuild-easyconfigs/pull/17980)), Safetensors ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), Sniffles ([#18048](https://github.com/easybuilders/easybuild-easyconfigs/pull/18048)), strace ([#14381](https://github.com/easybuilders/easybuild-easyconfigs/pull/14381)), + Structure_threader ([#18219](https://github.com/easybuilders/easybuild-easyconfigs/pull/18219)), subset-bam ([#18032](https://github.com/easybuilders/easybuild-easyconfigs/pull/18032)), SVclone ([#18084](https://github.com/easybuilders/easybuild-easyconfigs/pull/18084)), SVIM ([#18071](https://github.com/easybuilders/easybuild-easyconfigs/pull/18071)), Tapenade ([#18109](https://github.com/easybuilders/easybuild-easyconfigs/pull/18109)), + TensorFlow-Graphics ([#17465](https://github.com/easybuilders/easybuild-easyconfigs/pull/17465)), timm ([#17787](https://github.com/easybuilders/easybuild-easyconfigs/pull/17787)), Trinotate ([#18124](https://github.com/easybuilders/easybuild-easyconfigs/pull/18124)), Ultralytics ([#17894](https://github.com/easybuilders/easybuild-easyconfigs/pull/17894)), visdom ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)), + wrapt ([#18125](https://github.com/easybuilders/easybuild-easyconfigs/pull/18125)), xclip ([#17055](https://github.com/easybuilders/easybuild-easyconfigs/pull/17055)), xdotool ([#17055](https://github.com/easybuilders/easybuild-easyconfigs/pull/17055)) +- added additional easyconfigs for various supported software packages, including: + - AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0, + boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10, + corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1, + datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3, + elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2, + FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1, + Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1, + hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2, + Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0, + lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1, + minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3, + Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2, + OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1, + PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6, + pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3, + python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4, + seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0, + tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0, + UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2, + XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7 +- minor enhancements, including: + - add CI check for `-DCMAKE_BUILD_TYPE`, should use `build_type` instead ([#14008](https://github.com/easybuilders/easybuild-easyconfigs/pull/14008)) + - enhance sanity check for recent LibTIFF easyconfigs ([#17975](https://github.com/easybuilders/easybuild-easyconfigs/pull/17975)) + - update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module ([#17982](https://github.com/easybuilders/easybuild-easyconfigs/pull/17982)) + - use custom easyblock for Rust 1.65.0 ([#18174](https://github.com/easybuilders/easybuild-easyconfigs/pull/18174)) and Rust 1.70.0 ([#18167](https://github.com/easybuilders/easybuild-easyconfigs/pull/18167)) + - update easyconfig for Nextflow 23.04.2 to use `install_cmds` ([#18173](https://github.com/easybuilders/easybuild-easyconfigs/pull/18173)) + - add extra packages to recent R easyconfigs ([#18029](https://github.com/easybuilders/easybuild-easyconfigs/pull/18029), [#18063](https://github.com/easybuilders/easybuild-easyconfigs/pull/18063), [#18122](https://github.com/easybuilders/easybuild-easyconfigs/pull/18122), [#18195](https://github.com/easybuilders/easybuild-easyconfigs/pull/18195), [#18245](https://github.com/easybuilders/easybuild-easyconfigs/pull/18245)) + - add extra packages to recent R-bundle-Bioconductor easyconfigs ([#18196](https://github.com/easybuilders/easybuild-easyconfigs/pull/18196), [#18246](https://github.com/easybuilders/easybuild-easyconfigs/pull/18246)) +- various bug fixes, including: + - add patches to fix TensorFlow 2.7.1 on POWER ([#16795](https://github.com/easybuilders/easybuild-easyconfigs/pull/16795)) + - fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ `foss/2021b` ([#17058](https://github.com/easybuilders/easybuild-easyconfigs/pull/17058)) + - stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 ([#17998](https://github.com/easybuilders/easybuild-easyconfigs/pull/17998)) + - add pkgconfig as build dependency for nodejs , required for finding ICU dependency ([#18007](https://github.com/easybuilders/easybuild-easyconfigs/pull/18007)) + - fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 ([#18030](https://github.com/easybuilders/easybuild-easyconfigs/pull/18030)) + - update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies ([#18041](https://github.com/easybuilders/easybuild-easyconfigs/pull/18041)) + - fix `--sanity-check-only` for MAGeCK v0.5.9.4 ([#18047](https://github.com/easybuilders/easybuild-easyconfigs/pull/18047)) + - enable building static libs and check for `libexslt.*` in libxslt ([#18064](https://github.com/easybuilders/easybuild-easyconfigs/pull/18064)) + - add `-pthread` flag for dorado ([#18072](https://github.com/easybuilders/easybuild-easyconfigs/pull/18072)) + - add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 ([#18087](https://github.com/easybuilders/easybuild-easyconfigs/pull/18087)) + - add missing pkgconf build dependency for XML-LibXML v2.0208 ([#18159](https://github.com/easybuilders/easybuild-easyconfigs/pull/18159)) + - update homepage for NWChem 7.x ([#18184](https://github.com/easybuilders/easybuild-easyconfigs/pull/18184)) + - update homepage for SUNDIALS 5.x and 6.x ([#18186](https://github.com/easybuilders/easybuild-easyconfigs/pull/18186)) + - add missing `source_urls` for SimpleITK ([#18212](https://github.com/easybuilders/easybuild-easyconfigs/pull/18212)) + - use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 ([#18230](https://github.com/easybuilders/easybuild-easyconfigs/pull/18230)) + - fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) ([#18231](https://github.com/easybuilders/easybuild-easyconfigs/pull/18231)) + - fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks ([#18235](https://github.com/easybuilders/easybuild-easyconfigs/pull/18235)) + - use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 ([#18236](https://github.com/easybuilders/easybuild-easyconfigs/pull/18236)) + - update `source_urls` for Velvet 1.2.10 ([#18237](https://github.com/easybuilders/easybuild-easyconfigs/pull/18237)) + - use upstream patch for symbol compatibility in XZ 5.2.5 ([#18250](https://github.com/easybuilders/easybuild-easyconfigs/pull/18250)) + - update source url for pkgconf ([#18271](https://github.com/easybuilders/easybuild-easyconfigs/pull/18271)) +- other changes: + - stop running easyconfig unit tests with Python 2.7 ([#18006](https://github.com/easybuilders/easybuild-easyconfigs/pull/18006)) + - fix toolchain for networkx-3.0 (`foss/2022b` -> `gfbf/2022b`) ([#18061](https://github.com/easybuilders/easybuild-easyconfigs/pull/18061)) + - remove unused PyTorch patch ([#18062](https://github.com/easybuilders/easybuild-easyconfigs/pull/18062)) + - allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match ([#18098](https://github.com/easybuilders/easybuild-easyconfigs/pull/18098)) + - bump OpenSSL 1.1 wrapper fallback to 1.1.1u ([#18188](https://github.com/easybuilders/easybuild-easyconfigs/pull/18188)) + - remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion ([#18222](https://github.com/easybuilders/easybuild-easyconfigs/pull/18222)) + - remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB ([#18223](https://github.com/easybuilders/easybuild-easyconfigs/pull/18223)) + - remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs ([#18260](https://github.com/easybuilders/easybuild-easyconfigs/pull/18260)) + - change base compiler for `intel/2023.03` to `GCCcore/12.3.0` (required to use it as intel/2023a) ([#18263](https://github.com/easybuilders/easybuild-easyconfigs/pull/18263)) ## EasyBuild v4.7.2 (27 May 2023) {: #release_notes_eb472 } diff --git a/docs/typical-workflow-example.md b/docs/typical-workflow-example.md index 5cf3e40e6..f8c6dd36a 100644 --- a/docs/typical-workflow-example.md +++ b/docs/typical-workflow-example.md @@ -146,7 +146,7 @@ we enable dependency resolution such that the entire software stack is handled: $ eb WRF-4.4.1-foss-2022b-dmpar.eb --robot == temporary log file in case of crash /tmp/eb-LfQa8b/easybuild-TBXLTy.log == resolving dependencies ... -== processing EasyBuild easyconfig /home/example/.local/easybuild/software/EasyBuild/4.7.2/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb +== processing EasyBuild easyconfig /home/example/.local/easybuild/software/EasyBuild/4.8.0/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb == building and installing ncurses/6.3-GCCcore-12.2.0... [...] == building and installing tcsh/6.20.00-GCCcore-12.2.0... @@ -183,7 +183,7 @@ $ module load WRF/4.4.1-foss-2022b-dmpar $ module list Currently Loaded Modules: - 1) EasyBuild/4.7.2 18) OpenBLAS/0.3.21-GCC-12.2.0 + 1) EasyBuild/4.8.0 18) OpenBLAS/0.3.21-GCC-12.2.0 2) GCCcore/12.2.0 19) FlexiBLAS/3.2.1-GCC-12.2.0 3) zlib/1.2.12-GCCcore-12.2.0 20) FFTW/3.3.10-GCC-12.2.0 foss/2018b 4) binutils/2.39-GCCcore-12.2.0 21) gompi/2022b diff --git a/mkdocs.yml b/mkdocs.yml index 141598c08..032df935a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -155,7 +155,7 @@ extra: provider: google property: G-BLVCH6991S easybuild: - version: 4.7.2 + version: 4.8.0 # add links in bottom right social: - icon: fontawesome/brands/twitter From 29050f02f5faee11e9ae921633463e1d244cadbe Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Tue, 8 Aug 2023 15:47:59 +0100 Subject: [PATCH 18/41] Add missing and future hooks with param descriptions --- docs/hooks.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index c350c95e9..7da9102b4 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -43,7 +43,7 @@ eb ... ## Available hooks -Currently (since EasyBuild v3.7.0), three types of hooks are supported: +Currently (since EasyBuild v3.7.0), five types of hooks are supported: * `start_hook` and `end_hook`, which are triggered *once* before starting software installations, and *once* right after completing all installations, respectively @@ -59,6 +59,7 @@ which can also be consulted using `eb --avail-hooks`, is: * `start_hook` *(only called once in an EasyBuild session)* * `parse_hook` *(available since EasyBuild v3.7.0)* +* `pre_build_and_install_loop` * `pre_fetch_hook`, `post_fetch_hook` * `pre_ready_hook`, `post_ready_hook` * `pre_source_hook`, `post_source_hook` @@ -68,7 +69,9 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_build_hook`, `post_build_hook` * `pre_test_hook`, `post_test_hook` * `pre_install_hook`, `post_install_hook` -* `pre_extensions_hook`, `post_extensions_hook` +* `pre_extensions_hook` +* `pre_single_extension_hook`, `post_single_extension_hook` +* `post_extensions_hook` * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` @@ -76,7 +79,11 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_permissions_hook`, `post_permissions_hook` * `pre_package_hook`, `post_package_hook` * `pre_testcases_hook`, `post_testcases_hook` +* `post_build_and_install_loop` * `end_hook` *(only called once in an EasyBuild session)* +* `fail_hook` +* `cancel_hook` +* `crash_hook` * `module_write_hook` *(called multiple times per installation, available since EasyBuild v4.4.1)* All functions implemented in the provided Python module for which the name ends with `_hook` are considered. @@ -107,6 +114,8 @@ Do take into account the following: * for `start_hook` and `end_hook`, no arguments are provided * for `parse_hook`, one argument is provided: the `EasyConfig` instance that corresponds to the easyconfig file being parsed (usually referred to as `ec`) +* for `pre_build_and_install_loop`, a list of easyconfigs is provided +* for `post_build_and_install_loop`, a list of easyconfigs with build results is provided * for `module_write_hook`, 3 arguments are provided: * the `EasyBlock` instance used to perform the installation (usually referred to as `self`) * the filepath of the module that will be written From c5d3f6d542c3cda1942e724e44e90f7133aee90c Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Tue, 8 Aug 2023 16:26:16 +0100 Subject: [PATCH 19/41] Add further information on failure hooks --- docs/hooks.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index 7da9102b4..667c2b455 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -45,14 +45,17 @@ eb ... Currently (since EasyBuild v3.7.0), five types of hooks are supported: -* `start_hook` and `end_hook`, which are triggered *once* before starting software installations, - and *once* right after completing all installations, respectively +* `start_hook`, `pre_build_and_install_loop`, `end_hook` and `post_build_and_install_loop` which are triggered *once* before starting software installations, + and *once* right after completing all installations, respectively. * `parse_hook`, which is triggered when an easyconfig file is being parsed * `module_write_hook`, which is triggered right before a module file is written. This includes the temporary module file used when installing extensions and during the sanity check, as well as the devel module. * "*step*" hooks that are triggered before and after every step of each installation procedure that is performed, - also aptly named '`pre`'- and '`post`'-hooks + also aptly named '`pre`'- and '`post`'- hooks. +* "*failure*" hooks, `fail_hook`, `cancel_hook`, `crash_hook`, are triggered when an `EasyBuildError`, `KeyboardInterrupt` or `Exception` is +encountered, respectively. `crash_hook` functions as a "catch all" for Python exceptions, and won't be called if either `fail_hook` or `cancel_hook` +is run. The list of currently available hooks in order of execution, which can also be consulted using `eb --avail-hooks`, is: From 517183c3bba779c41e2ac04c3e9ffa48712f42f4 Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Wed, 9 Aug 2023 09:50:54 +0100 Subject: [PATCH 20/41] Detail arguments passed to failure hooks --- docs/hooks.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/hooks.md b/docs/hooks.md index 667c2b455..7909e7db3 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -115,6 +115,8 @@ each named after an available hook. Do take into account the following: * for `start_hook` and `end_hook`, no arguments are provided +* for `fail_hook`, `cancel_hook` and `crash_hook`, the exception which caused the build to stop +is provided * for `parse_hook`, one argument is provided: the `EasyConfig` instance that corresponds to the easyconfig file being parsed (usually referred to as `ec`) * for `pre_build_and_install_loop`, a list of easyconfigs is provided From be22e3ca20dab090cc6c8d634218212ef2a6288f Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Wed, 9 Aug 2023 10:37:19 +0100 Subject: [PATCH 21/41] Add postiter step --- docs/hooks.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index 7909e7db3..d135435bc 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -62,7 +62,7 @@ which can also be consulted using `eb --avail-hooks`, is: * `start_hook` *(only called once in an EasyBuild session)* * `parse_hook` *(available since EasyBuild v3.7.0)* -* `pre_build_and_install_loop` +* `pre_build_and_install_loop` *(available since EasyBuild v?)* * `pre_fetch_hook`, `post_fetch_hook` * `pre_ready_hook`, `post_ready_hook` * `pre_source_hook`, `post_source_hook` @@ -73,8 +73,9 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_test_hook`, `post_test_hook` * `pre_install_hook`, `post_install_hook` * `pre_extensions_hook` -* `pre_single_extension_hook`, `post_single_extension_hook` +* `pre_single_extension_hook`, `post_single_extension_hook` *(available since EasyBuild v4.7.1)* * `post_extensions_hook` +* `pre_postiter_step`, `post_postiter_step` * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` @@ -82,11 +83,11 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_permissions_hook`, `post_permissions_hook` * `pre_package_hook`, `post_package_hook` * `pre_testcases_hook`, `post_testcases_hook` -* `post_build_and_install_loop` +* `post_build_and_install_loop` *(available since EasyBuild v?)* * `end_hook` *(only called once in an EasyBuild session)* -* `fail_hook` -* `cancel_hook` -* `crash_hook` +* `fail_hook` *(available since EasyBuild v?)* +* `cancel_hook` *(available since EasyBuild v?)* +* `crash_hook` *(available since EasyBuild v?)* * `module_write_hook` *(called multiple times per installation, available since EasyBuild v4.4.1)* All functions implemented in the provided Python module for which the name ends with `_hook` are considered. From 763748364aab536ec0d73da2bf09017a8169ac3f Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Wed, 9 Aug 2023 11:18:13 +0100 Subject: [PATCH 22/41] Remove postiter_hook as it is not callable --- docs/hooks.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index d135435bc..80776deeb 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -75,7 +75,6 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_extensions_hook` * `pre_single_extension_hook`, `post_single_extension_hook` *(available since EasyBuild v4.7.1)* * `post_extensions_hook` -* `pre_postiter_step`, `post_postiter_step` * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` From ad3889ccac53ad163511a04c19773d4eba293049 Mon Sep 17 00:00:00 2001 From: XavierCS-dev Date: Wed, 9 Aug 2023 13:33:28 +0100 Subject: [PATCH 23/41] Add postiter hooks to docs --- docs/hooks.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/hooks.md b/docs/hooks.md index 80776deeb..ae71ad55c 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -75,6 +75,7 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_extensions_hook` * `pre_single_extension_hook`, `post_single_extension_hook` *(available since EasyBuild v4.7.1)* * `post_extensions_hook` +* `pre_postiter_hook`, `post_postiter_hook` *(available since EasyBuild v?)* * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` From c0936bf40c2241b17ae413419ea2a5ef5df0b0ca Mon Sep 17 00:00:00 2001 From: XavierCS-dev <64903011+XavierCS-dev@users.noreply.github.com> Date: Wed, 9 Aug 2023 14:11:43 +0100 Subject: [PATCH 24/41] Update docs/hooks.md Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/hooks.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index ae71ad55c..64a51c596 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -43,7 +43,7 @@ eb ... ## Available hooks -Currently (since EasyBuild v3.7.0), five types of hooks are supported: +Currently, five types of hooks are supported: * `start_hook`, `pre_build_and_install_loop`, `end_hook` and `post_build_and_install_loop` which are triggered *once* before starting software installations, and *once* right after completing all installations, respectively. From 0032ad7a8c383def315516c6a8e2b96db971a8c0 Mon Sep 17 00:00:00 2001 From: XavierCS-dev <64903011+XavierCS-dev@users.noreply.github.com> Date: Wed, 9 Aug 2023 14:12:21 +0100 Subject: [PATCH 25/41] Update docs/hooks.md Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/hooks.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index 64a51c596..bc506168d 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -45,7 +45,8 @@ eb ... Currently, five types of hooks are supported: -* `start_hook`, `pre_build_and_install_loop`, `end_hook` and `post_build_and_install_loop` which are triggered *once* before starting software installations, +* `start_hook`, `pre_build_and_install_loop`, `post_build_and_install_loop` and `end_hook` which are triggered *once* before starting software + installations, *once* before looping over the easyconfigs to be built, *once* after completing the loop over the eayconfigs to be installed, and *once* right after completing all installations, respectively. * `parse_hook`, which is triggered when an easyconfig file is being parsed * `module_write_hook`, which is triggered right before a module file is written. From a1e455bfb46f134fb2b7771ca51a1f799ba1ef88 Mon Sep 17 00:00:00 2001 From: XavierCS-dev <64903011+XavierCS-dev@users.noreply.github.com> Date: Wed, 9 Aug 2023 14:12:44 +0100 Subject: [PATCH 26/41] Update docs/hooks.md Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/hooks.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index bc506168d..4ea2ab7af 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -118,7 +118,7 @@ Do take into account the following: * for `start_hook` and `end_hook`, no arguments are provided * for `fail_hook`, `cancel_hook` and `crash_hook`, the exception which caused the build to stop -is provided + is provided * for `parse_hook`, one argument is provided: the `EasyConfig` instance that corresponds to the easyconfig file being parsed (usually referred to as `ec`) * for `pre_build_and_install_loop`, a list of easyconfigs is provided From 5ea9c035483456561f8f9aaa5b7d6e21e19a31a7 Mon Sep 17 00:00:00 2001 From: XavierCS-dev <64903011+XavierCS-dev@users.noreply.github.com> Date: Wed, 9 Aug 2023 14:13:02 +0100 Subject: [PATCH 27/41] Update docs/hooks.md Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/hooks.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index 4ea2ab7af..1200a696d 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -55,8 +55,8 @@ Currently, five types of hooks are supported: * "*step*" hooks that are triggered before and after every step of each installation procedure that is performed, also aptly named '`pre`'- and '`post`'- hooks. * "*failure*" hooks, `fail_hook`, `cancel_hook`, `crash_hook`, are triggered when an `EasyBuildError`, `KeyboardInterrupt` or `Exception` is -encountered, respectively. `crash_hook` functions as a "catch all" for Python exceptions, and won't be called if either `fail_hook` or `cancel_hook` -is run. + encountered, respectively. `crash_hook` functions as a "catch all" for Python exceptions, and won't be called if either `fail_hook` + or `cancel_hook` is run. The list of currently available hooks in order of execution, which can also be consulted using `eb --avail-hooks`, is: From 0a4ac4e5af6801568050d322d2479bc78bcc607d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 09:54:43 +0200 Subject: [PATCH 28/41] use HPL easyconfig as example for --check-contrib --- docs/code-style.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/code-style.md b/docs/code-style.md index 37987e496..3ccf315c0 100644 --- a/docs/code-style.md +++ b/docs/code-style.md @@ -19,7 +19,7 @@ The only (major) exception to PEP8 is our preference for longer line lengths: li ## Notes Code style in easyconfig files can be **automatically checked** using `--check-contrib`, -for example: `eb --check-contrib DBD-mysql-4.050-GCC-11.3.0.eb` +for example: `eb --check-contrib HPL-2.3-foss-2022b.eb` (see [Code style review][contributing_review_process_code_style] for more details). Style guides that go a step beyond PEP8: From 3356119ad80e81cc6f1d7be8392ee9dfe9ae01f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 10:08:09 +0200 Subject: [PATCH 29/41] link to page with changes for EasyBuild 5.0 --- docs/python-2-3-compatibility.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/python-2-3-compatibility.md b/docs/python-2-3-compatibility.md index 1a0525d8b..234ae01d6 100644 --- a/docs/python-2-3-compatibility.md +++ b/docs/python-2-3-compatibility.md @@ -6,7 +6,8 @@ following Python versions are currently supported: - Python 2.6.x (support was removed in EasyBuild v4.4.0) - Python 2.7.x (support will be removed in EasyBuild v5.0.0) -- Python 3.5.x (support will be removed in EasyBuild v5.0.0) +- Python 2.7.x ([support will be removed in EasyBuild v5.0.0](easybuild-v5/overview-of-changes.md)) +- Python 3.5.x ([support will be removed in EasyBuild v5.0.0](easybuild-v5/overview-of-changes.md)) - Python 3.6.x - Python 3.7.x - Python 3.8.x (requires EasyBuild v4.1.0) From 0008f84e9b4439a70e203baa5439ed08d181f534 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 11:07:37 +0200 Subject: [PATCH 30/41] drop duplicate bullet point in list of supported Python versions --- docs/python-2-3-compatibility.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/python-2-3-compatibility.md b/docs/python-2-3-compatibility.md index 234ae01d6..e630b9812 100644 --- a/docs/python-2-3-compatibility.md +++ b/docs/python-2-3-compatibility.md @@ -5,7 +5,6 @@ compatible with both Python versions 2 and 3. More specifically, the following Python versions are currently supported: - Python 2.6.x (support was removed in EasyBuild v4.4.0) -- Python 2.7.x (support will be removed in EasyBuild v5.0.0) - Python 2.7.x ([support will be removed in EasyBuild v5.0.0](easybuild-v5/overview-of-changes.md)) - Python 3.5.x ([support will be removed in EasyBuild v5.0.0](easybuild-v5/overview-of-changes.md)) - Python 3.6.x From 1000b55f76f2018591d935ab1eb2cb049da60de9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 09:12:43 +0200 Subject: [PATCH 31/41] remove mention of crash_hook, which was removed since it doesn't work as intended + minor cleanup --- docs/hooks.md | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index 1200a696d..2138aad5d 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -43,27 +43,26 @@ eb ... ## Available hooks -Currently, five types of hooks are supported: +Since EasyBuild v4.8.1, five different types of hooks are supported: -* `start_hook`, `pre_build_and_install_loop`, `post_build_and_install_loop` and `end_hook` which are triggered *once* before starting software - installations, *once* before looping over the easyconfigs to be built, *once* after completing the loop over the eayconfigs to be installed, - and *once* right after completing all installations, respectively. +* `start_hook`, `pre_build_and_install_loop_hook`, `post_build_and_install_loop_hook`, and `end_hook` which are triggered *once* right after + EasyBuild starts, *once* before looping over the easyconfigs to be built, *once* after completing the loop over the eayconfigs to be installed, + and *once* shortly before EasyBuild completes, respectively. * `parse_hook`, which is triggered when an easyconfig file is being parsed * `module_write_hook`, which is triggered right before a module file is written. This includes the temporary module file used when installing extensions and during the sanity check, as well as the devel module. * "*step*" hooks that are triggered before and after every step of each installation procedure that is performed, - also aptly named '`pre`'- and '`post`'- hooks. -* "*failure*" hooks, `fail_hook`, `cancel_hook`, `crash_hook`, are triggered when an `EasyBuildError`, `KeyboardInterrupt` or `Exception` is - encountered, respectively. `crash_hook` functions as a "catch all" for Python exceptions, and won't be called if either `fail_hook` - or `cancel_hook` is run. + also aptly named '`pre`'- and '`post`' hooks. +* `cancel_hook` and `fail_hook` which are triggered when a `KeyboardInterrupt` or `EasyBuildError` is raised, + respectively. The list of currently available hooks in order of execution, which can also be consulted using `eb --avail-hooks`, is: * `start_hook` *(only called once in an EasyBuild session)* * `parse_hook` *(available since EasyBuild v3.7.0)* -* `pre_build_and_install_loop` *(available since EasyBuild v?)* +* `pre_build_and_install_loop` *(available since EasyBuild v4.8.1)* * `pre_fetch_hook`, `post_fetch_hook` * `pre_ready_hook`, `post_ready_hook` * `pre_source_hook`, `post_source_hook` @@ -76,7 +75,7 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_extensions_hook` * `pre_single_extension_hook`, `post_single_extension_hook` *(available since EasyBuild v4.7.1)* * `post_extensions_hook` -* `pre_postiter_hook`, `post_postiter_hook` *(available since EasyBuild v?)* +* `pre_postiter_hook`, `post_postiter_hook` *(available since EasyBuild v4.8.1)* * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` @@ -84,11 +83,10 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_permissions_hook`, `post_permissions_hook` * `pre_package_hook`, `post_package_hook` * `pre_testcases_hook`, `post_testcases_hook` -* `post_build_and_install_loop` *(available since EasyBuild v?)* +* `post_build_and_install_loop` *(available since EasyBuild v4.8.1)* * `end_hook` *(only called once in an EasyBuild session)* -* `fail_hook` *(available since EasyBuild v?)* -* `cancel_hook` *(available since EasyBuild v?)* -* `crash_hook` *(available since EasyBuild v?)* +* `cancel_hook` *(available since EasyBuild v4.8.1)* +* `fail_hook` *(available since EasyBuild v4.8.1)* * `module_write_hook` *(called multiple times per installation, available since EasyBuild v4.4.1)* All functions implemented in the provided Python module for which the name ends with `_hook` are considered. @@ -117,8 +115,7 @@ each named after an available hook. Do take into account the following: * for `start_hook` and `end_hook`, no arguments are provided -* for `fail_hook`, `cancel_hook` and `crash_hook`, the exception which caused the build to stop - is provided +* for `cancel_hook` and `fail_hook`, the `KeyboardInterrupt` or `EasyBuildError` exception that was raised is provided * for `parse_hook`, one argument is provided: the `EasyConfig` instance that corresponds to the easyconfig file being parsed (usually referred to as `ec`) * for `pre_build_and_install_loop`, a list of easyconfigs is provided From 291c7dbd55fb5622093afdabcc2c10650a2eb69b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 21:20:52 +0200 Subject: [PATCH 32/41] document pre_run_shell_cmd_hook and post_run_shell_cmd_hook --- docs/hooks.md | 112 ++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 90 insertions(+), 22 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index 2138aad5d..0c0b1168b 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -43,7 +43,7 @@ eb ... ## Available hooks -Since EasyBuild v4.8.1, five different types of hooks are supported: +Since EasyBuild v4.8.1, six different types of hooks are supported: * `start_hook`, `pre_build_and_install_loop_hook`, `post_build_and_install_loop_hook`, and `end_hook` which are triggered *once* right after EasyBuild starts, *once* before looping over the easyconfigs to be built, *once* after completing the loop over the eayconfigs to be installed, @@ -56,6 +56,8 @@ Since EasyBuild v4.8.1, five different types of hooks are supported: also aptly named '`pre`'- and '`post`' hooks. * `cancel_hook` and `fail_hook` which are triggered when a `KeyboardInterrupt` or `EasyBuildError` is raised, respectively. +* `pre_run_shell_cmd_hook` and `post_run_shell_cmd_hook` which are triggered right before and after running + a shell command, respectively. The list of currently available hooks in order of execution, which can also be consulted using `eb --avail-hooks`, is: @@ -79,7 +81,9 @@ which can also be consulted using `eb --avail-hooks`, is: * `pre_postproc_hook`, `post_postproc_hook` * `pre_sanitycheck_hook`, `post_sanitycheck_hook` * `pre_cleanup_hook`, `post_cleanup_hook` -* `pre_module_hook`, `post_module_hook` +* `pre_module_hook` +* `module_write_hook` *(called multiple times per installation, available since EasyBuild v4.4.1)* +* `post_module_hook` * `pre_permissions_hook`, `post_permissions_hook` * `pre_package_hook`, `post_package_hook` * `pre_testcases_hook`, `post_testcases_hook` @@ -87,7 +91,10 @@ which can also be consulted using `eb --avail-hooks`, is: * `end_hook` *(only called once in an EasyBuild session)* * `cancel_hook` *(available since EasyBuild v4.8.1)* * `fail_hook` *(available since EasyBuild v4.8.1)* -* `module_write_hook` *(called multiple times per installation, available since EasyBuild v4.4.1)* + +`pre_run_shell_cmd_hook` and `post_run_shell_cmd_hook` *(available since EasyBuild v4.8.1)* are not included in +the list above because they can not be put in a particular order relative to other hooks, since these hooks +are triggered several times throughout an EasyBuild session. All functions implemented in the provided Python module for which the name ends with `_hook` are considered. @@ -112,23 +119,46 @@ Run 'eb --avail-hooks' to get an overview of known hooks To implement hooks, simply define one or more functions in a Python module (`*.py`), each named after an available hook. +In hooks you have access to the full functionality provided by the EasyBuild framework, +so do `import` from `easybuild.tools.*` (or other `easybuild.*` namespaces) to leverage +those functions. + Do take into account the following: -* for `start_hook` and `end_hook`, no arguments are provided -* for `cancel_hook` and `fail_hook`, the `KeyboardInterrupt` or `EasyBuildError` exception that was raised is provided -* for `parse_hook`, one argument is provided: the `EasyConfig` instance - that corresponds to the easyconfig file being parsed (usually referred to as `ec`) -* for `pre_build_and_install_loop`, a list of easyconfigs is provided -* for `post_build_and_install_loop`, a list of easyconfigs with build results is provided -* for `module_write_hook`, 3 arguments are provided: - * the `EasyBlock` instance used to perform the installation (usually referred to as `self`) - * the filepath of the module that will be written - * the module text as a string - The return value of this hook, when set, will replace the original text that is then written to the module file. -* for the step hooks, one argument is provided: - the `EasyBlock` instance used to perform the installation (usually referred to as `self`) -* the parsed easyconfig file can be accessed in the step hooks via the `EasyBlock` instance, - i.e., via `self.cfg` +* [Hook arguments](#hooks_args) +* [Return value of hooks](#hooks_return_value) +* [Parse hook specifics](#hooks_parse_hook_specifics) + + +### Hook arguments { #hooks_args } + +* For both `start_hook` and `end_hook` no arguments are provided. +* For `cancel_hook` and `fail_hook` the `KeyboardInterrupt` or `EasyBuildError` exception that was raised + is provided as an argument. +* For `parse_hook` the `EasyConfig` instance that corresponds to the easyconfig file being parsed + (usually referred to as `ec`) is passed as an argument. +* For `pre_build_and_install_loop_hook` a list of easyconfigs is provided as an argument. +* For `post_build_and_install_loop_hook` a list of easyconfigs with build results is provided as an argument. +* For `pre_run_shell_cmd_hook`, multiple arguments are passed: + * An unnamed argument (often called `cmd`) that corresponds to the shell command that will be run, + which could be provided either as a string value (like `"echo hello"`) or a list value (like `['echo', 'hello']`). + * A named argument `work_dir` that specifies the path of the working directory in which the command will be run. + * For interactive commands (which are run via the `run_cmd_qa` function), an additional named argument + `interactive` is set to `True`. +* For `post_run_shell_cmd_hook`, multiple arguments are passed: + * An unnamed argument (often called `cmd`) that corresponds to the shell command that was run, + which could be provided either as a string value (like `"echo hello"`) or a list value (like `['echo', 'hello']`). + * A named argument `work_dir` that specifies the working directory in which the shell command was run. + * A named argument `exit_code` that specifies the exit code of the shell command that was run. + * A named argument `output` that specifies the output of the shell command that was run. + * For interactive commands (which are run via the `run_cmd_qa` function), an additional named argument + `interactive` is set to `True`. +* For `module_write_hook`, 3 arguments are provided: + * The `EasyBlock` instance used to perform the installation (usually referred to as `self`). + * The filepath of the module that will be written. + * The module text as a string. +* For the step hooks, the `EasyBlock` instance used to perform the installation (usually referred to as `self`). + The parsed easyconfig file can be accessed in the step hooks via the `EasyBlock` instance, i.e., via `self.cfg`. It is recommended to anticipate possible changes in the provided (named) arguments, using the `*args` and `**kwargs` mechanism commonly used in Python. This @@ -140,11 +170,22 @@ def pre_configure_hook(self, *args, **kwargs): ... ``` -In hooks you have access to the full functionality provided by the EasyBuild framework, -so do `import` from `easybuild.tools.*` (or other `easybuild.*` namespaces) to leverage -those functions. -### Parse hook specifics +### Return value of hooks { #hooks_return_value } + +The return value of a hook is usually ignored by EasyBuild, except in particular cases: + +* If the `module_write_hook` returns a (string) value, it **replaces the original text that was going to be + written to the module file**. This way the `module_write_hook` can extend, change, or entirely replace the + module text that was provided as an argument. + +* If the `pre_run_shell_cmd_hook` returns a value, it **replaces the shell command that was going to be run**. + Hence, this hook can change or entirely replace particular shell commands right before they are executed. + Note that the value type of the return value of `pre_run_shell_cmd_hook` *must* match with the type of the + first (unnamed) argument that provides the shell command that would have been run originally. + + +### Parse hook specifics { #hooks_parse_hook_specifics } `parse_hook` is triggered right *after* reading the easyconfig file, before further parsing of some easyconfig parameters (like `*dependencies`) into @@ -289,3 +330,30 @@ def module_write_hook(self, filepath, module_txt, *args, **kwargs): replace = 'prepend_path("EBPYTHONPREFIXES", root)' return re.sub(search, replace, module_txt) ``` + +### Log running of shell commands + preprend `make install` with `sudo` + +```py +shell_cmds_log = '/tmp/eb_shell_cmds.log' + +def pre_run_shell_cmd_hook(cmd, work_dir=None, interactive=None): + """ + Log shell commands before they are run, + and replace 'make install' with 'sudo make install'. + """ + with open(shell_cmds_log, 'a') as fp: + cmd_type = 'interactive' if interactive else 'non-interactive' + fp.write("%s command '%s' will be run in %s ...\n" % (cmd_type, cmd, work_dir)) + + if cmd == "make install": + return "sudo make install" + + +def post_run_shell_cmd_hook(cmd, work_dir=None, interactive=None, exit_code=None, output=None): + """ + Log shell commands that were run. + """ + with open(shell_cmds_log, 'a') as fp: + cmd_type = 'interactive' if interactive else 'non-interactive' + fp.write("%s command '%s' in %s exited with %s - output: %s\n" % (cmd_type, cmd, work_dir, exit_code, output)) +``` From 396af1eb03799ba9664fa1875cce0bb718cb0e40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 09:33:58 +0200 Subject: [PATCH 33/41] fix typo --- docs/hooks.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index 0c0b1168b..d4c6c9daa 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -331,7 +331,7 @@ def module_write_hook(self, filepath, module_txt, *args, **kwargs): return re.sub(search, replace, module_txt) ``` -### Log running of shell commands + preprend `make install` with `sudo` +### Log running of shell commands + prepend `make install` with `sudo` ```py shell_cmds_log = '/tmp/eb_shell_cmds.log' From 07c44407d54f5f66f995cf8a366721962f979637 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 09:39:17 +0200 Subject: [PATCH 34/41] fix links to subsections of 'Implementing hooks' section --- docs/hooks.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index d4c6c9daa..f049c4f4e 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -125,12 +125,12 @@ those functions. Do take into account the following: -* [Hook arguments](#hooks_args) -* [Return value of hooks](#hooks_return_value) -* [Parse hook specifics](#hooks_parse_hook_specifics) +* [Hook arguments](#hooks-arguments) +* [Return value of hooks](#hooks-return-value) +* [Parse hook specifics](#parse-hook-specifics) -### Hook arguments { #hooks_args } +### Hook arguments { #hooks-arguments } * For both `start_hook` and `end_hook` no arguments are provided. * For `cancel_hook` and `fail_hook` the `KeyboardInterrupt` or `EasyBuildError` exception that was raised @@ -171,7 +171,7 @@ def pre_configure_hook(self, *args, **kwargs): ``` -### Return value of hooks { #hooks_return_value } +### Return value of hooks { #hooks-return-value } The return value of a hook is usually ignored by EasyBuild, except in particular cases: @@ -185,7 +185,7 @@ The return value of a hook is usually ignored by EasyBuild, except in particular first (unnamed) argument that provides the shell command that would have been run originally. -### Parse hook specifics { #hooks_parse_hook_specifics } +### Parse hook specifics { #parse-hook-specifics } `parse_hook` is triggered right *after* reading the easyconfig file, before further parsing of some easyconfig parameters (like `*dependencies`) into From 2d27925ffdd3738932b9a915fc26f80ffcb2a2ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 09:44:59 +0200 Subject: [PATCH 35/41] use '{: #example }' to define custom subsection anchors --- docs/hooks.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/hooks.md b/docs/hooks.md index f049c4f4e..b5091053a 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -130,7 +130,7 @@ Do take into account the following: * [Parse hook specifics](#parse-hook-specifics) -### Hook arguments { #hooks-arguments } +### Hook arguments {: #hooks-arguments } * For both `start_hook` and `end_hook` no arguments are provided. * For `cancel_hook` and `fail_hook` the `KeyboardInterrupt` or `EasyBuildError` exception that was raised @@ -171,7 +171,7 @@ def pre_configure_hook(self, *args, **kwargs): ``` -### Return value of hooks { #hooks-return-value } +### Return value of hooks {: #hooks-return-value } The return value of a hook is usually ignored by EasyBuild, except in particular cases: @@ -185,7 +185,7 @@ The return value of a hook is usually ignored by EasyBuild, except in particular first (unnamed) argument that provides the shell command that would have been run originally. -### Parse hook specifics { #parse-hook-specifics } +### Parse hook specifics {: #parse-hook-specifics } `parse_hook` is triggered right *after* reading the easyconfig file, before further parsing of some easyconfig parameters (like `*dependencies`) into From ce34bff4b792bb401506ef48144785c11e085ee7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:08:41 +0200 Subject: [PATCH 36/41] disable MD051 rule in markdownlint, since it incorrectly complains about links to subsections with a custom anchor --- .markdownlint.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.markdownlint.yml b/.markdownlint.yml index a3524d917..f1022e9b6 100644 --- a/.markdownlint.yml +++ b/.markdownlint.yml @@ -11,6 +11,7 @@ "MD026": false # Trailing punctuation in header "MD036": false # Emphasis instead of header "MD046": false # Code block style. Doesn't like MkDocs admonitions or content tabs +"MD051": false # Link fragments should be valid. Reports false negatives when using custom anchor for subsections. "MD052": false # defined ref links. Doesn't like mkdocs-autorefs "MD024": From d6c6bc46c2d91342034439366b4d0e1e10de0ba5 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 1 Sep 2023 09:42:01 +0100 Subject: [PATCH 37/41] fixing internal links --- .markdownlint.yml | 1 - docs/hooks.md | 6 +++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.markdownlint.yml b/.markdownlint.yml index f1022e9b6..a3524d917 100644 --- a/.markdownlint.yml +++ b/.markdownlint.yml @@ -11,7 +11,6 @@ "MD026": false # Trailing punctuation in header "MD036": false # Emphasis instead of header "MD046": false # Code block style. Doesn't like MkDocs admonitions or content tabs -"MD051": false # Link fragments should be valid. Reports false negatives when using custom anchor for subsections. "MD052": false # defined ref links. Doesn't like mkdocs-autorefs "MD024": diff --git a/docs/hooks.md b/docs/hooks.md index b5091053a..7592503c9 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -125,9 +125,9 @@ those functions. Do take into account the following: -* [Hook arguments](#hooks-arguments) -* [Return value of hooks](#hooks-return-value) -* [Parse hook specifics](#parse-hook-specifics) +* [Hook arguments][hooks-arguments] +* [Return value of hooks][hooks-return-value] +* [Parse hook specifics][parse-hook-specifics] ### Hook arguments {: #hooks-arguments } From 98c01cf0cc28f6953da4d5d290ac39bb592345f9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 1 Sep 2023 09:43:50 +0100 Subject: [PATCH 38/41] fix link --- docs/hooks.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hooks.md b/docs/hooks.md index 7592503c9..1c4977561 100644 --- a/docs/hooks.md +++ b/docs/hooks.md @@ -274,7 +274,7 @@ To achieve the intended effect, you can either: ``` A better approach for manipulating easyconfig parameters is to use the `parse_hook` that -was introduced in EasyBuild v3.7.0 (see [Parse hook specifics](#parse-hook-specifics)), +was introduced in EasyBuild v3.7.0 (see [Parse hook specifics][parse-hook-specifics]), where these kind of surprises will not occur (because templating is automatically disabled before `parse_hook` is called and restored immediately afterwards). See also [Example hook to inject a custom patch file](#inject-a-custom-patch-file). From 37a18ae987db9b2e22760f0ecf9581773c309142 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 13:42:06 +0200 Subject: [PATCH 39/41] auto-update docs for EasyBuild v4.8.1 --- docs/version-specific/easyblocks.md | 4 + .../version-specific/easyconfig-parameters.md | 1 + docs/version-specific/eb-help.md | 5 +- docs/version-specific/generic-easyblocks.md | 20 +- docs/version-specific/supported-software.md | 1885 +++++++++++++---- docs/version-specific/toolchain-opts.md | 91 +- docs/version-specific/toolchains.md | 2 + 7 files changed, 1611 insertions(+), 397 deletions(-) diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index bfa627766..c1d7da071 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -265,7 +265,9 @@ - EB_PyZMQ - EB_scipy - EB_SEPP + - EB_sympy - EB_TensorFlow + - EB_tensorflow_minus_compression - EB_TensorRT - EB_torchvision - EB_VSC_minus_tools @@ -379,7 +381,9 @@ - EB_PyZMQ - EB_scipy - EB_SEPP + - EB_sympy - EB_TensorFlow + - EB_tensorflow_minus_compression - EB_TensorRT - EB_torchvision - EB_VSC_minus_tools diff --git a/docs/version-specific/easyconfig-parameters.md b/docs/version-specific/easyconfig-parameters.md index f9d3bfc9e..5f0f4bbf3 100644 --- a/docs/version-specific/easyconfig-parameters.md +++ b/docs/version-specific/easyconfig-parameters.md @@ -146,6 +146,7 @@ **Parameter name**|**Description** |**Default value** ------------------|---------------------------------------------------------------------------------------------------------------------------|----------------- `block` |List of other 'block' sections on which this block depends (only relevant in easyconfigs with subblocks) |`None` +`build_info_msg` |String with information to be printed to stdout and logged during the building of the easyconfig |`None` `buildstats` |A list of dicts with build statistics |`None` `deprecated` |String specifying reason why this easyconfig file is deprecated and will be archived in the next major release of EasyBuild|`False` diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index b89d065f9..95f4daa4a 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -31,8 +31,8 @@ Option flag |Option description ## Configfile options Option flag |Option description ------------------------------------------|---------------------------------------------------------------------------------------------------------------- -``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list; default: /home/example/.config/easybuild/config.cfg) +-----------------------------------------|---------------------------------------------------------- +``--configfiles=CONFIGFILES`` |Parse (additional) configfiles (type comma-separated list) ``--ignoreconfigfiles=IGNORECONFIGFILES``|Ignore configfiles (type comma-separated list) ## Basic options @@ -298,6 +298,7 @@ Option flag |Option ``--set-gid-bit`` |Set group ID bit on newly created directories (default: False) ``--show-progress-bar`` |Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` |Silence specified deprecation warnings out of (python2, Lmod6, easyconfig, toolchain) (type comma-separated list) +``--silence-hook-trigger`` |Supress printing of debug message every time a hook is triggered (default: False) ``--skip-extensions`` |Skip installation of extensions (default: False) ``-t, --skip-test-cases`` |Skip running test cases (default: False) ``--skip-test-step`` |Skip running the test step (e.g. unit tests) (default: False) diff --git a/docs/version-specific/generic-easyblocks.md b/docs/version-specific/generic-easyblocks.md index ffd79de33..91c8e57c5 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -278,11 +278,12 @@ Support for configuring with CMake, building and installing with MesonNinja. ### Extra easyconfig parameters specific to ``CMakeNinja`` easyblock easyconfig parameter |description |default value ---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------ +--------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------- ``abs_path_compilers`` |Specify compilers via absolute file path (not via command names) |``False`` ``allow_system_boost`` |Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) |``False`` -``build_cmd`` |Build command to use |``"make"`` +``build_cmd`` |Build command to use |``"ninja"`` ``build_cmd_targets`` |Target name (string) or list of target names to build |``""`` +``build_dir`` |build_dir to pass to meson |``None`` ``build_shared_libs`` |Build shared library (instead of static library)None can be used to add no flag (usually results in static library) |``None`` ``build_type`` |Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] |``None`` ``configure_cmd`` |Configure command to use |``"cmake"`` @@ -290,7 +291,7 @@ easyconfig parameter |description ``configure_without_installdir``|Avoid passing an install directory to the configure command (such as via --prefix) |``False`` ``generator`` |Build file generator to use. None to use CMakes default |``"Ninja"`` ``host_type`` |Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script)|``None`` -``install_cmd`` |Install command to use |``"make install"`` +``install_cmd`` |Install command to use |``"ninja"`` ``install_target_subdir`` |Subdirectory to use as installation target |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``separate_build_dir`` |Perform build in a separate directory |``True`` @@ -886,7 +887,10 @@ Support for building and installing software with 'meson' and 'ninja'. easyconfig parameter |description |default value ----------------------|-------------------------------------|------------- +``build_cmd`` |Build command to use |``"ninja"`` +``build_dir`` |build_dir to pass to meson |``None`` ``configure_cmd`` |Configure command to use |``"meson"`` +``install_cmd`` |Install command to use |``"ninja"`` ``separate_build_dir``|Perform build in a separate directory|``True`` ### Customised steps in ``MesonNinja`` easyblock @@ -994,6 +998,7 @@ easyconfig parameter |description ``default_component_specs`` |Default specs to use for every component |``{}`` ``default_easyblock`` |Default easyblock to use for components |``None`` ``options`` |Dictionary with extension options. |``{}`` +``prefix_opt`` |String to use for option to set installation prefix (default is 'PREFIX') |``None`` ``runtest`` |Run unit tests. |``"test"`` ``sanity_check_all_components``|Enable sanity checks for all components |``False`` ``sanity_check_components`` |List of components for which to run sanity checks |``[]`` @@ -1006,10 +1011,11 @@ Builds and installs a Perl module, and can provide a dedicated module file. ### Extra easyconfig parameters specific to ``PerlModule`` easyblock -easyconfig parameter|description |default value ---------------------|----------------------------------|------------- -``options`` |Dictionary with extension options.|``{}`` -``runtest`` |Run unit tests. |``"test"`` +easyconfig parameter|description |default value +--------------------|-------------------------------------------------------------------------|------------- +``options`` |Dictionary with extension options. |``{}`` +``prefix_opt`` |String to use for option to set installation prefix (default is 'PREFIX')|``None`` +``runtest`` |Run unit tests. |``"test"`` ### Customised steps in ``PerlModule`` easyblock diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index 2a08950d1..0da9e33bf 100644 --- a/docs/version-specific/supported-software.md +++ b/docs/version-specific/supported-software.md @@ -5,7 +5,7 @@ This page contains a lot of information, it may take a while to load. -EasyBuild supports 3161 different software packages (incl. toolchains, bundles): +EasyBuild supports 3244 different software packages (incl. toolchains, bundles): [a](#a) - [b](#b) - [c](#c) - [d](#d) - [e](#e) - [f](#f) - [g](#g) - [h](#h) - [i](#i) - [j](#j) - [k](#k) - [l](#l) - [m](#m) - [n](#n) - [o](#o) - [p](#p) - [q](#q) - [r](#r) - [s](#s) - [t](#t) - [u](#u) - [v](#v) - [w](#w) - [x](#x) - [y](#y) - [z](#z) @@ -56,7 +56,7 @@ version |toolchain ## A -[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [axel](#axel) +[ABAQUS](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [ACT](#act) - [ACTC](#actc) - [ada](#ada) - [AdapterRemoval](#adapterremoval) - [ADDA](#adda) - [ADF](#adf) - [ADIOS](#adios) - [adjustText](#adjusttext) - [ADMIXTURE](#admixture) - [ADOL-C](#adol-c) - [Advisor](#advisor) - [affinity](#affinity) - [AFNI](#afni) - [AGAT](#agat) - [AGeNT](#agent) - [AGFusion](#agfusion) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [alleleCount](#allelecount) - [alleleIntegrator](#alleleintegrator) - [Allinea](#allinea) - [ALLPATHS-LG](#allpaths-lg) - [almosthere](#almosthere) - [Alpha](#alpha) - [AlphaFold](#alphafold) - [AlphaPulldown](#alphapulldown) - [ALPS](#alps) - [alsa-lib](#alsa-lib) - [AMAPVox](#amapvox) - [Amara](#amara) - [amask](#amask) - [Amber](#amber) - [AmberMini](#ambermini) - [AmberTools](#ambertools) - [AMD-LibM](#amd-libm) - [AMD-RNG](#amd-rng) - [AMD-SecureRNG](#amd-securerng) - [AMD-uProf](#amd-uprof) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [aNCI](#anci) - [andi](#andi) - [ANGEL](#angel) - [angsd](#angsd) - [ANIcalculator](#anicalculator) - [anndata](#anndata) - [Annif](#annif) - [Annocript](#annocript) - [annovar](#annovar) - [ANSYS](#ansys) - [ANSYS_CFD](#ansys_cfd) - [ant](#ant) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOMP](#aomp) - [APBS](#apbs) - [apex](#apex) - [APR](#apr) - [APR-util](#apr-util) - [AptaSUITE](#aptasuite) - [ARAGORN](#aragorn) - [Arb](#arb) - [Arcade-Learning-Environment](#arcade-learning-environment) - [arcasHLA](#arcashla) - [ARCH](#arch) - [Archive-Zip](#archive-zip) - [ArchR](#archr) - [archspec](#archspec) - [ARGoS](#argos) - [argtable](#argtable) - [aria2](#aria2) - [Arlequin](#arlequin) - [Armadillo](#armadillo) - [arosics](#arosics) - [ARPACK++](#arpack++) - [arpack-ng](#arpack-ng) - [ArrayFire](#arrayfire) - [Arriba](#arriba) - [Arrow](#arrow) - [arrow-R](#arrow-r) - [ART](#art) - [artic-ncov2019](#artic-ncov2019) - [ARTS](#arts) - [ArviZ](#arviz) - [ARWEN](#arwen) - [ASAP](#asap) - [ASAP3](#asap3) - [ASCAT](#ascat) - [ASE](#ase) - [ASF-SearchAPI](#asf-searchapi) - [ASHS](#ashs) - [Aspera-CLI](#aspera-cli) - [Aspera-Connect](#aspera-connect) - [assimp](#assimp) - [Assimulo](#assimulo) - [ASTRID](#astrid) - [astro-tulips](#astro-tulips) - [astropy](#astropy) - [at-spi2-atk](#at-spi2-atk) - [at-spi2-core](#at-spi2-core) - [ATAT](#atat) - [ATK](#atk) - [ATLAS](#atlas) - [atomate](#atomate) - [AtomPAW](#atompaw) - [atools](#atools) - [atropos](#atropos) - [ATSAS](#atsas) - [attr](#attr) - [attrdict](#attrdict) - [attrdict3](#attrdict3) - [augur](#augur) - [AUGUSTUS](#augustus) - [Austin](#austin) - [AUTO-07p](#auto-07p) - [Autoconf](#autoconf) - [Autoconf-archive](#autoconf-archive) - [AutoDock](#autodock) - [AutoDock-GPU](#autodock-gpu) - [AutoDock-Vina](#autodock-vina) - [AutoDockSuite](#autodocksuite) - [AutoGeneS](#autogenes) - [AutoGrid](#autogrid) - [Automake](#automake) - [AutoMap](#automap) - [autopep8](#autopep8) - [Autotools](#autotools) - [Avogadro2](#avogadro2) - [avro-cpp](#avro-cpp) - [awscli](#awscli) - [Ax](#ax) - [axel](#axel) ### ABAQUS @@ -102,6 +102,7 @@ version |versionsuffix |toolchain ``9.4.1`` | |``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``9.4.2`` | |``foss/2021a``, ``intel/2021a`` ``9.6.2`` | |``foss/2022a``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` +``9.10.3``| |``intel/2022a`` ### ABRA2 @@ -307,6 +308,8 @@ version |toolchain ``2021.2.0`` |``system`` ``2021.4.0`` |``system`` ``2022.1.0`` |``system`` +``2023.0.0`` |``system`` +``2023.2.0`` |``system`` ### affinity @@ -383,6 +386,7 @@ version |versionsuffix |toolchain ``3.5.4``|``-Python-3.6.6``|``foss/2018b`` ``3.8.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.8.3``| |``GCCcore/11.3.0`` +``3.8.5``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ALADIN @@ -394,6 +398,16 @@ version |toolchain ---------------|--------------- ``36t1_op2bf1``|``intel/2016a`` +### ALAMODE + +ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. + +*homepage*: + +version |toolchain +---------|-------------- +``1.4.2``|``foss/2022b`` + ### Albacore Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms. @@ -689,6 +703,7 @@ version |toolchain -----------|---------- ``3.4.502``|``system`` ``3.5.671``|``system`` +``4.1.424``|``system`` ### AMOS @@ -740,6 +755,16 @@ version |toolchain ---------|-------------- ``1.5.4``|``foss/2021b`` +### AMRFinderPlus + +This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences. + +*homepage*: + +version |toolchain +-----------|-------------------------------- +``3.11.18``|``gompi/2021b``, ``gompi/2022b`` + ### AmrPlusPlus AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database. @@ -807,6 +832,7 @@ version |toolchain ``2022.05`` |``system`` ``2022.10`` |``system`` ``2023.03-1``|``system`` +``2023.07-2``|``system`` ### aNCI @@ -872,6 +898,7 @@ anndata is a Python package for handling annotated data matrices in memory and o version |toolchain ---------|-------------- ``0.8.0``|``foss/2022a`` +``0.9.2``|``foss/2021a`` ### Annif @@ -1039,7 +1066,7 @@ version |toolchain ``3.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.1.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.2.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### AOMP @@ -1082,16 +1109,18 @@ version |toolchain ---------|-------------------------------------------------------------------------------------------------------------------- ``1.6.3``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` ``1.7.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``1.7.4``|``GCCcore/12.3.0`` ### APR-util Apache Portable Runtime (APR) util libraries. -*homepage*: +*homepage*: version |toolchain ---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.6.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` +``1.6.3``|``GCCcore/12.3.0`` ### AptaSUITE @@ -1137,6 +1166,7 @@ The Arcade Learning Environment (ALE) is a simple framework that allows research version |toolchain ---------|-------------- ``0.7.3``|``foss/2021b`` +``0.8.1``|``foss/2022a`` ### arcasHLA @@ -1192,6 +1222,7 @@ version |versionsuffix |toolchain ``0.1.3``| |``GCCcore/11.2.0`` ``0.1.4``| |``GCCcore/11.3.0`` ``0.2.0``| |``GCCcore/12.2.0`` +``0.2.1``| |``GCCcore/12.3.0`` ### ARGoS @@ -1255,6 +1286,7 @@ version |versionsuffix |toolchain ``10.5.3`` | |``foss/2020b`` ``10.7.5`` | |``foss/2021a`` ``11.4.3`` | |``foss/2022a``, ``foss/2022b`` +``12.6.2`` | |``foss/2023a`` ### arosics @@ -1290,6 +1322,7 @@ version |toolchain ``3.6.2``|``intel/2018a`` ``3.7.0``|``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``3.8.0``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b`` +``3.9.0``|``foss/2023a`` ### ArrayFire @@ -1527,8 +1560,9 @@ Open Asset Import Library (assimp) is a library to import and export various 3d *homepage*: version |toolchain ----------|----------------- +---------|------------------ ``5.0.1``|``GCCcore/8.3.0`` +``5.2.5``|``GCCcore/12.3.0`` ### Assimulo @@ -1585,12 +1619,12 @@ AT-SPI 2 toolkit bridge *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------------------------- +----------|---------------------------------------------------------------------------------------------------------------------- ``2.26.3``|``fosscuda/2018b`` ``2.32.0``|``GCCcore/8.2.0`` ``2.34.1``|``GCCcore/8.3.0`` ``2.34.2``|``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.38.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### at-spi2-core @@ -1598,17 +1632,18 @@ Assistive Technology Service Provider Interface. *homepage*: -version |toolchain -----------|------------------ -``2.26.3``|``fosscuda/2018b`` -``2.32.0``|``GCCcore/8.2.0`` -``2.34.0``|``GCCcore/8.3.0`` -``2.36.0``|``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/10.2.0`` -``2.40.2``|``GCCcore/10.3.0`` -``2.40.3``|``GCCcore/11.2.0`` -``2.44.1``|``GCCcore/11.3.0`` -``2.46.0``|``GCCcore/12.2.0`` +version |toolchain +-----------|------------------ +``2.26.3`` |``fosscuda/2018b`` +``2.32.0`` |``GCCcore/8.2.0`` +``2.34.0`` |``GCCcore/8.3.0`` +``2.36.0`` |``GCCcore/9.3.0`` +``2.38.0`` |``GCCcore/10.2.0`` +``2.40.2`` |``GCCcore/10.3.0`` +``2.40.3`` |``GCCcore/11.2.0`` +``2.44.1`` |``GCCcore/11.3.0`` +``2.46.0`` |``GCCcore/12.2.0`` +``2.49.91``|``GCCcore/12.3.0`` ### ATAT @@ -1638,7 +1673,7 @@ version |toolchain ``2.32.0``|``GCCcore/8.2.0`` ``2.34.1``|``GCCcore/8.3.0`` ``2.36.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.38.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.38.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ATLAS @@ -1735,8 +1770,8 @@ AttrDict is a Python library that provides mapping objects that allow their elem *homepage*: version |toolchain ----------|------------------ -``2.0.2``|``GCCcore/11.2.0`` +---------|-------------------------------------- +``2.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### augur @@ -1796,7 +1831,7 @@ version |toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.68``|``foss/2016b`` ``2.69``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.71``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Autoconf-archive @@ -1889,7 +1924,7 @@ version |toolchain ``1.16.2``|``GCCcore/10.2.0`` ``1.16.3``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``1.16.4``|``GCCcore/11.2.0`` -``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``1.16.5``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### AutoMap @@ -1926,7 +1961,7 @@ version |toolchain ``20200321``|``GCCcore/10.2.0`` ``20210128``|``FCC/4.5.0``, ``GCCcore/10.3.0`` ``20210726``|``GCCcore/11.2.0`` -``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``20220317``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Avogadro2 @@ -1964,6 +1999,16 @@ version |versionsuffix |toolchain ``2.0.55`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``2.11.21`` | |``GCCcore/11.3.0`` +### Ax + +Ax is an accessible, general-purpose platform for understanding, managing, deploying, and automating adaptive experiments. Adaptive experimentation is the machine-learning guided process of iteratively exploring a (possibly infinite) parameter space in order to identify optimal configurations in a resource-efficient manner. Ax currently supports Bayesian optimization and bandit optimization as exploration strategies. Bayesian optimization in Ax is powered by BoTorch, a modern library for Bayesian optimization research built on PyTorch. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2022a`` + ### axel Lightweight CLI download accelerator @@ -1977,7 +2022,7 @@ version |toolchain ## B -[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) +[BA3-SNPS-autotune](#ba3-snps-autotune) - [BabelStream](#babelstream) - [babl](#babl) - [Bader](#bader) - [BAGEL](#bagel) - [BAli-Phy](#bali-phy) - [bam-readcount](#bam-readcount) - [Bambi](#bambi) - [bamFilters](#bamfilters) - [BAMM](#bamm) - [BAMSurgeon](#bamsurgeon) - [bamtofastq](#bamtofastq) - [BamTools](#bamtools) - [BamUtil](#bamutil) - [Bandage](#bandage) - [barrnap](#barrnap) - [basemap](#basemap) - [Bash](#bash) - [bashplotlib](#bashplotlib) - [bat](#bat) - [batchgenerators](#batchgenerators) - [BatMeth2](#batmeth2) - [BayesAss](#bayesass) - [BayesAss3-SNPs](#bayesass3-snps) - [BayeScan](#bayescan) - [BayeScEnv](#bayescenv) - [BayesPrism](#bayesprism) - [BayesTraits](#bayestraits) - [Bazel](#bazel) - [bbcp](#bbcp) - [bbFTP](#bbftp) - [BBMap](#bbmap) - [bc](#bc) - [BCALM](#bcalm) - [bcbio-gff](#bcbio-gff) - [BCEL](#bcel) - [BCFtools](#bcftools) - [bcgTree](#bcgtree) - [bcl-convert](#bcl-convert) - [bcl2fastq2](#bcl2fastq2) - [bcolz](#bcolz) - [bcrypt](#bcrypt) - [BDBag](#bdbag) - [Beagle](#beagle) - [beagle-lib](#beagle-lib) - [Beast](#beast) - [BeautifulSoup](#beautifulsoup) - [BEDOPS](#bedops) - [BEDTools](#bedtools) - [BEEF](#beef) - [behave](#behave) - [bench](#bench) - [BerkeleyGW](#berkeleygw) - [BFAST](#bfast) - [BFC](#bfc) - [BGC-Bayesian-genomic-clines](#bgc-bayesian-genomic-clines) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [bibtexparser](#bibtexparser) - [BiG-SCAPE](#big-scape) - [BigDFT](#bigdft) - [BinSanity](#binsanity) - [binutils](#binutils) - [Bio-DB-HTS](#bio-db-hts) - [Bio-EUtilities](#bio-eutilities) - [Bio-SamTools](#bio-samtools) - [Bio-SearchIO-hmmer](#bio-searchio-hmmer) - [bioawk](#bioawk) - [biobambam2](#biobambam2) - [biogeme](#biogeme) - [biom-format](#biom-format) - [biomart-perl](#biomart-perl) - [BioPerl](#bioperl) - [BioPP](#biopp) - [Biopython](#biopython) - [BioServices](#bioservices) - [BirdNET](#birdnet) - [biscuit](#biscuit) - [Bismark](#bismark) - [Bison](#bison) - [bitarray](#bitarray) - [BLACS](#blacs) - [BLASR](#blasr) - [blasr_libcpp](#blasr_libcpp) - [BLAST](#blast) - [BLAST+](#blast+) - [BLAT](#blat) - [Blender](#blender) - [BLIS](#blis) - [Blitz++](#blitz++) - [BlobTools](#blobtools) - [Block](#block) - [Blosc](#blosc) - [Blosc2](#blosc2) - [BLT](#blt) - [bmtagger](#bmtagger) - [bnpy](#bnpy) - [BOINC](#boinc) - [bokeh](#bokeh) - [BoltzTraP](#boltztrap) - [BoltzTraP2](#boltztrap2) - [Bonito](#bonito) - [Bonmin](#bonmin) - [Bonnie++](#bonnie++) - [Boost](#boost) - [Boost.MPI](#boost.mpi) - [Boost.Python](#boost.python) - [Boost.Python-NumPy](#boost.python-numpy) - [boost_histogram](#boost_histogram) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-meth](#bwa-meth) - [bwakit](#bwakit) - [bwidget](#bwidget) - [BWISE](#bwise) - [bx-python](#bx-python) - [BXH_XCEDE_TOOLS](#bxh_xcede_tools) - [byacc](#byacc) - [byobu](#byobu) - [bzip2](#bzip2) ### BA3-SNPS-autotune @@ -2024,13 +2069,14 @@ version |toolchain ### BAGEL -BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program. +BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program. *homepage*: version |toolchain ---------|--------------- ``1.1.1``|``intel/2016b`` +``1.2.2``|``foss/2021a`` ### BAli-Phy @@ -2051,6 +2097,7 @@ Count DNA sequence reads in BAM files version |toolchain ---------|--------------------------------------------- ``0.8.0``|``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +``1.0.1``|``GCC/12.2.0`` ### Bambi @@ -2114,7 +2161,7 @@ version |toolchain ``2.4.1``|``intel/2017a`` ``2.5.0``|``foss/2016b``, ``intel/2017b`` ``2.5.1``|``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` -``2.5.2``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` +``2.5.2``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` ### BamUtil @@ -2305,6 +2352,7 @@ version |versionsuffix|toolchain ``3.7.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` ``4.2.2`` | |``GCCcore/11.2.0`` ``5.1.1`` | |``GCCcore/11.3.0`` +``6.3.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### bbcp @@ -2333,14 +2381,14 @@ BBMap short read aligner, and other bioinformatic tools. *homepage*: version |versionsuffix |toolchain -----------|-------------------|------------------------------- +----------|-------------------|--------------------------------------------- ``36.62`` |``-Java-1.8.0_112``|``intel/2016b`` ``37.93`` | |``foss/2018a``, ``intel/2018a`` ``38.26`` | |``foss/2018b`` ``38.50b``| |``GCC/8.2.0-2.31.1`` ``38.76`` | |``GCC/8.2.0-2.31.1`` ``38.79`` | |``GCC/8.3.0`` -``38.87`` | |``iccifort/2020.1.217`` +``38.87`` | |``GCC/8.2.0-2.31.1``, ``iccifort/2020.1.217`` ``38.90`` | |``GCC/10.2.0``, ``GCC/9.3.0`` ``38.96`` | |``GCC/10.3.0`` ``38.98`` | |``GCC/11.2.0`` @@ -2408,6 +2456,7 @@ version |toolchain ``1.14`` |``GCC/11.2.0`` ``1.15.1``|``GCC/11.3.0`` ``1.17`` |``GCC/12.2.0`` +``1.18`` |``GCC/12.3.0`` ### bcgTree @@ -2437,9 +2486,9 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: version |versionsuffix |toolchain -----------|------------------|----------------------------------------------------------------------------------------------------------------------------- +----------|------------------|--------------------------------------------------------------------------------------------------------------------------------------------- ``2.19.1``|``-Python-2.7.12``|``foss/2016b`` -``2.20.0``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` ``2.20.0``|``-Python-2.7.12``|``foss/2016b`` ``2.20.0``|``-Python-2.7.14``|``intel/2017b`` @@ -2455,6 +2504,16 @@ version |versionsuffix |toolchain ``1.2.1``| |``foss/2020b`` ``1.2.1``|``-Python-3.8.2`` |``foss/2020a`` +### bcrypt + +Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt) + +*homepage*: + +version |toolchain +---------|------------------ +``4.0.1``|``GCCcore/12.3.0`` + ### BDBag The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles. @@ -2530,6 +2589,7 @@ version |versionsuffix |toolchain ``4.9.3`` | |``GCCcore/10.2.0`` ``4.10.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``4.11.1``| |``GCCcore/12.2.0`` +``4.12.2``| |``GCCcore/12.3.0`` ### BEDOPS @@ -2562,6 +2622,7 @@ version |toolchain ``2.28.0``|``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.29.2``|``GCC/8.3.0``, ``GCC/9.3.0`` ``2.30.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``iccifort/2020.4.304`` +``2.31.0``|``GCC/12.3.0`` ### BEEF @@ -2584,6 +2645,16 @@ version |versionsuffix |toolchain ``1.2.5``|``-Python-2.7.12``|``foss/2016b`` ``1.2.6``|``-Python-3.6.4`` |``intel/2018a`` +### bench + +Tools to accurately benchmark and analyze execution times for R expressions. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``1.1.2``|``-R-4.2.1`` |``foss/2022a`` + ### BerkeleyGW The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. @@ -2629,6 +2700,16 @@ version |toolchain --------|--------------- ``1.03``|``gompi/2021a`` +### BgeeDB + +Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology. + +*homepage*: + +version |versionsuffix |toolchain +----------|---------------|-------------- +``2.26.0``|``-R-%(rver)s``|``foss/2021a`` + ### bgen A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. @@ -2714,7 +2795,7 @@ version |toolchain ``2.37`` |``GCCcore/11.2.0``, ``system`` ``2.38`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ``2.39`` |``GCCcore/12.2.0``, ``system`` -``2.40`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.40`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### Bio-DB-HTS @@ -2757,8 +2838,8 @@ Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with *homepage*: version |toolchain ----------|-------------------------------------------------------------- -``1.7.3``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +---------|------------------------------------------------------------------------------ +``1.7.3``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### bioawk @@ -2804,6 +2885,7 @@ version |versionsuffix |toolchain ``2.1.10``|``-Python-3.8.2``|``foss/2020a`` ``2.1.12``| |``foss/2021b`` ``2.1.14``| |``foss/2022a`` +``2.1.15``| |``foss/2022b`` ### biomart-perl @@ -2870,7 +2952,7 @@ version |versionsuffix |toolchain ``1.74``| |``foss/2019a`` ``1.75``|``-Python-2.7.16``|``foss/2019b`` ``1.75``|``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.76``|``-Python-2.7.18``|``foss/2020b`` +``1.76``|``-Python-2.7.18``|``foss/2020b``, ``foss/2021b`` ``1.78``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``1.79``| |``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` @@ -2940,7 +3022,7 @@ version |toolchain ``3.6.1``|``GCCcore/10.1.0`` ``3.7.1``|``GCCcore/10.2.0``, ``system`` ``3.7.6``|``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.5.0``, ``system`` +``3.8.2``|``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/9.5.0``, ``system`` ### bitarray @@ -3196,6 +3278,7 @@ version |versionsuffix |toolchain ``2.4.1`` | |``foss/2021a`` ``2.4.2`` | |``foss/2021b`` ``2.4.3`` | |``foss/2022a`` +``3.2.1`` | |``foss/2022b`` ### BoltzTraP @@ -3311,6 +3394,7 @@ version |versionsuffix |toolchain ``1.77.0``| |``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ``1.79.0``| |``GCC/11.2.0``, ``GCC/11.3.0`` ``1.81.0``| |``GCC/12.2.0`` +``1.82.0``| |``GCC/12.3.0`` ### Boost.MPI @@ -3346,6 +3430,16 @@ version |versionsuffix |toolchain ``1.77.0``| |``GCC/11.2.0`` ``1.79.0``| |``GCC/11.3.0`` +### Boost.Python-NumPy + +Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. + +*homepage*: + +version |toolchain +----------|-------------- +``1.79.0``|``foss/2022a`` + ### boost_histogram Boost-histogram is a Python package providing Python bindings for Boost.Histogram. @@ -3798,7 +3892,7 @@ version |toolchain ## C -[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) +[c-ares](#c-ares) - [C3D](#c3d) - [cadaver](#cadaver) - [CaDiCaL](#cadical) - [CAFE5](#cafe5) - [Caffe](#caffe) - [cairo](#cairo) - [cairomm](#cairomm) - [Calcam](#calcam) - [CalculiX-CrunchiX](#calculix-crunchix) - [Calendrical](#calendrical) - [Calib](#calib) - [CAMPARI](#campari) - [Cantera](#cantera) - [canu](#canu) - [Canvas](#canvas) - [CAP3](#cap3) - [CapnProto](#capnproto) - [captum](#captum) - [Cargo](#cargo) - [Carma](#carma) - [carputils](#carputils) - [Cartopy](#cartopy) - [CASA](#casa) - [casacore](#casacore) - [Casanovo](#casanovo) - [CaSpER](#casper) - [CASPR](#caspr) - [CASTEP](#castep) - [CastXML](#castxml) - [CAT-BAT](#cat-bat) - [CatBoost](#catboost) - [Catch2](#catch2) - [category_encoders](#category_encoders) - [CatLearn](#catlearn) - [CatMAP](#catmap) - [causallift](#causallift) - [causalml](#causalml) - [CaVEMan](#caveman) - [CAVIAR](#caviar) - [Cbc](#cbc) - [CBLAS](#cblas) - [ccache](#ccache) - [CCfits](#ccfits) - [CCL](#ccl) - [cclib](#cclib) - [cctbx-base](#cctbx-base) - [cctools](#cctools) - [CD-HIT](#cd-hit) - [CDAT](#cdat) - [cdbfasta](#cdbfasta) - [CDBtools](#cdbtools) - [cddlib](#cddlib) - [CDFlib](#cdflib) - [cDNA_Cupcake](#cdna_cupcake) - [CDO](#cdo) - [cdo-bindings](#cdo-bindings) - [cdsapi](#cdsapi) - [cell2location](#cell2location) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [centerline](#centerline) - [Centrifuge](#centrifuge) - [Cereal](#cereal) - [CESM-deps](#cesm-deps) - [CFDEMcoupling](#cfdemcoupling) - [cffi](#cffi) - [CFITSIO](#cfitsio) - [cftime](#cftime) - [CGAL](#cgal) - [cget](#cget) - [Cgl](#cgl) - [CGmapTools](#cgmaptools) - [CGNS](#cgns) - [CharLS](#charls) - [CHASE](#chase) - [Check](#check) - [CheckM](#checkm) - [CheckM-Database](#checkm-database) - [Cheetah](#cheetah) - [Chemaxon-Marvin](#chemaxon-marvin) - [chemprop](#chemprop) - [CheMPS2](#chemps2) - [CHERAB](#cherab) - [chewBBACA](#chewbbaca) - [chi2comb](#chi2comb) - [Chimera](#chimera) - [ChimPipe](#chimpipe) - [ChIPseeker](#chipseeker) - [Chromaprint](#chromaprint) - [cicero](#cicero) - [CIF2Cell](#cif2cell) - [cimfomfa](#cimfomfa) - [CIRCexplorer](#circexplorer) - [CIRCexplorer2](#circexplorer2) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [CLISP](#clisp) - [ClonalFrameML](#clonalframeml) - [CLooG](#cloog) - [CloudCompare](#cloudcompare) - [Clp](#clp) - [Clustal-Omega](#clustal-omega) - [ClustalW2](#clustalw2) - [Cluster-Buster](#cluster-buster) - [ClusterShell](#clustershell) - [CMake](#cmake) - [CMAverse](#cmaverse) - [CmdStanR](#cmdstanr) - [cmocean](#cmocean) - [CMSeq](#cmseq) - [CNT-ILP](#cnt-ilp) - [CNVkit](#cnvkit) - [CNVnator](#cnvnator) - [Co-phylog](#co-phylog) - [COBRApy](#cobrapy) - [CoCoALib](#cocoalib) - [CodAn](#codan) - [code-server](#code-server) - [CODEX2](#codex2) - [CodingQuarry](#codingquarry) - [Cogent](#cogent) - [Coin](#coin) - [CoinUtils](#coinutils) - [ColabFold](#colabfold) - [colossalai](#colossalai) - [Commet](#commet) - [CompareM](#comparem) - [Compress-Raw-Zlib](#compress-raw-zlib) - [COMSOL](#comsol) - [Con3F](#con3f) - [conan](#conan) - [CONCOCT](#concoct) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [Control-FREEC](#control-freec) - [cooler](#cooler) - [CoordgenLibs](#coordgenlibs) - [Coot](#coot) - [CopyKAT](#copykat) - [core-counter](#core-counter) - [Coreutils](#coreutils) - [corner](#corner) - [CoSymLib](#cosymlib) - [coverage](#coverage) - [cowsay](#cowsay) - [CP2K](#cp2k) - [CPB](#cpb) - [CPC2](#cpc2) - [CPLEX](#cplex) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppzmq](#cppzmq) - [cpu_features](#cpu_features) - [cram](#cram) - [cramtools](#cramtools) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [crb-blast](#crb-blast) - [CREST](#crest) - [CRF++](#crf++) - [CRISPR-DAV](#crispr-dav) - [CRISPResso2](#crispresso2) - [cromwell](#cromwell) - [crossguid](#crossguid) - [CrossMap](#crossmap) - [CrossTalkZ](#crosstalkz) - [CRPropa](#crpropa) - [Crumble](#crumble) - [cryoCARE](#cryocare) - [cryoDRGN](#cryodrgn) - [cryptography](#cryptography) - [CryptoMiniSat](#cryptominisat) - [CrystFEL](#crystfel) - [CSB](#csb) - [CSBDeep](#csbdeep) - [CSBLAST](#csblast) - [cscope](#cscope) - [csvkit](#csvkit) - [ctags](#ctags) - [ctffind](#ctffind) - [CTPL](#ctpl) - [Cube](#cube) - [CubeGUI](#cubegui) - [CubeLib](#cubelib) - [CubeWriter](#cubewriter) - [CuCLARK](#cuclark) - [CUDA](#cuda) - [CUDA-Samples](#cuda-samples) - [CUDAcompat](#cudacompat) - [CUDAcore](#cudacore) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVglasso](#cvglasso) - [CVS](#cvs) - [CVXOPT](#cvxopt) - [CVXPY](#cvxpy) - [CWIPI](#cwipi) - [cwltool](#cwltool) - [cxxopts](#cxxopts) - [cysignals](#cysignals) - [Cython](#cython) - [cython-blis](#cython-blis) - [cytoolz](#cytoolz) - [Cytoscape](#cytoscape) - [cytosim](#cytosim) - [cyvcf2](#cyvcf2) ### c-ares @@ -3811,6 +3905,7 @@ version |toolchain ----------|-------------------------------------- ``1.17.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.18.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.19.1``|``GCCcore/12.3.0`` ### C3D @@ -3880,6 +3975,7 @@ version |versionsuffix |toolchain ``1.14.12``| |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16.0`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.17.4`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.17.8`` | |``GCCcore/12.3.0`` ### cairomm @@ -3909,8 +4005,8 @@ A Free Software Three-Dimensional Structural Finite Element Program *homepage*: version |toolchain ---------|-------------- -``2.20``|``foss/2021a`` +--------|------------------------------ +``2.20``|``foss/2021a``, ``foss/2022b`` ### Calendrical @@ -3966,7 +4062,7 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: version |versionsuffix |toolchain ----------|----------------|------------------------------------------------------------------------------ +---------|----------------|-------------------------------------------------------------------------- ``1.4`` | |``foss/2016b`` ``1.7`` | |``intel/2018a`` ``1.8`` |``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` @@ -3975,7 +4071,7 @@ version |versionsuffix |toolchain ``1.9`` |``-Java-11`` |``GCCcore/8.3.0`` ``2.1.1``| |``GCCcore/10.2.0`` ``2.1.1``|``-Java-11`` |``GCCcore/9.3.0`` -``2.2`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.2`` | |``GCC/12.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``2.2`` |``-Java-11`` |``GCCcore/10.3.0`` ### Canvas @@ -4155,6 +4251,16 @@ version |toolchain ---------|-------------- ``5.2.3``|``GCC/10.3.0`` +### CatBoost + +CatBoost is a high-performance open source library for gradient boosting on decision trees + +*homepage*: + +version|toolchain +-------|-------------- +``1.2``|``gfbf/2023a`` + ### Catch2 A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) @@ -4246,9 +4352,9 @@ Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``2.10.3``|``foss/2018b`` -``2.10.5``|``foss/2020b``, ``foss/2021a`` +``2.10.5``|``foss/2020b``, ``foss/2021a``, ``foss/2022b`` ### CBLAS @@ -4276,6 +4382,8 @@ version |versionsuffix|toolchain ``4.2.1`` | |``system`` ``4.6.1`` | |``GCCcore/11.2.0`` ``4.6.3`` | |``GCCcore/11.3.0``, ``system`` +``4.7.5`` | |``system`` +``4.8.3`` | |``system`` ### CCfits @@ -4425,6 +4533,7 @@ version |toolchain ``2.0.5`` |``gompi/2021b`` ``2.0.6`` |``gompi/2022a`` ``2.1.1`` |``gompi/2021a`` +``2.2.2`` |``gompi/2023a`` ### cdo-bindings @@ -4566,6 +4675,16 @@ version |toolchain ---------|-------------- ``1.0.0``|``foss/2021b`` +### centerline + +Roads, rivers and similar linear structures are often represented by long and complex polygons. Since one of the most important attributes of a linear structure is its length, extracting that attribute from a polygon can prove to be more or less difficult. This library tries to solve this problem by creating the the polygon's centerline using the Voronoi diagram. For more info on how to use this package, see the official documentation. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.1``|``foss/2022a`` + ### Centrifuge Classifier for metagenomic sequences @@ -4606,14 +4725,24 @@ CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to c *homepage*: version |toolchain ----------|-------------- -``3.8.0``|``foss/2018a`` +---------|------------------------------ +``3.8.0``|``foss/2018a``, ``foss/2019b`` + +### cffi + +C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation. + +*homepage*: + +version |toolchain +----------|------------------ +``1.15.1``|``GCCcore/12.3.0`` ### CFITSIO -CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. +CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. -*homepage*: +*homepage*: version |toolchain ---------|---------------------------------------------------------- @@ -4625,6 +4754,7 @@ version |toolchain ``3.48`` |``GCCcore/9.3.0`` ``3.49`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.2.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.3.0``|``GCCcore/12.3.0`` ### cftime @@ -4660,10 +4790,12 @@ version |versionsuffix |toolchain ``4.11.1``|``-Python-3.6.4`` |``foss/2018a`` ``4.11.1``|``-Python-3.6.6`` |``foss/2018b`` ``4.14`` |``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` +``4.14.1``|``-Python-2.7.16``|``foss/2019b`` ``4.14.1``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` ``4.14.3``| |``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2021a`` ``4.14.3``|``-Python-3.8.2`` |``gompi/2020a``, ``iimpi/2020a`` ``5.2`` | |``gompi/2020b`` +``5.5.2`` | |``GCCcore/12.2.0`` ### cget @@ -4685,6 +4817,7 @@ version |toolchain ----------|------------------------------ ``0.60.2``|``foss/2018b`` ``0.60.3``|``foss/2020b``, ``foss/2021a`` +``0.60.7``|``foss/2022b`` ### CGmapTools @@ -4720,6 +4853,7 @@ version |toolchain ``2.2.0``|``GCCcore/10.2.0`` ``2.3.4``|``GCCcore/10.3.0`` ``2.4.1``|``GCCcore/11.3.0`` +``2.4.2``|``GCCcore/12.2.0`` ### CHASE @@ -4873,6 +5007,16 @@ version |versionsuffix |toolchain ``0.9.5``| |``foss/2018b`` ``0.9.5``|``-Python-2.7.12``|``foss/2016b`` +### ChIPseeker + +This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.32.1``|``-R-4.2.1`` |``foss/2022a`` + ### Chromaprint Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source. @@ -4892,6 +5036,7 @@ Cicero is an R package that provides tools for analyzing single-cell chromatin a version |versionsuffix |toolchain ------------|---------------------|-------------- ``1.3.4.11``|``-R-4.0.3-Monocle3``|``foss/2020b`` +``1.3.8`` |``-R-4.2.1-Monocle3``|``foss/2022a`` ### CIF2Cell @@ -5037,6 +5182,8 @@ version |versionsuffix |toolchain ``13.0.1``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``13.0.1``|``-CUDA-11.4.1`` |``GCCcore/11.2.0`` ``15.0.5``| |``GCCcore/11.3.0`` +``16.0.4``| |``GCCcore/12.2.0`` +``16.0.6``| |``GCCcore/12.3.0`` ### Clang-AOMP @@ -5173,6 +5320,7 @@ version |toolchain ``1.17.3``|``foss/2018b`` ``1.17.6``|``foss/2020b``, ``foss/2021a`` ``1.17.7``|``foss/2021b`` +``1.17.8``|``foss/2022b`` ### Clustal-Omega @@ -5197,13 +5345,14 @@ version|toolchain ### Cluster-Buster -Cluster-Buster: Finding dense clusters of motifs in DNA sequences +Cluster-Buster is a program for finding interesting functional regions, such as transcriptional enhancers, in DNA sequences. -*homepage*: +*homepage*: version |toolchain ------------|--------------- ``20160106``|``intel/2016a`` +``20200507``|``GCC/12.2.0`` ### ClusterShell @@ -5251,7 +5400,7 @@ version |toolchain ``3.10.2``|``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.10.3``|``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.11.1``|``GCCcore/6.4.0`` -``3.11.4``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``3.11.4``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``3.12.1``|``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` ``3.13.3``|``GCCcore/8.2.0`` ``3.15.1``|``system`` @@ -5444,6 +5593,7 @@ version |toolchain ``2.11.3``|``GCCcore/7.3.0``, ``foss/2018b`` ``2.11.4``|``GCC/10.3.0``, ``GCCcore/10.2.0`` ``2.11.6``|``GCC/11.2.0`` +``2.11.9``|``GCC/12.2.0`` ### ColabFold @@ -5526,6 +5676,7 @@ Decentralized, open-source (MIT), C/C++ package manager. version |toolchain ----------|------------------ ``1.58.0``|``GCCcore/11.3.0`` +``1.60.2``|``GCCcore/12.3.0`` ### CONCOCT @@ -5567,6 +5718,8 @@ version |versionsuffix |toolchain ``4.2.1``| |``GCCcore/10.2.0`` ``4.4.0``| |``GCCcore/10.3.0`` ``4.5.3``| |``GCCcore/11.3.0`` +``4.5.5``| |``GCCcore/12.2.0`` +``4.5.6``| |``GCCcore/12.3.0`` ### CONN @@ -5578,6 +5731,16 @@ version|versionsuffix |toolchain -------|-----------------|---------- ``21a``|``-MATLAB-2021a``|``system`` +### connected-components-3d + +cc3d is an implementation of connected components in three dimensions using a 26, 18, or 6-connected neighborhood in 3D or 4 and 8-connected in 2D. + +*homepage*: + +version |toolchain +----------|-------------- +``3.12.1``|``foss/2022b`` + ### ConnectomeWorkbench Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. @@ -5700,6 +5863,7 @@ version |versionsuffix |toolchain ``4.5.1``|``-Python-2.7.14``|``intel/2017b`` ``5.5`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``7.2.3``| |``GCCcore/12.2.0`` +``7.2.7``| |``GCCcore/11.3.0`` ### cowsay @@ -5731,6 +5895,7 @@ version |versionsuffix|toolchain ``8.2`` | |``foss/2021a``, ``intel/2021a`` ``9.1`` | |``foss/2022a`` ``2022.1``| |``foss/2022a`` +``2023.1``| |``foss/2022b`` ### CPB @@ -5802,9 +5967,9 @@ A small C++ header library which makes it easier to write Python extension modul *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.1.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### cppzmq @@ -6024,6 +6189,16 @@ version |versionsuffix |toolchain ``0.3.5`` |``-CUDA-11.3.1``|``foss/2021a`` ``1.0.0-beta``|``-CUDA-11.3.1``|``foss/2021a`` +### cryptography + +cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. + +*homepage*: + +version |toolchain +----------|------------------ +``41.0.1``|``GCCcore/12.3.0`` + ### CryptoMiniSat CryptoMiniSat is an advanced SAT solver @@ -6161,6 +6336,7 @@ version |toolchain ``4.4.4``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``4.8`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.8.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### CubeWriter @@ -6173,6 +6349,7 @@ version |toolchain ``4.4.3``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``4.8`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.8.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### CuCLARK @@ -6224,6 +6401,7 @@ version |toolchain ``12.1.0`` |``system`` ``12.1.1`` |``system`` ``12.2.0`` |``system`` +``12.2.2`` |``system`` ### CUDA-Samples @@ -6451,6 +6629,16 @@ version |toolchain ---------|-------------- ``2.0.3``|``foss/2022a`` +### CVglasso + +CVglasso is an R package that estimates a lasso-penalized precision matrix via block-wise coordinate descent – also known as the graphical lasso (glasso) algorithm. + +*homepage*: + +version|versionsuffix|toolchain +-------|-------------|-------------- +``1.0``|``-R-4.2.1`` |``foss/2022a`` + ### CVS CVS is a version control system, an important component of Source Configuration Management (SCM). @@ -6604,7 +6792,7 @@ version |versionsuffix |toolchain ## D -[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) +[dadi](#dadi) - [dagitty](#dagitty) - [Dakota](#dakota) - [DALI](#dali) - [DaliLite](#dalilite) - [Dalton](#dalton) - [damageproto](#damageproto) - [dammit](#dammit) - [DANPOS2](#danpos2) - [DAS_Tool](#das_tool) - [dask](#dask) - [dask-labextension](#dask-labextension) - [datamash](#datamash) - [davix](#davix) - [DB](#db) - [DB_File](#db_file) - [DBCSR](#dbcsr) - [DBD-mysql](#dbd-mysql) - [DBG2OLC](#dbg2olc) - [DBus](#dbus) - [dbus-glib](#dbus-glib) - [dclone](#dclone) - [dcm2niix](#dcm2niix) - [DCMTK](#dcmtk) - [dd](#dd) - [deal.II](#deal.ii) - [deap](#deap) - [decona](#decona) - [deconf](#deconf) - [DeconICA](#deconica) - [deepdiff](#deepdiff) - [DeepLabCut](#deeplabcut) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delly](#delly) - [DeMixT](#demixt) - [DendroPy](#dendropy) - [DensPart](#denspart) - [Deprecated](#deprecated) - [destiny](#destiny) - [Detectron2](#detectron2) - [detonate](#detonate) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [DGL](#dgl) - [DIAL](#dial) - [DIALOGUE](#dialogue) - [DIAMOND](#diamond) - [Dice](#dice) - [DiCE-ML](#dice-ml) - [dicom2nifti](#dicom2nifti) - [DicomBrowser](#dicombrowser) - [DiffBind](#diffbind) - [Diffutils](#diffutils) - [dijitso](#dijitso) - [dill](#dill) - [DIRAC](#dirac) - [distributed](#distributed) - [DistributedStream](#distributedstream) - [DL_POLY_4](#dl_poly_4) - [DL_POLY_Classic](#dl_poly_classic) - [dlb](#dlb) - [dlib](#dlib) - [DLPack](#dlpack) - [dm-haiku](#dm-haiku) - [dm-reverb](#dm-reverb) - [dm-tree](#dm-tree) - [DMCfun](#dmcfun) - [DMLC-Core](#dmlc-core) - [DMTCP](#dmtcp) - [DOLFIN](#dolfin) - [dominate](#dominate) - [dorado](#dorado) - [Doris](#doris) - [DosageConvertor](#dosageconvertor) - [dotNET-Core-Runtime](#dotnet-core-runtime) - [dotNET-SDK](#dotnet-sdk) - [double-conversion](#double-conversion) - [DoubletFinder](#doubletfinder) - [Doxygen](#doxygen) - [DRAGMAP](#dragmap) - [Drake](#drake) - [dRep](#drep) - [drmaa-python](#drmaa-python) - [DROP](#drop) - [dropEst](#dropest) - [DSA](#dsa) - [dSFMT](#dsfmt) - [DSRC](#dsrc) - [Dsuite](#dsuite) - [dtcmp](#dtcmp) - [dtcwt](#dtcwt) - [DualSPHysics](#dualsphysics) - [DUBStepR](#dubstepr) - [dune-core](#dune-core) - [dune-fem](#dune-fem) - [duplex-tools](#duplex-tools) - [dx-toolkit](#dx-toolkit) - [dxpy](#dxpy) - [DyMat](#dymat) ### dadi @@ -6741,6 +6929,7 @@ version |versionsuffix |toolchain ``2021.9.1`` | |``foss/2021a`` ``2022.1.0`` | |``foss/2021b`` ``2022.10.0``| |``foss/2022a`` +``2023.7.1`` | |``foss/2022b`` ### dask-labextension @@ -6903,6 +7092,7 @@ version |toolchain ``1.0.20201102``|``GCCcore/8.3.0`` ``1.0.20211006``|``GCCcore/10.3.0`` ``1.0.20220720``|``GCCcore/11.3.0`` +``1.0.20230411``|``GCCcore/12.2.0`` ### DCMTK @@ -7071,6 +7261,7 @@ version |versionsuffix |toolchain ``0.7.8``|``-linux_x86_64``|``system`` ``0.8.7``| |``gompi/2020b`` ``1.1.5``| |``GCC/11.3.0`` +``1.1.6``| |``GCC/12.2.0`` ### DeMixT @@ -7260,7 +7451,7 @@ version |toolchain ``2.0.11``|``GCC/10.3.0`` ``2.0.13``|``GCC/10.3.0``, ``GCC/11.2.0`` ``2.1.0`` |``GCC/11.3.0`` -``2.1.8`` |``GCC/10.3.0`` +``2.1.8`` |``GCC/10.3.0``, ``GCC/12.2.0`` ### Dice @@ -7303,6 +7494,16 @@ version |versionsuffix |toolchain -----------|------------------|---------- ``1.7.0b5``|``-Java-1.7.0_80``|``system`` +### DiffBind + +Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``3.6.5``|``-R-4.2.1`` |``foss/2022a`` + ### Diffutils Diffutils: GNU diff utilities - find the differences between files @@ -7335,6 +7536,7 @@ version |toolchain ``0.3.3``|``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ``0.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``0.3.6``|``GCCcore/11.3.0`` +``0.3.7``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### DIRAC @@ -7435,6 +7637,7 @@ Haiku is a simple neural network library for JAX developed by some of the author version |versionsuffix |toolchain ---------|----------------|-------------- +``0.0.9``| |``foss/2022a`` ``0.0.9``|``-CUDA-11.3.1``|``foss/2021a`` ### dm-reverb @@ -7653,6 +7856,16 @@ version |toolchain ``3.0.0``|``foss/2021a`` ``3.4.2``|``foss/2022a`` +### drmaa-python + +Distributed Resource Management Application API (DRMAA) bindings for Python. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|------------------ +``0.7.9``|``-slurm`` |``GCCcore/12.2.0`` + ### DROP Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders @@ -7824,7 +8037,7 @@ version|versionsuffix |toolchain ## E -[E-ANTIC](#e-antic) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) +[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ED2](#ed2) - [EDirect](#edirect) - [edlib](#edlib) - [EggLib](#egglib) - [eggnog-mapper](#eggnog-mapper) - [EGTtools](#egttools) - [eht-imaging](#eht-imaging) - [Eigen](#eigen) - [EigenExa](#eigenexa) - [EIGENSOFT](#eigensoft) - [einops](#einops) - [elastix](#elastix) - [elbencho](#elbencho) - [ELFIO](#elfio) - [elfutils](#elfutils) - [Elk](#elk) - [ELPA](#elpa) - [ELPH](#elph) - [elprep](#elprep) - [ELSI](#elsi) - [ELSI-RCI](#elsi-rci) - [Emacs](#emacs) - [EMAN2](#eman2) - [EMBOSS](#emboss) - [Embree](#embree) - [emcee](#emcee) - [EMU](#emu) - [enaBrowserTool](#enabrowsertool) - [enchant](#enchant) - [enchant-2](#enchant-2) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [eQuilibrator](#equilibrator) - [EricScript](#ericscript) - [ESL-Bundle](#esl-bundle) - [ESM-2](#esm-2) - [ESMF](#esmf) - [ESMPy](#esmpy) - [ESMValTool](#esmvaltool) - [eSpeak-NG](#espeak-ng) - [ESPResSo](#espresso) - [Essentia](#essentia) - [ETE](#ete) - [ETSF_IO](#etsf_io) - [eudev](#eudev) - [Evcxr-REPL](#evcxr-repl) - [EvidentialGene](#evidentialgene) - [evmix](#evmix) - [ExaBayes](#exabayes) - [ExaML](#examl) - [Excel-Writer-XLSX](#excel-writer-xlsx) - [ExifTool](#exiftool) - [exiv2](#exiv2) - [Exonerate](#exonerate) - [expat](#expat) - [expect](#expect) - [expecttest](#expecttest) - [eXpress](#express) - [Extrae](#extrae) - [EZC3D](#ezc3d) ### E-ANTIC @@ -7838,6 +8051,16 @@ version |toolchain ``0.1.2``|``GCC/8.2.0-2.31.1`` ``0.1.5``|``GCC/8.3.0`` +### e3nn + +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3). + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2022a`` + ### ea-utils Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. @@ -7972,6 +8195,7 @@ version |toolchain ``4.7.0`` |``system`` ``4.7.1`` |``system`` ``4.7.2`` |``system`` +``4.8.0`` |``system`` ### EasyQC @@ -7992,6 +8216,7 @@ A CMake-based build system, consisting of a collection of CMake macros and funct version |toolchain ---------|---------- ``3.7.0``|``system`` +``3.8.0``|``system`` ### ecCodes @@ -8013,6 +8238,7 @@ version |versionsuffix |toolchain ``2.22.1``| |``gompi/2021a`` ``2.24.2``| |``gompi/2021b``, ``iimpi/2021b`` ``2.27.0``| |``gompi/2022a`` +``2.31.0``| |``gompi/2023a`` ### eccodes-python @@ -8256,6 +8482,7 @@ version |versionsuffix |toolchain ``2022.05.001`` | |``foss/2022a``, ``foss/2022b``, ``intel/2022a``, ``intel/2022b`` ``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ``2022.05.001`` |``-CUDA-12.0.0``|``foss/2022b`` +``2023.05.001`` | |``foss/2023a`` ### ELPH @@ -8563,8 +8790,10 @@ A software package for performing and analyzing scientific Molecular Dynamics si *homepage*: version |versionsuffix |toolchain ----------|----------------|-------------- +---------|----------------|------------------------------ +``4.2.1``| |``foss/2021a``, ``foss/2022a`` ``4.2.1``|``-CUDA-11.3.1``|``foss/2021a`` +``4.2.1``|``-CUDA-11.8.0``|``foss/2022a`` ### Essentia @@ -8685,14 +8914,15 @@ version |toolchain ### exiv2 -Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. +Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and with a commercial license, and is used in many projects. -*homepage*: +*homepage*: version |toolchain ----------|------------------ ``0.27.4``|``GCCcore/10.3.0`` ``0.27.5``|``GCCcore/11.2.0`` +``0.28.0``|``GCCcore/12.3.0`` ### Exonerate @@ -8742,8 +8972,9 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``0.1.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|-------------------------------------------------------------------------------------------------- +``0.1.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.1.5``|``GCCcore/12.3.0`` ### eXpress @@ -8782,7 +9013,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) +[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastp](#fastp) - [fastparquet](#fastparquet) - [fastPHASE](#fastphase) - [fastq-pair](#fastq-pair) - [fastq-tools](#fastq-tools) - [FastQ_Screen](#fastq_screen) - [FastQC](#fastqc) - [fastqsplitter](#fastqsplitter) - [FastQTL](#fastqtl) - [fastqz](#fastqz) - [FastRFS](#fastrfs) - [fastStructure](#faststructure) - [FastTree](#fasttree) - [FastViromeExplorer](#fastviromeexplorer) - [FASTX-Toolkit](#fastx-toolkit) - [fatslim](#fatslim) - [fbm](#fbm) - [FBPIC](#fbpic) - [FCC](#fcc) - [FCM](#fcm) - [fdict](#fdict) - [FDS](#fds) - [fdstools](#fdstools) - [FDTD_Solutions](#fdtd_solutions) - [feh](#feh) - [FEniCS](#fenics) - [fermi-lite](#fermi-lite) - [Ferret](#ferret) - [festival](#festival) - [fetchMG](#fetchmg) - [FFC](#ffc) - [FFLAS-FFPACK](#fflas-ffpack) - [FFmpeg](#ffmpeg) - [ffmpi](#ffmpi) - [ffnet](#ffnet) - [ffnvcodec](#ffnvcodec) - [fftlib](#fftlib) - [FFTW](#fftw) - [FFTW.MPI](#fftw.mpi) - [fgbio](#fgbio) - [FGSL](#fgsl) - [FHI-aims](#fhi-aims) - [FIAT](#fiat) - [FIGARO](#figaro) - [FigureGen](#figuregen) - [Fiji](#fiji) - [file](#file) - [filevercmp](#filevercmp) - [Filtlong](#filtlong) - [find_circ](#find_circ) - [finder](#finder) - [findhap](#findhap) - [findutils](#findutils) - [fineRADstructure](#fineradstructure) - [fineSTRUCTURE](#finestructure) - [fio](#fio) - [Fiona](#fiona) - [Firefox](#firefox) - [FIRESTARTER](#firestarter) - [FireWorks](#fireworks) - [FIt-SNE](#fit-sne) - [FIX](#fix) - [fixesproto](#fixesproto) - [FLAC](#flac) - [FLAIR](#flair) - [flair-NLP](#flair-nlp) - [FLANN](#flann) - [FLASH](#flash) - [Flask](#flask) - [flatbuffers](#flatbuffers) - [flatbuffers-python](#flatbuffers-python) - [FLEUR](#fleur) - [flex](#flex) - [Flexbar](#flexbar) - [FlexiBLAS](#flexiblas) - [FlexiDot](#flexidot) - [Flink](#flink) - [FLINT](#flint) - [flit](#flit) - [flook](#flook) - [flowFDA](#flowfda) - [FLTK](#fltk) - [FLUENT](#fluent) - [Flye](#flye) - [FMILibrary](#fmilibrary) - [FMM3D](#fmm3d) - [FMPy](#fmpy) - [FMRIprep](#fmriprep) - [FMS](#fms) - [fmt](#fmt) - [FoBiS](#fobis) - [FoldX](#foldx) - [fontconfig](#fontconfig) - [fontsproto](#fontsproto) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [FPM](#fpm) - [fpocket](#fpocket) - [fqtrim](#fqtrim) - [fqzcomp](#fqzcomp) - [FragGeneScan](#fraggenescan) - [FragPipe](#fragpipe) - [FRANz](#franz) - [FreeBarcodes](#freebarcodes) - [freebayes](#freebayes) - [FreeFEM](#freefem) - [FreeFem++](#freefem++) - [freeglut](#freeglut) - [FreeImage](#freeimage) - [FreeSASA](#freesasa) - [FreeSurfer](#freesurfer) - [FreeTDS](#freetds) - [freetype](#freetype) - [freetype-py](#freetype-py) - [FreeXL](#freexl) - [freud-analysis](#freud-analysis) - [FriBidi](#fribidi) - [FRUIT](#fruit) - [FRUIT_processor](#fruit_processor) - [FSL](#fsl) - [FSLeyes](#fsleyes) - [fsom](#fsom) - [FSON](#fson) - [FTGL](#ftgl) - [Fujitsu](#fujitsu) - [fullrmc](#fullrmc) - [fumi_tools](#fumi_tools) - [funannotate](#funannotate) - [FunGAP](#fungap) - [FUNWAVE-TVD](#funwave-tvd) - [FUSE](#fuse) - [FuSeq](#fuseq) - [FusionCatcher](#fusioncatcher) - [futhark](#futhark) - [futile](#futile) - [future](#future) - [fxtract](#fxtract) ### f90cache @@ -8886,8 +9117,8 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- -``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +---------|------------------------------------------------------------------------------------------------- +``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### fastai @@ -8995,10 +9226,11 @@ fastparquet is a python implementation of the parquet format, aiming to integrat *homepage*: -version |toolchain ----------|-------------- -``0.7.2``|``foss/2021a`` -``0.8.0``|``foss/2021b`` +version |toolchain +------------|-------------- +``0.7.2`` |``foss/2021a`` +``0.8.0`` |``foss/2021b`` +``2023.4.0``|``gfbf/2022b`` ### fastPHASE @@ -9366,6 +9598,7 @@ version |toolchain ``4.4.2`` |``GCCcore/11.3.0`` ``5.0.1`` |``GCCcore/11.3.0`` ``5.1.2`` |``GCCcore/12.2.0`` +``6.0`` |``GCCcore/12.3.0`` ### ffmpi @@ -9393,9 +9626,10 @@ FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and *homepage*: -version |toolchain -------------|---------- -``11.1.5.2``|``system`` +version |toolchain +-------------|---------- +``11.1.5.2`` |``system`` +``12.0.16.0``|``system`` ### fftlib @@ -9414,7 +9648,7 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: version |versionsuffix|toolchain -----------|-------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|-------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.0.0`` |``-fujitsu`` |``FCC/4.5.0`` ``2.1.5`` | |``intel/2016b``, ``intel/2017a``, ``intel/2018b`` ``3.3.4`` | |``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -9422,7 +9656,7 @@ version |versionsuffix|toolchain ``3.3.6`` | |``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``3.3.7`` | |``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` ``3.3.7`` |``-serial`` |``GCC/6.4.0-2.28`` -``3.3.8`` | |``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b``, ``iomkl/2020b`` +``3.3.8`` | |``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b``, ``iomkl/2020b``, ``iompi/2020b`` ``3.3.8`` |``-amd`` |``gompi/2020a`` ``3.3.8`` |``-serial`` |``GCC/9.3.0`` ``3.3.9`` | |``gompi/2021a``, ``intel/2021a`` @@ -9542,9 +9776,9 @@ filevercmp function as in sort --version-sort. *homepage*: version |toolchain -------------|---------------------------------------------------------- +------------|------------------------------------------------------------------------------ ``20141119``|``GCCcore/9.3.0`` -``20191210``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``20191210``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### Filtlong @@ -9785,12 +10019,13 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: -version |toolchain -----------|---------------------------------------------------------- -``1.12.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.0.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``2.0.7`` |``GCCcore/11.3.0`` -``23.1.4``|``GCCcore/12.2.0`` +version |toolchain +-----------|---------------------------------------------------------- +``1.12.0`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.7`` |``GCCcore/11.3.0`` +``23.1.4`` |``GCCcore/12.2.0`` +``23.5.26``|``GCCcore/12.3.0`` ### flatbuffers-python @@ -9798,11 +10033,13 @@ Python Flatbuffers runtime library. *homepage*: -version |versionsuffix |toolchain ---------|-----------------|---------------------------------------------------------- -``1.12``| |``GCCcore/10.2.0`` -``1.12``|``-Python-3.7.4``|``GCCcore/8.3.0`` -``2.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +version |versionsuffix |toolchain +-----------|-----------------|---------------------------------------------------------- +``1.12`` | |``GCCcore/10.2.0`` +``1.12`` |``-Python-3.7.4``|``GCCcore/8.3.0`` +``2.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``23.1.4`` | |``GCCcore/12.2.0`` +``23.5.26``| |``GCCcore/12.3.0`` ### FLEUR @@ -9821,14 +10058,14 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ``2.5.35``|``system`` ``2.5.38``|``GCC/4.8.2`` ``2.5.39``|``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` ``2.6.0`` |``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` |``intel/2016b`` ``2.6.3`` |``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` +``2.6.4`` |``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` ### Flexbar @@ -9887,6 +10124,16 @@ version |toolchain ``2.8.4``|``foss/2021b`` ``2.9.0``|``gfbf/2022a`` +### flit + +A simple packaging tool for simple packages. + +*homepage*: + +version |toolchain +---------|------------------ +``3.9.0``|``GCCcore/12.3.0`` + ### flook The fortran-Lua-hook library. @@ -9920,7 +10167,7 @@ version |toolchain ``1.3.5``|``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.3.6``|``GCCcore/10.3.0`` ``1.3.7``|``GCCcore/11.2.0`` -``1.3.8``|``GCCcore/11.3.0`` +``1.3.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### FLUENT @@ -10298,8 +10545,8 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------------------------------------------- -``3.18.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +----------|----------------------------------------------------------------------------------------------------------------------------------------------------------- +``3.18.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### FreeSASA @@ -10334,6 +10581,10 @@ version |versionsuffix |toolchain ``7.4.0``|``-centos8_x86_64``|``system`` ``7.4.0``|``-ubuntu20_amd64``|``system`` ``7.4.0``|``-ubuntu22_amd64``|``system`` +``7.4.1``|``-centos7_x86_64``|``system`` +``7.4.1``|``-centos8_x86_64``|``system`` +``7.4.1``|``-ubuntu20_amd64``|``system`` +``7.4.1``|``-ubuntu22_amd64``|``system`` ### FreeTDS @@ -10416,7 +10667,7 @@ version |toolchain ``1.0.5`` |``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.0.9`` |``GCCcore/9.3.0`` ``1.0.10``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.0.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.0.12``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### FRUIT @@ -10480,6 +10731,7 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. version |toolchain ------------|----------------------------------------------------------------------------- ``20141119``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``20151117``|``GCCcore/11.3.0`` ### FSON @@ -10643,7 +10895,7 @@ version|toolchain ## G -[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) +[G-PhoCS](#g-phocs) - [g2clib](#g2clib) - [g2lib](#g2lib) - [g2log](#g2log) - [Gaia](#gaia) - [GAMESS-US](#gamess-us) - [gap](#gap) - [GapCloser](#gapcloser) - [GapFiller](#gapfiller) - [gappa](#gappa) - [GAPPadder](#gappadder) - [GARLI](#garli) - [garnett](#garnett) - [GAT](#gat) - [GATB-Core](#gatb-core) - [GATE](#gate) - [GATK](#gatk) - [Gaussian](#gaussian) - [gawk](#gawk) - [gbasis](#gbasis) - [Gblocks](#gblocks) - [GBprocesS](#gbprocess) - [gbs2ploidy](#gbs2ploidy) - [gc](#gc) - [GC3Pie](#gc3pie) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gcloud](#gcloud) - [GConf](#gconf) - [GCTA](#gcta) - [Gctf](#gctf) - [GD](#gd) - [GDAL](#gdal) - [GDB](#gdb) - [gdbgui](#gdbgui) - [gdbm](#gdbm) - [gdc-client](#gdc-client) - [GDCHART](#gdchart) - [GDCM](#gdcm) - [GDGraph](#gdgraph) - [gdist](#gdist) - [Gdk-Pixbuf](#gdk-pixbuf) - [GDRCopy](#gdrcopy) - [Geant4](#geant4) - [Geant4-data](#geant4-data) - [gearshifft](#gearshifft) - [GEGL](#gegl) - [GEM](#gem) - [GEM-library](#gem-library) - [gemelli](#gemelli) - [GEMMA](#gemma) - [gemmi](#gemmi) - [gencore_variant_detection](#gencore_variant_detection) - [GeneMark-ET](#genemark-et) - [GenerativeModels](#generativemodels) - [gengetopt](#gengetopt) - [GenMap](#genmap) - [Genome_Profiler](#genome_profiler) - [GenomeMapper](#genomemapper) - [genomepy](#genomepy) - [GenomeTester4](#genometester4) - [GenomeThreader](#genomethreader) - [GenomeTools](#genometools) - [GenomeWorks](#genomeworks) - [GenotypeHarmonizer](#genotypeharmonizer) - [genozip](#genozip) - [gensim](#gensim) - [geocube](#geocube) - [geopandas](#geopandas) - [geopy](#geopy) - [georges](#georges) - [GEOS](#geos) - [geosphere](#geosphere) - [Gerris](#gerris) - [GETORB](#getorb) - [GetOrganelle](#getorganelle) - [gettext](#gettext) - [gexiv2](#gexiv2) - [gfbf](#gfbf) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [Gibbs2](#gibbs2) - [giflib](#giflib) - [gifsicle](#gifsicle) - [GIMIC](#gimic) - [gimkl](#gimkl) - [GimmeMotifs](#gimmemotifs) - [GIMP](#gimp) - [gimpi](#gimpi) - [gimpic](#gimpic) - [GIMPS](#gimps) - [giolf](#giolf) - [giolfc](#giolfc) - [Giotto-Suite](#giotto-suite) - [git](#git) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [gkmSVM](#gkmsvm) - [GL2PS](#gl2ps) - [Glade](#glade) - [glew](#glew) - [GLFW](#glfw) - [GLI](#gli) - [GLib](#glib) - [glib-networking](#glib-networking) - [glibc](#glibc) - [GLibmm](#glibmm) - [GLIMMER](#glimmer) - [GlimmerHMM](#glimmerhmm) - [GLIMPSE](#glimpse) - [GLM](#glm) - [GLM-AED](#glm-aed) - [GlobalArrays](#globalarrays) - [Globus-CLI](#globus-cli) - [GlobusConnectPersonal](#globusconnectpersonal) - [glog](#glog) - [GLPK](#glpk) - [glproto](#glproto) - [Glucose](#glucose) - [GMAP-GSNAP](#gmap-gsnap) - [GMP](#gmp) - [gmpich](#gmpich) - [gmpolf](#gmpolf) - [gmpy2](#gmpy2) - [gmsh](#gmsh) - [GMT](#gmt) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [gnuplot](#gnuplot) - [GnuTLS](#gnutls) - [Go](#go) - [goalign](#goalign) - [GOATOOLS](#goatools) - [gobff](#gobff) - [GObject-Introspection](#gobject-introspection) - [goblf](#goblf) - [GOBNILP](#gobnilp) - [Godon](#godon) - [gofasta](#gofasta) - [golf](#golf) - [gomkl](#gomkl) - [gompi](#gompi) - [gompic](#gompic) - [google-java-format](#google-java-format) - [googletest](#googletest) - [gotree](#gotree) - [GP2C](#gp2c) - [GPAW](#gpaw) - [GPAW-setups](#gpaw-setups) - [gperf](#gperf) - [gperftools](#gperftools) - [gpustat](#gpustat) - [GPy](#gpy) - [GPyOpt](#gpyopt) - [GPyTorch](#gpytorch) - [Grace](#grace) - [Gradle](#gradle) - [gradunwarp](#gradunwarp) - [graph-tool](#graph-tool) - [GraphDB](#graphdb) - [Graphene](#graphene) - [GraphicsMagick](#graphicsmagick) - [graphite2](#graphite2) - [GraPhlAn](#graphlan) - [GraphMap](#graphmap) - [GraphMap2](#graphmap2) - [Graphviz](#graphviz) - [graphviz-python](#graphviz-python) - [GRASP](#grasp) - [GRASS](#grass) - [Greenlet](#greenlet) - [Grep](#grep) - [gretl](#gretl) - [grib_api](#grib_api) - [grid](#grid) - [GRIDSS](#gridss) - [GRIT](#grit) - [GRNBoost](#grnboost) - [groff](#groff) - [GroIMP](#groimp) - [GROMACS](#gromacs) - [GromacsWrapper](#gromacswrapper) - [Groovy](#groovy) - [gRPC](#grpc) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gsport](#gsport) - [GST-plugins-bad](#gst-plugins-bad) - [GST-plugins-base](#gst-plugins-base) - [GStreamer](#gstreamer) - [gsutil](#gsutil) - [gsw](#gsw) - [GTDB-Tk](#gtdb-tk) - [GTK+](#gtk+) - [GTK2](#gtk2) - [GTK3](#gtk3) - [GTK4](#gtk4) - [GtkSourceView](#gtksourceview) - [GTOOL](#gtool) - [GTS](#gts) - [gubbins](#gubbins) - [guenomu](#guenomu) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -10756,6 +11008,16 @@ version |toolchain ---------|-------------- ``0.7.1``|``GCC/10.3.0`` +### GAPPadder + +GAPPadder is tool for closing gaps on draft genomes with short sequencing data + +*homepage*: + +version |versionsuffix |toolchain +------------|------------------|-------------- +``20170601``|``-Python-2.7.18``|``foss/2021b`` + ### GARLI GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. @@ -10944,6 +11206,7 @@ version |toolchain ``8.0.4`` |``GCCcore/10.3.0`` ``8.2.0`` |``GCCcore/11.2.0`` ``8.2.2`` |``GCCcore/10.2.0``, ``GCCcore/11.3.0`` +``8.2.4`` |``GCCcore/12.3.0`` ### GC3Pie @@ -11029,6 +11292,7 @@ version |versionsuffix |toolchain ``12.2.0``| |``system`` ``12.3.0``| |``system`` ``13.1.0``| |``system`` +``13.2.0``| |``system`` ``system``| |``system`` ``system``|``-2.29`` |``system`` @@ -11075,6 +11339,7 @@ version |toolchain ``12.2.0``|``system`` ``12.3.0``|``system`` ``13.1.0``|``system`` +``13.2.0``|``system`` ``system``|``system`` ### gcccuda @@ -11111,8 +11376,8 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``3.2.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +---------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``3.2.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ### GCTA @@ -11211,6 +11476,7 @@ version |versionsuffix |toolchain ``10.2`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` ``11.1`` | |``GCCcore/11.2.0`` ``12.1`` | |``GCCcore/11.3.0`` +``13.2`` | |``GCCcore/12.3.0`` ### gdbgui @@ -11314,7 +11580,7 @@ version |toolchain ``2.40.0`` |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.42.6`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.42.8`` |``GCCcore/11.3.0`` -``2.42.10``|``GCCcore/12.2.0`` +``2.42.10``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### GDRCopy @@ -11461,6 +11727,16 @@ version |toolchain ``4.65``|``GCCcore/10.2.0`` ``4.71``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +### GenerativeModels + + + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.2.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### gengetopt Gengetopt is a tool to write command line option parsing code for C programs. @@ -11663,6 +11939,17 @@ version |versionsuffix |toolchain ``3.9.1`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` ``3.10.3``| |``GCC/11.3.0`` ``3.11.1``| |``GCC/12.2.0`` +``3.12.0``| |``GCC/12.3.0`` + +### geosphere + +Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.5-18``|``-R-4.2.1`` |``foss/2022a`` ### Gerris @@ -11716,6 +12003,7 @@ version |versionsuffix |toolchain ``0.20.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``0.21`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` ``0.21.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``0.22`` | |``GCCcore/13.2.0``, ``system`` ### gexiv2 @@ -11766,6 +12054,16 @@ version |toolchain ``0.11.6``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.12.7``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.2.0`` +### gffutils + +Gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. + +*homepage*: + +version |toolchain +--------|-------------- +``0.12``|``foss/2022b`` + ### gflags The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. @@ -11809,6 +12107,7 @@ version |versionsuffix|toolchain ----------|-------------|---------- ``6.12.3``| |``system`` ``8.6.5`` |``-x86_64`` |``system`` +``9.2.2`` |``-x86_64`` |``system`` ### Ghostscript @@ -11816,22 +12115,23 @@ Ghostscript is a versatile processor for PostScript data with the ability to ren *homepage*: -version |versionsuffix |toolchain -----------|------------------|-------------------------------------------------- -``9.19`` | |``intel/2016a``, ``intel/2016b`` -``9.20`` | |``foss/2016b``, ``intel/2016b`` -``9.21`` | |``intel/2017a`` -``9.22`` | |``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``9.22`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` -``9.23`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``9.23`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` -``9.27`` | |``GCCcore/8.2.0`` -``9.50`` | |``GCCcore/8.3.0`` -``9.52`` | |``GCCcore/9.3.0`` -``9.53.3``| |``GCCcore/10.2.0`` -``9.54.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``9.56.1``| |``GCCcore/11.3.0`` -``10.0.0``| |``GCCcore/12.2.0`` +version |versionsuffix |toolchain +-----------|------------------|-------------------------------------------------- +``9.19`` | |``intel/2016a``, ``intel/2016b`` +``9.20`` | |``foss/2016b``, ``intel/2016b`` +``9.21`` | |``intel/2017a`` +``9.22`` | |``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` +``9.22`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` +``9.23`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``9.23`` |``-cairo-1.14.12``|``GCCcore/6.4.0`` +``9.27`` | |``GCCcore/8.2.0`` +``9.50`` | |``GCCcore/8.3.0`` +``9.52`` | |``GCCcore/9.3.0`` +``9.53.3`` | |``GCCcore/10.2.0`` +``9.54.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.56.1`` | |``GCCcore/11.3.0`` +``10.0.0`` | |``GCCcore/12.2.0`` +``10.01.2``| |``GCCcore/12.3.0`` ### Gibbs2 @@ -11850,9 +12150,9 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------ ``5.1.4``|``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.2.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### gifsicle @@ -12074,6 +12374,16 @@ version |versionsuffix |toolchain ------------|-----------------|-------------- ``20220803``|``-Python-3.8.2``|``foss/2020a`` +### gkmSVM + +Gapped-Kmer Support Vector Machine. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``0.82.0``|``-R-4.2.1`` |``foss/2022a`` + ### GL2PS GL2PS: an OpenGL to PostScript printing library @@ -12162,6 +12472,7 @@ version |toolchain ``2.69.1``|``GCCcore/11.2.0`` ``2.72.1``|``GCCcore/11.3.0`` ``2.75.0``|``GCCcore/12.2.0`` +``2.77.1``|``GCCcore/12.3.0`` ### glib-networking @@ -12235,11 +12546,11 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: version |toolchain ------------|------------------------------------------------------------------------------------------------- +-----------|----------------------------------------------------------------------------------------------------------------------------------------- ``0.9.7.6``|``intel/2016a`` ``0.9.8.3``|``GCCcore/5.4.0``, ``GCCcore/7.3.0`` ``0.9.9.0``|``GCCcore/6.4.0`` -``0.9.9.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +``0.9.9.8``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0`` ### GLM-AED @@ -12315,7 +12626,7 @@ version |toolchain ``4.60``|``GCCcore/5.4.0``, ``intel/2016b`` ``4.61``|``intel/2017a`` ``4.65``|``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### glproto @@ -12403,7 +12714,7 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: version |versionsuffix |toolchain ------------|------------------|---------------------------------------------------------------------- +-----------|------------------|------------------------------------------------------------------------------------------ ``2.0.8`` |``-Python-2.7.13``|``intel/2017a`` ``2.0.8`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` ``2.0.8`` |``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` @@ -12411,7 +12722,8 @@ version |versionsuffix |toolchain ``2.1.0b1``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` ``2.1.0b4``| |``GCC/8.3.0`` ``2.1.0b5``| |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``2.1.2`` | |``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` +``2.1.2`` | |``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.4.0``, ``intel-compilers/2022.1.0`` +``2.1.5`` | |``GCC/12.3.0`` ### gmsh @@ -12498,6 +12810,7 @@ version |toolchain ``5.4.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``5.4.4``|``GCCcore/11.3.0`` ``5.4.6``|``GCCcore/12.2.0`` +``5.4.8``|``GCCcore/12.3.0`` ### GnuTLS @@ -12601,6 +12914,7 @@ version |versionsuffix |toolchain ``1.68.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.72.0``| |``GCCcore/11.3.0`` ``1.74.0``| |``GCCcore/12.2.0`` +``1.76.1``| |``GCCcore/12.3.0`` ### goblf @@ -12820,6 +13134,7 @@ version |toolchain ``2.8`` |``GCCcore/9.3.0`` ``2.9.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.10`` |``GCCcore/11.3.0`` +``2.12`` |``GCCcore/12.3.0`` ### gpustat @@ -12929,9 +13244,9 @@ Graphene is a a thin layer of types for graphic libraries *homepage*: version |toolchain -----------|-------------------------------------- +----------|---------------------------------------------------------- ``1.6.0`` |``intel/2017a`` -``1.10.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.10.8``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### GraphicsMagick @@ -12995,7 +13310,7 @@ Graphviz is open source graph visualization software. Graph visualization is a *homepage*: version |versionsuffix |toolchain -----------|-------------------------|------------------------------- +----------|-------------------------|-------------------------------------- ``2.38.0``| |``foss/2016b``, ``intel/2016b`` ``2.40.1``| |``foss/2018b``, ``intel/2018a`` ``2.40.1``|``-Python-2.7.15`` |``foss/2018b`` @@ -13008,6 +13323,7 @@ version |versionsuffix |toolchain ``2.47.2``| |``GCCcore/10.3.0`` ``2.50.0``| |``GCCcore/11.2.0`` ``5.0.0`` | |``GCCcore/11.3.0`` +``8.1.0`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### graphviz-python @@ -13016,11 +13332,11 @@ Simple Python interface for Graphviz *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------- +----------|------------------|-------------------------------------- ``0.5.1`` |``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` ``0.5.1`` |``-Python-3.5.2`` |``intel/2016b`` ``0.8.2`` |``-Python-3.6.4`` |``intel/2018a`` -``0.20.1``| |``GCCcore/11.3.0`` +``0.20.1``| |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### GRASP @@ -13051,12 +13367,12 @@ The greenlet package is a spin-off of Stackless, a version of CPython that suppo *homepage*: version |versionsuffix |toolchain -----------|------------------|--------------- +----------|------------------|------------------------------ ``0.4.9`` |``-Python-2.7.11``|``intel/2016a`` ``0.4.9`` |``-Python-3.5.1`` |``intel/2016a`` ``0.4.11``|``-Python-2.7.12``|``intel/2016b`` ``0.4.12``|``-Python-2.7.14``|``intel/2017b`` -``2.0.2`` | |``foss/2022a`` +``2.0.2`` | |``foss/2022a``, ``foss/2022b`` ### Grep @@ -13230,6 +13546,7 @@ gRPC is a modern, open source, high-performance remote procedure call (RPC) fram version |toolchain ----------|------------------ ``1.44.0``|``GCCcore/11.2.0`` +``1.57.0``|``GCCcore/12.3.0`` ### GSEA @@ -13258,7 +13575,7 @@ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmer *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ +---------|------------------------------------------------------------------------------------------------------------------------------------------ ``1.16`` |``foss/2016a``, ``intel/2016a`` ``2.1`` |``GCC/5.4.0-2.26``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.2.1``|``intel/2016a``, ``intel/2016b`` @@ -13266,7 +13583,7 @@ version |toolchain ``2.4`` |``GCCcore/6.4.0`` ``2.5`` |``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` |``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``2.7`` |``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ### gSOAP @@ -13298,6 +13615,7 @@ GStreamer is a library for constructing graphs of media-handling components. Th version |toolchain ----------|-------------- ``1.20.2``|``GCC/11.3.0`` +``1.22.5``|``GCC/12.2.0`` ### GST-plugins-base @@ -13315,7 +13633,8 @@ version |toolchain ``1.18.4`` |``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` |``GCC/11.2.0`` ``1.20.2`` |``GCC/11.3.0`` -``1.22.1`` |``GCCcore/12.2.0`` +``1.22.1`` |``GCC/12.2.0`` +``1.22.5`` |``GCC/12.3.0`` ### GStreamer @@ -13334,7 +13653,8 @@ version |toolchain ``1.18.4`` |``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` |``GCC/11.2.0`` ``1.20.2`` |``GCC/11.3.0`` -``1.22.1`` |``GCCcore/12.2.0`` +``1.22.1`` |``GCC/12.2.0`` +``1.22.5`` |``GCC/12.3.0`` ### gsutil @@ -13414,6 +13734,7 @@ version |toolchain ``3.24.31``|``GCCcore/11.2.0`` ``3.24.33``|``GCCcore/11.3.0`` ``3.24.35``|``GCCcore/12.2.0`` +``3.24.37``|``GCCcore/12.3.0`` ### GTK4 @@ -13421,9 +13742,10 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It prov *homepage*: -version |toolchain ----------|-------------- -``4.7.0``|``GCC/11.3.0`` +version |toolchain +----------|-------------- +``4.7.0`` |``GCC/11.3.0`` +``4.11.3``|``GCC/12.2.0`` ### GtkSourceView @@ -13453,8 +13775,8 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: version |toolchain -------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.7.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.7.6`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` ``20121130``|``foss/2017b`` ### gubbins @@ -13492,7 +13814,7 @@ version |toolchain ``2.2.7`` |``GCCcore/10.3.0`` ``3.0.7`` |``GCCcore/11.2.0`` ``3.0.8`` |``GCCcore/11.3.0`` -``3.0.9`` |``GCCcore/10.2.0`` +``3.0.9`` |``GCCcore/10.2.0``, ``GCCcore/12.3.0`` ### GULP @@ -13558,7 +13880,7 @@ version |toolchain ## H -[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [HBase](#hbase) - [HD-BET](#hd-bet) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [HOOMD-blue](#hoomd-blue) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [HTSplotter](#htsplotter) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) +[h4toh5](#h4toh5) - [H5hut](#h5hut) - [h5netcdf](#h5netcdf) - [h5py](#h5py) - [Hadoop](#hadoop) - [HAL](#hal) - [hampel](#hampel) - [hanythingondemand](#hanythingondemand) - [HAPGEN2](#hapgen2) - [HarfBuzz](#harfbuzz) - [Harminv](#harminv) - [harmony](#harmony) - [hatchling](#hatchling) - [HBase](#hbase) - [HD-BET](#hd-bet) - [HDBSCAN](#hdbscan) - [HDDM](#hddm) - [HDF](#hdf) - [HDF-EOS](#hdf-eos) - [HDF-EOS2](#hdf-eos2) - [HDF-EOS5](#hdf-eos5) - [HDF5](#hdf5) - [hdf5storage](#hdf5storage) - [HDFView](#hdfview) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [HiCExplorer](#hicexplorer) - [HiCMatrix](#hicmatrix) - [hierfstat](#hierfstat) - [hifiasm](#hifiasm) - [HighFive](#highfive) - [Highway](#highway) - [HIP](#hip) - [hipify-clang](#hipify-clang) - [HIPS](#hips) - [hipSYCL](#hipsycl) - [hiredis](#hiredis) - [HISAT2](#hisat2) - [histolab](#histolab) - [hivtrace](#hivtrace) - [hl7apy](#hl7apy) - [HLAminer](#hlaminer) - [HMMER](#hmmer) - [HMMER2](#hmmer2) - [hmmlearn](#hmmlearn) - [HOME](#home) - [HOOMD-blue](#hoomd-blue) - [Horovod](#horovod) - [horton](#horton) - [how_are_we_stranded_here](#how_are_we_stranded_here) - [HPCG](#hpcg) - [HPCX](#hpcx) - [HPDBSCAN](#hpdbscan) - [HPL](#hpl) - [htop](#htop) - [HTSeq](#htseq) - [HTSlib](#htslib) - [HTSplotter](#htsplotter) - [hub](#hub) - [humann](#humann) - [hunspell](#hunspell) - [hwloc](#hwloc) - [Hybpiper](#hybpiper) - [Hydra](#hydra) - [Hyperopt](#hyperopt) - [HyperQueue](#hyperqueue) - [hyperspy](#hyperspy) - [HyPhy](#hyphy) - [HyPo](#hypo) - [hypothesis](#hypothesis) - [Hypre](#hypre) ### h4toh5 @@ -13571,6 +13893,7 @@ version |versionsuffix |toolchain ---------|------------------------|------------------------------------------------ ``2.2.2``|``-linux-x86_64-static``|``system`` ``2.2.3``| |``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` +``2.2.5``| |``gompi/2022a`` ### H5hut @@ -13591,6 +13914,7 @@ A Python interface for the netCDF4 file-format that reads and writes local or re version |toolchain ---------|-------------- ``1.1.0``|``foss/2021b`` +``1.2.0``|``foss/2022a`` ### h5py @@ -13637,6 +13961,7 @@ version |versionsuffix |toolchain ``3.6.0`` | |``foss/2021b``, ``intel/2021b`` ``3.7.0`` | |``foss/2022a``, ``intel/2022a`` ``3.8.0`` | |``foss/2022b`` +``3.9.0`` | |``foss/2023a`` ### Hadoop @@ -13666,6 +13991,16 @@ version|toolchain -------|-------------- ``2.1``|``foss/2020b`` +### hampel + +The Hampel filter is generally used to detect anomalies in data with a timeseries structure. It basically consists of a sliding window of a parameterizable size. For each window, each observation will be compared with the Median Absolute Deviation (MAD). The observation will be considered an outlier in the case in which it exceeds the MAD by n times (the parameter n is also parameterizable). + +*homepage*: + +version |toolchain +---------|-------------- +``0.0.5``|``foss/2022a`` + ### hanythingondemand HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation. @@ -13726,7 +14061,7 @@ version |toolchain ``2.8.1``|``GCCcore/10.3.0`` ``2.8.2``|``GCCcore/11.2.0`` ``4.2.1``|``GCCcore/11.3.0`` -``5.3.1``|``GCCcore/12.2.0`` +``5.3.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Harminv @@ -13750,6 +14085,16 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.0.0-20200224``|``-R-4.0.0`` |``foss/2020a`` +### hatchling + +Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. + +*homepage*: + +version |toolchain +----------|------------------ +``1.18.0``|``GCCcore/12.3.0`` + ### HBase Apache HBase. is the Hadoop database, a distributed, scalable, big data store. @@ -13820,6 +14165,16 @@ version |toolchain --------|-------------------------------------------------------- ``2.20``|``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +### HDF-EOS2 + +HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. + +*homepage*: + +version|toolchain +-------|------------------ +``3.0``|``GCCcore/11.3.0`` + ### HDF-EOS5 HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. @@ -13864,7 +14219,7 @@ version |versionsuffix|toolchain ``1.12.2`` |``-serial`` |``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` ``1.13.1`` | |``gompi/2022a``, ``iimpi/2022a`` ``1.13.1`` |``-serial`` |``GCC/11.3.0`` -``1.14.0`` | |``gompi/2022b``, ``iimpi/2022b`` +``1.14.0`` | |``gompi/2022b``, ``gompi/2023a``, ``iimpi/2022b``, ``iimpi/2023a`` ### hdf5storage @@ -13967,7 +14322,7 @@ version |toolchain ``1.47.16``|``GCCcore/10.2.0`` ``1.48.3`` |``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` ``1.49.2`` |``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` -``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``1.49.3`` |``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0`` ### HepMC3 @@ -14116,6 +14471,7 @@ Hiredis is a minimalistic C client library for the Redis database. It is minima version |toolchain ---------|-------------------------------------- ``1.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.0``|``GCCcore/12.3.0`` ### HISAT2 @@ -14222,9 +14578,10 @@ HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecu *homepage*: -version |toolchain ----------|-------------- -``4.0.1``|``foss/2022a`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``4.0.1``| |``foss/2022a`` +``4.0.1``|``-CUDA-11.7.0``|``foss/2022a`` ### Horovod @@ -14248,12 +14605,23 @@ version |versionsuffix |toolchain ``0.21.3``|``-PyTorch-1.7.1`` |``fosscuda/2020b`` ``0.21.3``|``-TensorFlow-2.3.1-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a`` ``0.22.0``|``-PyTorch-1.8.1`` |``fosscuda/2020b`` +``0.22.1``|``-CUDA-11.3.1-TensorFlow-2.5.3`` |``foss/2021a`` ``0.22.1``|``-CUDA-11.3.1-TensorFlow-2.6.0`` |``foss/2021a`` ``0.22.1``|``-TensorFlow-2.5.0`` |``fosscuda/2020b`` ``0.22.1``|``-TensorFlow-2.5.0-Python-3.7.4`` |``fosscuda/2019b`` ``0.23.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` ``0.23.0``|``-TensorFlow-2.5.0`` |``fosscuda/2020b`` ``0.25.0``|``-CUDA-11.3.1-PyTorch-1.10.0`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.3.1-PyTorch-1.11.0`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.3.1-PyTorch-1.12.1`` |``foss/2021a`` +``0.28.1``|``-CUDA-11.4.1-TensorFlow-2.7.1`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.4.1-TensorFlow-2.8.4`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.5.2-PyTorch-1.12.1`` |``foss/2021b`` +``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.0`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-PyTorch-1.12.1`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.11.0`` |``foss/2022a`` +``0.28.1``|``-CUDA-11.7.0-TensorFlow-2.9.1`` |``foss/2022a`` +``0.28.1``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` ### horton @@ -14315,10 +14683,10 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: version|toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1``|``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2``|``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` +``2.3``|``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``gomkl/2022a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022.12``, ``intel/2022a``, ``intel/2022b``, ``intel/2023.03``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a``, ``iomkl/2021b`` ### htop @@ -14327,10 +14695,11 @@ An interactive process viewer for Unix *homepage*: version |toolchain ----------|---------- +---------|------------------ ``2.0.0``|``system`` ``2.0.1``|``system`` ``3.2.1``|``system`` +``3.2.2``|``GCCcore/11.3.0`` ### HTSeq @@ -14378,6 +14747,7 @@ version |versionsuffix|toolchain ``1.14`` | |``GCC/11.2.0`` ``1.15.1`` | |``GCC/11.3.0`` ``1.17`` | |``GCC/12.2.0`` +``1.18`` | |``GCC/12.3.0`` ``20160107``|``-PacBio`` |``intel/2017a`` ### HTSplotter @@ -14457,16 +14827,28 @@ version |toolchain ``2.7.1`` |``GCCcore/11.3.0`` ``2.8.0`` |``GCCcore/12.2.0`` ``2.9.1`` |``GCCcore/12.3.0`` +``2.9.2`` |``GCCcore/13.2.0`` + +### Hybpiper + +HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts/modules that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. + +*homepage*: + +version |toolchain +---------|-------------- +``2.1.6``|``foss/2022b`` ### Hydra -Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. +Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. *homepage*: version |toolchain ---------|------------------ ``1.1.1``|``GCCcore/10.3.0`` +``1.3.2``|``GCCcore/11.3.0`` ### Hyperopt @@ -14546,6 +14928,7 @@ version |versionsuffix |toolchain ``6.14.6``| |``GCCcore/11.2.0`` ``6.46.7``| |``GCCcore/11.3.0`` ``6.68.2``| |``GCCcore/12.2.0`` +``6.82.0``| |``GCCcore/12.3.0`` ### Hypre @@ -14564,11 +14947,12 @@ version |toolchain ``2.24.0``|``intel/2021b`` ``2.25.0``|``foss/2022a`` ``2.27.0``|``foss/2022b`` +``2.29.0``|``foss/2023a`` ## I -[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoNet](#isonet) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) +[i-cisTarget](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [IGVTools](#igvtools) - [iibff](#iibff) - [iimkl](#iimkl) - [iimpi](#iimpi) - [iimpic](#iimpic) - [IJulia](#ijulia) - [ILAMB](#ilamb) - [IMa2](#ima2) - [IMa2p](#ima2p) - [imagecodecs](#imagecodecs) - [imageio](#imageio) - [ImageJ](#imagej) - [ImageMagick](#imagemagick) - [imake](#imake) - [Imath](#imath) - [IMB](#imb) - [imbalanced-learn](#imbalanced-learn) - [imgaug](#imgaug) - [imkl](#imkl) - [imkl-FFTW](#imkl-fftw) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [Infomap](#infomap) - [inih](#inih) - [inline](#inline) - [InParanoid](#inparanoid) - [inputproto](#inputproto) - [Inspector](#inspector) - [IntaRNA](#intarna) - [INTEGRATE](#integrate) - [INTEGRATE-Neo](#integrate-neo) - [intel](#intel) - [intel-compilers](#intel-compilers) - [IntelClusterChecker](#intelclusterchecker) - [intelcuda](#intelcuda) - [IntelDAAL](#inteldaal) - [IntelPython](#intelpython) - [InterProScan](#interproscan) - [InterProScan_data](#interproscan_data) - [intervaltree](#intervaltree) - [intervaltree-python](#intervaltree-python) - [intltool](#intltool) - [io_lib](#io_lib) - [ioapi](#ioapi) - [iodata](#iodata) - [iomkl](#iomkl) - [iompi](#iompi) - [IOR](#ior) - [IOzone](#iozone) - [IPM](#ipm) - [Ipopt](#ipopt) - [ipp](#ipp) - [IPy](#ipy) - [ipympl](#ipympl) - [ipyparallel](#ipyparallel) - [ipyrad](#ipyrad) - [IPython](#ipython) - [IQ-TREE](#iq-tree) - [Iris](#iris) - [IRkernel](#irkernel) - [irodsfs](#irodsfs) - [IronPython](#ironpython) - [ISA-L](#isa-l) - [ISL](#isl) - [isoCirc](#isocirc) - [IsoformSwitchAnalyzeR](#isoformswitchanalyzer) - [IsoNet](#isonet) - [IsoQuant](#isoquant) - [IsoSeq](#isoseq) - [ispc](#ispc) - [itac](#itac) - [ITK](#itk) - [itpp](#itpp) - [ITSTool](#itstool) - [ITSx](#itsx) - [iVar](#ivar) ### i-cisTarget @@ -14759,6 +15143,7 @@ version |toolchain ``69.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``71.1``|``GCCcore/11.3.0`` ``72.1``|``GCCcore/12.2.0`` +``73.2``|``GCCcore/12.3.0`` ### IDBA-UD @@ -14864,6 +15249,7 @@ version |toolchain ``0.9.4`` |``foss/2021a`` ``0.9.5`` |``foss/2021b`` ``0.10.3``|``foss/2022a`` +``0.10.6``|``foss/2022b`` ### IGV @@ -14924,6 +15310,7 @@ version |toolchain ---------|---------- ``2018a``|``system`` ``2022b``|``system`` +``2023a``|``system`` ### iimpi @@ -15061,6 +15448,7 @@ version |versionsuffix |toolchain ``2.10.5``| |``foss/2021a`` ``2.13.5``| |``foss/2021b`` ``2.22.2``| |``foss/2022a`` +``2.31.1``| |``foss/2022b`` ### ImageJ @@ -15106,6 +15494,7 @@ version |versionsuffix |toolchain ``7.1.0-4`` | |``GCCcore/11.2.0`` ``7.1.0-37`` | |``GCCcore/11.3.0`` ``7.1.0-53`` | |``GCCcore/12.2.0`` +``7.1.1-15`` | |``GCCcore/12.3.0`` ### imake @@ -15373,6 +15762,8 @@ version |versionsuffix |toolchain ``1.3.3`` | |``foss/2020b``, ``foss/2021a`` ``1.3.3`` |``-Python-3.8.2`` |``foss/2020a`` ``1.10.1``|``-R-4.1.2`` |``foss/2021b`` +``1.12.0``|``-R-4.2.1`` |``foss/2022a`` +``1.14.2``|``-R-4.2.2`` |``foss/2022b`` ### infercnvpy @@ -15416,6 +15807,16 @@ version |toolchain ------------|-------------------- ``20190308``|``GCC/8.2.0-2.31.1`` +### inih + +Direct Rendering Manager runtime library. + +*homepage*: + +version|toolchain +-------|------------------ +``57`` |``GCCcore/12.3.0`` + ### inline Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions. @@ -15650,8 +16051,8 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: version|toolchain --------|----------------------------------------------------------------------------- -``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +-------|------------------------------------------------------------------------------------------------- +``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### intervaltree-python @@ -15660,9 +16061,9 @@ A mutable, self-balancing interval tree. Queries may be by point, by range over *homepage*: version |versionsuffix |toolchain ----------|-----------------|-------------------------------------- +---------|-----------------|---------------------------------------------------------- ``3.0.2``|``-Python-3.6.6``|``foss/2018b`` -``3.1.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.1.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### intltool @@ -15888,6 +16289,7 @@ version |versionsuffix |toolchain ``7.25.0``| |``GCCcore/10.3.0`` ``7.26.0``| |``GCCcore/11.2.0`` ``8.5.0`` | |``GCCcore/11.3.0`` +``8.14.0``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### IQ-TREE @@ -15968,7 +16370,7 @@ version |toolchain isl is a library for manipulating sets and relations of integer points bounded by linear constraints. -*homepage*: +*homepage*: version |toolchain --------|--------------------------------------------------------- @@ -15978,6 +16380,7 @@ version |toolchain ``0.17``|``foss/2016a`` ``0.23``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.24``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.26``|``GCCcore/12.3.0`` ### isoCirc @@ -15989,6 +16392,16 @@ version |toolchain ---------|-------------- ``1.0.4``|``foss/2020b`` +### IsoformSwitchAnalyzeR + +Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``1.18.0``|``-R-4.2.1`` |``foss/2022a`` + ### IsoNet IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis sing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic. @@ -15999,6 +16412,16 @@ version |toolchain ---------------------------|------------------ ``0.1_20210822_04_674f67f``|``fosscuda/2020b`` +### IsoQuant + +IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon and intron quantification. If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping. + +*homepage*: + +version |toolchain +---------|-------------- +``3.3.0``|``foss/2022b`` + ### IsoSeq IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added. @@ -16113,7 +16536,7 @@ version |toolchain ## J -[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JWM](#jwm) - [jxrlib](#jxrlib) +[JAGS](#jags) - [Jansson](#jansson) - [Jasmine](#jasmine) - [JasPer](#jasper) - [Java](#java) - [JavaFX](#javafx) - [jax](#jax) - [JAXFrontCE](#jaxfrontce) - [jbigkit](#jbigkit) - [Jellyfish](#jellyfish) - [jemalloc](#jemalloc) - [jhbuild](#jhbuild) - [JiTCODE](#jitcode) - [jModelTest](#jmodeltest) - [Jorg](#jorg) - [joypy](#joypy) - [jq](#jq) - [json-c](#json-c) - [json-fortran](#json-fortran) - [JSON-GLib](#json-glib) - [JsonCpp](#jsoncpp) - [JUBE](#jube) - [Judy](#judy) - [Julia](#julia) - [JUnit](#junit) - [Jupyter-bundle](#jupyter-bundle) - [jupyter-contrib-nbextensions](#jupyter-contrib-nbextensions) - [jupyter-matlab-proxy](#jupyter-matlab-proxy) - [jupyter-resource-usage](#jupyter-resource-usage) - [jupyter-server](#jupyter-server) - [jupyter-server-proxy](#jupyter-server-proxy) - [JupyterHub](#jupyterhub) - [JupyterLab](#jupyterlab) - [jupyterlab-lmod](#jupyterlab-lmod) - [jupyterlmod](#jupyterlmod) - [JupyterNotebook](#jupyternotebook) - [JWM](#jwm) - [jxrlib](#jxrlib) ### JAGS @@ -16232,6 +16655,7 @@ version |versionsuffix |toolchain ``11.0.8`` |``-aarch64`` |``system`` ``11.0.16`` | |``system`` ``11.0.18`` | |``system`` +``11.0.20`` | |``system`` ``13`` | |``system`` ``13.0.2`` | |``system`` ``15`` | |``system`` @@ -16387,9 +16811,9 @@ jq is a lightweight and flexible command-line JSON processor. *homepage*: version|toolchain --------|---------------------------------------------------------- +-------|------------------------------------------------------------------------------ ``1.5``|``GCCcore/10.2.0``, ``GCCcore/6.4.0`` -``1.6``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.6``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### json-c @@ -16409,8 +16833,8 @@ JSON-Fortran: A Modern Fortran JSON API *homepage*: version |toolchain ----------|------------------ -``8.3.0``|``GCCcore/11.2.0`` +---------|-------------------------------------- +``8.3.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### JSON-GLib @@ -16433,7 +16857,7 @@ version |toolchain ``0.10.7``|``GCCcore/8.2.0`` ``1.9.3`` |``GCCcore/8.3.0`` ``1.9.4`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``1.9.5`` |``GCCcore/11.3.0`` +``1.9.5`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### JUBE @@ -16490,6 +16914,8 @@ version |versionsuffix |toolchain ``1.8.2``|``-linux-x86_64``|``system`` ``1.8.5``|``-linux-x86_64``|``system`` ``1.9.0``|``-linux-x86_64``|``system`` +``1.9.2``|``-linux-x86_64``|``system`` +``1.9.3``|``-linux-x86_64``|``system`` ### JUnit @@ -16518,6 +16944,16 @@ version |versionsuffix |toolchain ``4.12``|``-Java-1.8.0_77`` |``system`` ``4.12``|``-Java-1.8.0_92`` |``system`` +### Jupyter-bundle + +This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub. + +*homepage*: + +version |toolchain +------------|------------------ +``20230823``|``GCCcore/12.3.0`` + ### jupyter-contrib-nbextensions A collection of various notebook extensions for Jupyter @@ -16550,6 +16986,7 @@ version |toolchain ``0.6.1``|``GCCcore/10.3.0`` ``0.6.2``|``GCCcore/10.3.0`` ``0.6.3``|``GCCcore/11.3.0`` +``1.0.0``|``GCCcore/12.3.0`` ### jupyter-server @@ -16560,6 +16997,8 @@ The Jupyter Server provides the backend (i.e. the core services, APIs, and REST version |toolchain ----------|------------------ ``1.21.0``|``GCCcore/11.3.0`` +``2.7.0`` |``GCCcore/12.2.0`` +``2.7.2`` |``GCCcore/12.3.0`` ### jupyter-server-proxy @@ -16568,9 +17007,10 @@ Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``3.2.1``|``GCCcore/10.3.0`` -``3.2.2``|``GCCcore/11.3.0`` +``3.2.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/12.3.0`` ### JupyterHub @@ -16585,6 +17025,8 @@ version |versionsuffix |toolchain ``1.1.0``| |``GCCcore/10.2.0`` ``1.4.1``| |``GCCcore/10.3.0`` ``3.0.0``| |``GCCcore/11.3.0`` +``4.0.1``| |``GCCcore/12.2.0`` +``4.0.2``| |``GCCcore/12.3.0`` ### JupyterLab @@ -16600,6 +17042,8 @@ version |versionsuffix |toolchain ``3.1.6`` | |``GCCcore/11.2.0`` ``3.2.8`` | |``GCCcore/10.3.0`` ``3.5.0`` | |``GCCcore/11.3.0`` +``4.0.3`` | |``GCCcore/12.2.0`` +``4.0.5`` | |``GCCcore/12.3.0`` ### jupyterlab-lmod @@ -16618,9 +17062,19 @@ Jupyter interactive notebook server extension that allows users to interact with *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``3.0.0``|``GCCcore/11.3.0`` -``4.0.3``|``GCCcore/11.3.0`` +``4.0.3``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` + +### JupyterNotebook + +The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. + +*homepage*: + +version |toolchain +---------|------------------ +``7.0.2``|``GCCcore/12.3.0`` ### JWM @@ -16731,8 +17185,8 @@ kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. *homepage*: version |toolchain -----------|-------------- -``0.27.3``|``foss/2021b`` +----------|------------------------------ +``0.27.3``|``foss/2021b``, ``foss/2022a`` ### kbproto @@ -16874,9 +17328,10 @@ KMA is a mapping method designed to map raw reads directly against redundant dat *homepage*: -version |toolchain -----------|--------------- -``1.2.22``|``intel/2019b`` +version |toolchain +-----------|--------------- +``1.2.22`` |``intel/2019b`` +``1.4.12a``|``GCC/12.2.0`` ### KMC @@ -16884,12 +17339,14 @@ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/F *homepage*: -version |versionsuffix |toolchain -------------|-----------------|------------------------------ -``3.1.0`` | |``foss/2018a``, ``foss/2018b`` -``3.1.1`` |``-Python-3.7.2``|``GCC/8.2.0-2.31.1`` -``3.1.2rc1``|``-Python-3.7.4``|``GCC/8.3.0`` -``3.2.1`` | |``GCC/11.2.0`` +version |versionsuffix |toolchain +------------|------------------|------------------------------ +``3.1.0`` | |``foss/2018a``, ``foss/2018b`` +``3.1.1`` |``-Python-3.7.2`` |``GCC/8.2.0-2.31.1`` +``3.1.2rc1``|``-Python-3.7.4`` |``GCC/8.3.0`` +``3.2.1`` | |``GCC/11.2.0`` +``3.2.1`` |``-Python-2.7.18``|``GCC/11.2.0`` +``3.2.2`` | |``GCC/12.2.0`` ### KMCP @@ -17049,7 +17506,7 @@ version |toolchain ## L -[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) +[L_RNA_scaffolder](#l_rna_scaffolder) - [Lace](#lace) - [LADR](#ladr) - [lagrangian-filtering](#lagrangian-filtering) - [LAME](#lame) - [LAMMPS](#lammps) - [lancet](#lancet) - [LAPACK](#lapack) - [LASSO-Python](#lasso-python) - [LAST](#last) - [LASTZ](#lastz) - [lavaan](#lavaan) - [LayoutParser](#layoutparser) - [LBFGS++](#lbfgs++) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcpuset](#libcpuset) - [libcroco](#libcroco) - [libctl](#libctl) - [libdap](#libdap) - [libde265](#libde265) - [libdeflate](#libdeflate) - [libdivsufsort](#libdivsufsort) - [libdrm](#libdrm) - [libdrs](#libdrs) - [libdwarf](#libdwarf) - [libedit](#libedit) - [libelf](#libelf) - [libemf](#libemf) - [libepoxy](#libepoxy) - [libev](#libev) - [libevent](#libevent) - [libexif](#libexif) - [libfabric](#libfabric) - [libfdf](#libfdf) - [libffcall](#libffcall) - [libffi](#libffi) - [libFLAME](#libflame) - [libfontenc](#libfontenc) - [libgcrypt](#libgcrypt) - [libgd](#libgd) - [libgdiplus](#libgdiplus) - [libGDSII](#libgdsii) - [libgeotiff](#libgeotiff) - [libgit2](#libgit2) - [libglade](#libglade) - [libGLU](#libglu) - [libglvnd](#libglvnd) - [libgpg-error](#libgpg-error) - [libgpuarray](#libgpuarray) - [libGridXC](#libgridxc) - [libgtextutils](#libgtextutils) - [libharu](#libharu) - [libheif](#libheif) - [libibmad](#libibmad) - [libibumad](#libibumad) - [libICE](#libice) - [libiconv](#libiconv) - [libidn](#libidn) - [libidn2](#libidn2) - [Libint](#libint) - [LiBis](#libis) - [libjpeg-turbo](#libjpeg-turbo) - [libjxl](#libjxl) - [libleidenalg](#libleidenalg) - [LibLZF](#liblzf) - [libmad](#libmad) - [libmatheval](#libmatheval) - [libmaus2](#libmaus2) - [libmbd](#libmbd) - [libMemcached](#libmemcached) - [libmicrohttpd](#libmicrohttpd) - [libmo_unpack](#libmo_unpack) - [libmypaint](#libmypaint) - [libnsl](#libnsl) - [libobjcryst](#libobjcryst) - [libogg](#libogg) - [libopus](#libopus) - [libosmium](#libosmium) - [libpci](#libpci) - [libpciaccess](#libpciaccess) - [libplinkio](#libplinkio) - [libpng](#libpng) - [libpsl](#libpsl) - [libPSML](#libpsml) - [libpsortb](#libpsortb) - [libpspio](#libpspio) - [libpthread-stubs](#libpthread-stubs) - [libQGLViewer](#libqglviewer) - [libreadline](#libreadline) - [libRmath](#librmath) - [librosa](#librosa) - [librsb](#librsb) - [librsvg](#librsvg) - [librttopo](#librttopo) - [libsamplerate](#libsamplerate) - [libSBML](#libsbml) - [libsigc++](#libsigc++) - [libsigsegv](#libsigsegv) - [libSM](#libsm) - [libsndfile](#libsndfile) - [libsodium](#libsodium) - [LibSoup](#libsoup) - [libspatialindex](#libspatialindex) - [libspatialite](#libspatialite) - [libssh](#libssh) - [libStatGen](#libstatgen) - [LIBSVM](#libsvm) - [LIBSVM-Python](#libsvm-python) - [libtar](#libtar) - [libtasn1](#libtasn1) - [libtecla](#libtecla) - [LibTIFF](#libtiff) - [libtirpc](#libtirpc) - [libtool](#libtool) - [libtree](#libtree) - [libunistring](#libunistring) - [libunwind](#libunwind) - [libutempter](#libutempter) - [LibUUID](#libuuid) - [libuv](#libuv) - [libvdwxc](#libvdwxc) - [libvorbis](#libvorbis) - [libvori](#libvori) - [libWallModelledLES](#libwallmodelledles) - [libwebp](#libwebp) - [libwpe](#libwpe) - [libX11](#libx11) - [libXau](#libxau) - [libxc](#libxc) - [libxcb](#libxcb) - [libXcursor](#libxcursor) - [libXdamage](#libxdamage) - [libXdmcp](#libxdmcp) - [libXext](#libxext) - [libXfixes](#libxfixes) - [libXfont](#libxfont) - [libXft](#libxft) - [libXi](#libxi) - [libXinerama](#libxinerama) - [libxkbcommon](#libxkbcommon) - [libxml++](#libxml++) - [libxml2](#libxml2) - [libxml2-python](#libxml2-python) - [libXmu](#libxmu) - [libXp](#libxp) - [libXpm](#libxpm) - [libXrandr](#libxrandr) - [libXrender](#libxrender) - [libxslt](#libxslt) - [libxsmm](#libxsmm) - [libXt](#libxt) - [libXxf86vm](#libxxf86vm) - [libyaml](#libyaml) - [libzeep](#libzeep) - [libzip](#libzip) - [lie_learn](#lie_learn) - [lifelines](#lifelines) - [Lighter](#lighter) - [liknorm](#liknorm) - [likwid](#likwid) - [limix](#limix) - [LinBox](#linbox) - [line_profiler](#line_profiler) - [Lingeling](#lingeling) - [LISFLOOD-FP](#lisflood-fp) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [LncLOOM](#lncloom) - [LocARNA](#locarna) - [LoFreq](#lofreq) - [Log-Log4perl](#log-log4perl) - [logaddexp](#logaddexp) - [LOHHLA](#lohhla) - [Loki](#loki) - [longestrunsubsequence](#longestrunsubsequence) - [longread_umi](#longread_umi) - [Longshot](#longshot) - [loompy](#loompy) - [loomR](#loomr) - [LoRDEC](#lordec) - [LPeg](#lpeg) - [LPJmL](#lpjml) - [lpsolve](#lpsolve) - [lrslib](#lrslib) - [LS-PrePost](#ls-prepost) - [LSD2](#lsd2) - [LSMS](#lsms) - [LTR_retriever](#ltr_retriever) - [LtrDetector](#ltrdetector) - [Lua](#lua) - [LuaJIT](#luajit) - [LuaJIT2-OpenResty](#luajit2-openresty) - [LuaRocks](#luarocks) - [Lucene-Geo-Gazetteer](#lucene-geo-gazetteer) - [LUMPY](#lumpy) - [LUSCUS](#luscus) - [lwgrp](#lwgrp) - [lxml](#lxml) - [lynx](#lynx) - [lz4](#lz4) - [LZO](#lzo) ### L_RNA_scaffolder @@ -17100,9 +17557,9 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``3.99.5``|``foss/2016b``, ``intel/2017a`` -``3.100`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +``3.100`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` ### LAMMPS @@ -17253,19 +17710,30 @@ version |toolchain ---------|---------- ``2.1.9``|``system`` +### leafcutter + +Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. For details please see our bioRxiv preprint and corresponding Nature Genetics publication. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.2.9``|``-R-4.2.2`` |``foss/2022b`` + ### leidenalg Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. *homepage*: -version |versionsuffix |toolchain ----------|-----------------|---------------------------------- -``0.8.2``|``-Python-3.8.2``|``foss/2020a`` -``0.8.3``| |``foss/2020b``, ``fosscuda/2020b`` -``0.8.7``| |``foss/2021a`` -``0.8.8``| |``foss/2021b`` -``0.9.1``| |``foss/2022a`` +version |versionsuffix |toolchain +----------|-----------------|---------------------------------- +``0.8.2`` |``-Python-3.8.2``|``foss/2020a`` +``0.8.3`` | |``foss/2020b``, ``fosscuda/2020b`` +``0.8.7`` | |``foss/2021a`` +``0.8.8`` | |``foss/2021b`` +``0.9.1`` | |``foss/2022a`` +``0.10.1``| |``foss/2022b`` ### LEMON @@ -17297,9 +17765,9 @@ LERC is an open-source image or raster format which supports rapid encoding and *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``3.0`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### less @@ -17362,8 +17830,8 @@ Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsig *homepage*: version |toolchain ----------|------------------------------------------------------------------------------ -``1.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|-------------------------------------------------------------------------------------------------- +``1.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### libaio @@ -17375,7 +17843,7 @@ version |toolchain -----------|------------------------------------------------------------------------------ ``0.3.111``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.3.112``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.3.113``|``GCCcore/12.2.0`` +``0.3.113``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libarchive @@ -17409,9 +17877,9 @@ This library aims to be a friendly, portable C implementation of the AV1 Image F *homepage*: version |toolchain -----------|------------------------------ +----------|-------------------------------------------------- ``0.9.0`` |``foss/2020b`` -``0.11.1``|``foss/2021a``, ``foss/2022a`` +``0.11.1``|``GCCcore/11.3.0``, ``foss/2021a``, ``foss/2022a`` ### libBigWig @@ -17461,7 +17929,7 @@ version |toolchain ``1.15``|``GCCcore/10.3.0`` ``1.17``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.1`` |``GCCcore/11.3.0`` -``2.3`` |``GCCcore/12.2.0`` +``2.3`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libcint @@ -17619,6 +18087,7 @@ version |toolchain ``2.4.107``|``GCCcore/11.2.0`` ``2.4.110``|``GCCcore/11.3.0`` ``2.4.114``|``GCCcore/12.2.0`` +``2.4.115``|``GCCcore/12.3.0`` ### libdrs @@ -17639,6 +18108,7 @@ The DWARF Debugging Information Format is of interest to programmers working on version |toolchain ------------|--------------------------------------------------- ``0.4.1`` |``GCCcore/11.3.0`` +``0.7.0`` |``GCCcore/12.3.0`` ``20140805``|``GCC/4.9.2`` ``20150310``|``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529``|``GCCcore/8.2.0`` @@ -17686,12 +18156,12 @@ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: version |toolchain -----------|-------------------------------------------------------- +----------|---------------------------------------------------------- ``1.5.2`` |``foss/2018a`` ``1.5.3`` |``GCCcore/8.2.0``, ``fosscuda/2018b`` ``1.5.4`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.5.8`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.5.10``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.5.10``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libev @@ -17710,11 +18180,11 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------ ``2.0.22``|``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``2.1.11``|``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``system`` +``2.1.12``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``system`` ### libexif @@ -17744,6 +18214,7 @@ version |toolchain ``1.15.1``|``GCCcore/11.3.0`` ``1.16.1``|``GCCcore/12.2.0`` ``1.18.0``|``GCCcore/12.3.0`` +``1.19.0``|``GCCcore/13.2.0`` ### libfdf @@ -17831,7 +18302,7 @@ version |toolchain ``2.2.5``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.3.1``|``GCCcore/10.3.0`` -``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libgdiplus @@ -17880,6 +18351,7 @@ version |toolchain ``1.1.1``|``GCCcore/11.2.0`` ``1.4.3``|``GCCcore/11.3.0`` ``1.5.0``|``GCCcore/12.2.0`` +``1.7.1``|``GCCcore/12.3.0`` ### libglade @@ -17903,6 +18375,7 @@ version |versionsuffix |toolchain ``9.0.0``|``-Mesa-11.2.1``|``foss/2016a``, ``intel/2016a`` ``9.0.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``9.0.2``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``9.0.3``| |``GCCcore/12.3.0`` ### libglvnd @@ -17916,7 +18389,7 @@ version |toolchain ``1.3.2``|``GCCcore/10.2.0`` ``1.3.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.4.0``|``GCCcore/11.3.0`` -``1.6.0``|``GCCcore/12.2.0`` +``1.6.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libgpg-error @@ -18075,7 +18548,7 @@ version |versionsuffix |toolchain ``2.4.2``| |``intel/2018a`` ``2.5.0``| |``gompi/2019a``, ``iimpi/2019a`` ``2.6.0``|``-lmax-6-cp2k``|``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` -``2.7.2``|``-lmax-6-cp2k``|``GCC/11.3.0`` +``2.7.2``|``-lmax-6-cp2k``|``GCC/11.3.0``, ``GCC/12.2.0`` ### LiBis @@ -18123,6 +18596,16 @@ version |toolchain ``0.6.1``|``GCCcore/10.2.0`` ``0.8.1``|``foss/2022a`` +### libleidenalg + +Implements the Leiden algorithm in C++ + +*homepage*: + +version |toolchain +----------|-------------- +``0.11.1``|``foss/2022b`` + ### LibLZF LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C. @@ -18223,9 +18706,9 @@ The libnsl package contains the public client interface for NIS(YP). *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``1.3.0``|``GCCcore/10.3.0`` -``2.0.0``|``GCCcore/11.3.0`` +``2.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### libobjcryst @@ -18292,7 +18775,7 @@ version |toolchain ``0.13.4``|``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` |``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.16`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``0.17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``0.17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### libplinkio @@ -18545,6 +19028,7 @@ version |toolchain ``1.0.31``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.1.0`` |``GCCcore/11.3.0`` ``1.2.0`` |``GCCcore/12.2.0`` +``1.2.2`` |``GCCcore/12.3.0`` ### libsodium @@ -18553,7 +19037,7 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------------------------------------------------------------------ ``1.0.6`` |``intel/2016a`` ``1.0.8`` |``foss/2016a`` ``1.0.11``|``foss/2016b``, ``intel/2016b`` @@ -18561,7 +19045,7 @@ version |toolchain ``1.0.13``|``GCCcore/6.4.0``, ``foss/2017a`` ``1.0.16``|``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17``|``GCCcore/8.2.0`` -``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.18``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### LibSoup @@ -18637,6 +19121,16 @@ version |toolchain ``3.25``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.30``|``GCCcore/11.3.0`` +### LIBSVM-Python + +This tool provides a simple Python interface to LIBSVM, a library for support vector machines (http://www.csie.ntu.edu.tw/~cjlin/libsvm). The interface is very easy to use as the usage is the same as that of LIBSVM. The interface is developed with the built-in Python library "ctypes". + +*homepage*: + +version |toolchain +--------|-------------- +``3.30``|``foss/2022a`` + ### libtar C library for manipulating POSIX tar files @@ -18717,7 +19211,7 @@ version |toolchain ``2.4.2``|``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5``|``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6``|``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``2.4.7``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### libtree @@ -18743,7 +19237,7 @@ version |toolchain ``0.9.7`` |``GCCcore/6.4.0`` ``0.9.10``|``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.1`` |``GCCcore/10.2.0`` +``1.1`` |``GCCcore/10.2.0``, ``GCCcore/12.3.0`` ### libunwind @@ -18811,6 +19305,16 @@ version |toolchain ---------|---------------------------------------------------------------------------------------------------------------------- ``1.3.7``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +### libvori + +C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package. + +*homepage*: + +version |toolchain +----------|-------------------------------------- +``220621``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` + ### libWallModelledLES libWallModelledLES is a library based on OpenFOAM® technology, extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). This is a turbulence modelling methodology, which allows to make LES cheaper by not resolving the inner region of turbulent boundary layers. @@ -18834,6 +19338,7 @@ version |toolchain ``1.1.0``|``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.4``|``GCCcore/11.3.0`` +``1.3.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### libwpe @@ -18844,6 +19349,7 @@ WPE is the reference WebKit port for embedded and low-consumption computer devic version |toolchain ----------|------------------ ``1.13.3``|``GCCcore/11.2.0`` +``1.14.1``|``GCCcore/11.3.0`` ### libX11 @@ -19037,6 +19543,7 @@ version |versionsuffix |toolchain ``2.9.13``| |``GCCcore/11.3.0`` ``2.10.3``| |``GCCcore/12.2.0`` ``2.11.4``| |``GCCcore/12.3.0`` +``2.11.5``| |``GCCcore/13.2.0`` ### libxml2-python @@ -19135,7 +19642,7 @@ version |toolchain ``1.10`` |``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.16.1``|``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``1.16.2``|``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``1.17`` |``GCC/11.2.0``, ``GCC/11.3.0`` +``1.17`` |``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ### libXt @@ -19322,6 +19829,7 @@ version |toolchain ``2.12`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.13.1``|``GCCcore/11.3.0`` ``2.14`` |``GCCcore/12.2.0`` +``2.15`` |``GCCcore/12.3.0`` ### LLDB @@ -19363,6 +19871,7 @@ version |toolchain ``12.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``14.0.3``|``GCCcore/11.3.0`` ``15.0.5``|``GCCcore/12.2.0`` +``16.0.6``|``GCCcore/12.3.0`` ### LMDB @@ -19672,6 +20181,7 @@ version |toolchain ``5.4.2`` |``GCCcore/10.2.0`` ``5.4.3`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``5.4.4`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``5.4.6`` |``GCCcore/12.3.0`` ### LuaJIT @@ -19811,7 +20321,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) +[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [MACH](#mach) - [MACS2](#macs2) - [MACSE](#macse) - [maeparser](#maeparser) - [MAFFT](#mafft) - [MAGeCK](#mageck) - [magick](#magick) - [Magics](#magics) - [magma](#magma) - [MAGMA-gene-analysis](#magma-gene-analysis) - [MagresPython](#magrespython) - [mahotas](#mahotas) - [MAJIQ](#majiq) - [make](#make) - [makedepend](#makedepend) - [makedepf90](#makedepf90) - [makeinfo](#makeinfo) - [MAKER](#maker) - [Mako](#mako) - [Mamba](#mamba) - [mandrake](#mandrake) - [mannkendall](#mannkendall) - [manta](#manta) - [mapDamage](#mapdamage) - [Maple](#maple) - [MapSplice](#mapsplice) - [Maq](#maq) - [MariaDB](#mariadb) - [MariaDB-connector-c](#mariadb-connector-c) - [MARS](#mars) - [Mash](#mash) - [MaSuRCA](#masurca) - [Mathematica](#mathematica) - [MathGL](#mathgl) - [MATIO](#matio) - [MATLAB](#matlab) - [MATLAB-Engine](#matlab-engine) - [matlab-proxy](#matlab-proxy) - [matplotlib](#matplotlib) - [matplotlib-inline](#matplotlib-inline) - [MATSim](#matsim) - [maturin](#maturin) - [Maude](#maude) - [mauveAligner](#mauvealigner) - [Maven](#maven) - [mawk](#mawk) - [MaxBin](#maxbin) - [MaxQuant](#maxquant) - [mayavi](#mayavi) - [maze](#maze) - [MbedTLS](#mbedtls) - [MBROLA](#mbrola) - [mbuffer](#mbuffer) - [mc](#mc) - [MCL](#mcl) - [MCR](#mcr) - [mctc-lib](#mctc-lib) - [mcu](#mcu) - [MDAnalysis](#mdanalysis) - [MDBM](#mdbm) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [meboot](#meboot) - [medaka](#medaka) - [medImgProc](#medimgproc) - [MedPy](#medpy) - [Meep](#meep) - [MEGA](#mega) - [MEGACC](#megacc) - [MEGAHIT](#megahit) - [Megalodon](#megalodon) - [MEGAN](#megan) - [Meld](#meld) - [MEM](#mem) - [MEME](#meme) - [memkind](#memkind) - [memory-profiler](#memory-profiler) - [MEMOTE](#memote) - [memtester](#memtester) - [meRanTK](#merantk) - [MERCKX](#merckx) - [Mercurial](#mercurial) - [Mesa](#mesa) - [Mesa-demos](#mesa-demos) - [meshalyzer](#meshalyzer) - [meshio](#meshio) - [meshtool](#meshtool) - [Meson](#meson) - [meson-python](#meson-python) - [Mesquite](#mesquite) - [MESS](#mess) - [MetaBAT](#metabat) - [MetaboAnalystR](#metaboanalystr) - [metaerg](#metaerg) - [MetaEuk](#metaeuk) - [MetaGeneAnnotator](#metageneannotator) - [Metagenome-Atlas](#metagenome-atlas) - [Metal](#metal) - [MetaMorpheus](#metamorpheus) - [MetaPhlAn](#metaphlan) - [MetaPhlAn2](#metaphlan2) - [metaWRAP](#metawrap) - [Metaxa2](#metaxa2) - [methylartist](#methylartist) - [MethylDackel](#methyldackel) - [methylpy](#methylpy) - [METIS](#metis) - [mgen](#mgen) - [mgltools](#mgltools) - [mhcflurry](#mhcflurry) - [mhcnuggets](#mhcnuggets) - [MicrobeAnnotator](#microbeannotator) - [microctools](#microctools) - [MiGEC](#migec) - [MIGRATE-N](#migrate-n) - [Mikado](#mikado) - [Miller](#miller) - [mimalloc](#mimalloc) - [MINC](#minc) - [MinCED](#minced) - [Mini-XML](#mini-xml) - [miniasm](#miniasm) - [minibar](#minibar) - [MiniCARD](#minicard) - [Miniconda2](#miniconda2) - [Miniconda3](#miniconda3) - [minieigen](#minieigen) - [Minimac4](#minimac4) - [minimap2](#minimap2) - [Minipolish](#minipolish) - [MiniSat](#minisat) - [minizip](#minizip) - [MINPACK](#minpack) - [MinPath](#minpath) - [MIRA](#mira) - [miRDeep2](#mirdeep2) - [Mish-Cuda](#mish-cuda) - [misha](#misha) - [MITgcmutils](#mitgcmutils) - [MITObim](#mitobim) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLxtend](#mlxtend) - [mm-common](#mm-common) - [Mmg](#mmg) - [MMSEQ](#mmseq) - [MMseqs2](#mmseqs2) - [mmtf-cpp](#mmtf-cpp) - [MNE-Python](#mne-python) - [MOABB](#moabb) - [MOABS](#moabs) - [MOB-suite](#mob-suite) - [ModelTest-NG](#modeltest-ng) - [modred](#modred) - [Molcas](#molcas) - [mold](#mold) - [Molden](#molden) - [molecularGSM](#moleculargsm) - [Molekel](#molekel) - [molmod](#molmod) - [Molpro](#molpro) - [MONA](#mona) - [MONAI](#monai) - [MONAI-Label](#monai-label) - [mongolite](#mongolite) - [Mono](#mono) - [Monocle3](#monocle3) - [moonjit](#moonjit) - [MOOSE](#moose) - [mordecai](#mordecai) - [MoreRONN](#moreronn) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [MPB](#mpb) - [MPC](#mpc) - [MPFR](#mpfr) - [mpi4py](#mpi4py) - [MPICH](#mpich) - [MPICH2](#mpich2) - [mpifileutils](#mpifileutils) - [mpiP](#mpip) - [MPJ-Express](#mpj-express) - [mpmath](#mpmath) - [MrBayes](#mrbayes) - [mrcfile](#mrcfile) - [MRChem](#mrchem) - [MRCPP](#mrcpp) - [MRIcron](#mricron) - [MRPRESSO](#mrpresso) - [MRtrix](#mrtrix) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MuSiC](#music) - [MUST](#must) - [MuTect](#mutect) - [mutil](#mutil) - [MVAPICH2](#mvapich2) - [MView](#mview) - [mxml](#mxml) - [mxmlplus](#mxmlplus) - [MXNet](#mxnet) - [MyCC](#mycc) - [mygene](#mygene) - [MyMediaLite](#mymedialite) - [mympingpong](#mympingpong) - [Myokit](#myokit) - [mypy](#mypy) - [MySQL](#mysql) - [MySQL-python](#mysql-python) - [mysqlclient](#mysqlclient) ### M1QN3 @@ -19845,7 +20355,7 @@ version |toolchain ``1.4.16``|``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17``|``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` +``1.4.19``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/11.4.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ### MACH @@ -19870,6 +20380,7 @@ version |versionsuffix |toolchain ``2.1.2.1`` |``-Python-2.7.15``|``intel/2019a`` ``2.2.5`` |``-Python-3.6.6`` |``foss/2018b`` ``2.2.7.1`` | |``foss/2021b`` +``2.2.9.1`` | |``foss/2022b`` ### MACSE @@ -19961,6 +20472,7 @@ version |versionsuffix |toolchain ``2.6.2``|``-CUDA-11.4.1``|``foss/2021b`` ``2.6.2``|``-CUDA-11.5.2``|``foss/2021b`` ``2.6.2``|``-CUDA-11.7.0``|``foss/2022a`` +``2.7.1``|``-CUDA-12.0.0``|``foss/2022b`` ### MAGMA-gene-analysis @@ -19990,9 +20502,10 @@ Mahotas is a computer vision and image processing library for Python *homepage*: -version |versionsuffix |toolchain ----------|------------------|--------------- -``1.4.3``|``-Python-2.7.12``|``intel/2016b`` +version |versionsuffix |toolchain +----------|------------------|--------------- +``1.4.3`` |``-Python-2.7.12``|``intel/2016b`` +``1.4.13``| |``foss/2022a`` ### MAJIQ @@ -20046,11 +20559,12 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: -version|versionsuffix|toolchain --------|-------------|------------------------------------------------------------------------------------------- -``6.7``| |``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.7``|``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.8``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +version |versionsuffix|toolchain +---------|-------------|------------------------------------------------------------------------------------------- +``6.7`` | |``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.7`` |``-minimal`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.8`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``7.0.3``| |``GCCcore/12.3.0`` ### MAKER @@ -20082,7 +20596,7 @@ version |versionsuffix |toolchain ``1.1.3``| |``GCCcore/10.2.0`` ``1.1.4``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.2.0``| |``GCCcore/11.3.0`` -``1.2.4``| |``GCCcore/12.2.0`` +``1.2.4``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Mamba @@ -20093,6 +20607,7 @@ Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, version |toolchain ------------|---------- ``4.14.0-0``|``system`` +``23.1.0-4``|``system`` ### mandrake @@ -20287,14 +20802,14 @@ matio is an C library for reading and writing Matlab MAT files. *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``1.5.9`` |``GCCcore/5.4.0`` ``1.5.11``|``foss/2017b`` ``1.5.12``|``GCCcore/6.4.0`` ``1.5.17``|``GCCcore/8.3.0`` ``1.5.19``|``GCCcore/9.3.0`` ``1.5.21``|``GCCcore/10.2.0`` -``1.5.23``|``GCCcore/11.3.0`` +``1.5.23``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### MATLAB @@ -20395,6 +20910,7 @@ version |versionsuffix |toolchain ``3.5.1``| |``foss/2020b``, ``intel/2020b`` ``3.5.2``| |``foss/2021b``, ``foss/2022a``, ``intel/2022a`` ``3.7.0``| |``gfbf/2022b`` +``3.7.2``| |``gfbf/2023a`` ### matplotlib-inline @@ -20417,6 +20933,16 @@ version |versionsuffix |toolchain ``0.8.1``|``-Java-1.8.0_112``|``intel/2016b`` ``14.0`` |``-Java-11`` |``GCCcore/11.2.0``, ``system`` +### maturin + +This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support. + +*homepage*: + +version |toolchain +---------|-------------------------------------- +``1.1.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` + ### Maude Maude is a high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications. Maude has been influenced in important ways by the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational specification and programming, Maude also supports rewriting logic computation. @@ -20700,6 +21226,16 @@ version |versionsuffix |toolchain ``1.9.5``| |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.9.7``| |``foss/2021a``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +### meboot + +Maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|-------------- +``1.4-9.2``|``-R-4.2.1`` |``foss/2022a`` + ### medaka medaka is a tool to create a consensus sequence from nanopore sequencing data. @@ -20718,6 +21254,8 @@ version |versionsuffix |toolchain ``1.4.3`` |``-Python-3.7.4``|``foss/2019b`` ``1.5.0`` | |``foss/2021a`` ``1.6.0`` | |``foss/2021b`` +``1.8.1`` | |``foss/2022a`` +``1.9.1`` | |``foss/2022a`` ### medImgProc @@ -20923,6 +21461,7 @@ version |versionsuffix |toolchain ``5.7.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``5.8`` | |``GCCcore/10.3.0`` ``6.2`` | |``GCCcore/11.3.0`` +``6.4.5``| |``GCCcore/12.3.0`` ### Mesa @@ -20949,6 +21488,7 @@ version |toolchain ``21.1.7``|``GCCcore/11.2.0`` ``22.0.3``|``GCCcore/11.3.0`` ``22.2.4``|``GCCcore/12.2.0`` +``23.1.4``|``GCCcore/12.3.0`` ### Mesa-demos @@ -21029,6 +21569,7 @@ Python build backend (PEP 517) for Meson projects version |toolchain ----------|------------------ ``0.11.0``|``GCCcore/12.2.0`` +``0.13.2``|``GCCcore/12.3.0`` ### Mesquite @@ -21226,6 +21767,16 @@ version |versionsuffix|toolchain ``5.1.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``5.1.0``|``-32bitIDX``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +### mgen + +Convenient matrix generation functions + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.1``|``foss/2022a`` + ### mgltools The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment). @@ -21300,6 +21851,16 @@ version |toolchain ``4.2.14``|``foss/2018a`` ``5.0.4`` |``foss/2021b`` +### Mikado + +Mikado is a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS. + +*homepage*: + +version |toolchain +---------|-------------- +``2.3.4``|``foss/2022b`` + ### Miller Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON @@ -21412,6 +21973,7 @@ version |toolchain ``4.9.2`` |``system`` ``4.12.0`` |``system`` ``22.11.1-1``|``system`` +``23.5.2-0`` |``system`` ### minieigen @@ -21950,6 +22512,7 @@ version |versionsuffix |toolchain ---------|-------------------------|-------------- ``0.2.0``|``-Python-3.7.2-R-3.6.0``|``foss/2019a`` ``0.2.3``|``-R-4.0.3`` |``foss/2020b`` +``1.3.1``|``-R-4.2.1`` |``foss/2022a`` ### moonjit @@ -22087,6 +22650,7 @@ version |versionsuffix |toolchain ``1.0.3``|``-MPFR-3.1.6``|``foss/2017b``, ``intel/2017b`` ``1.1.0``| |``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` ``1.2.1``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.3.1``| |``GCCcore/12.3.0`` ### MPFR @@ -22121,7 +22685,7 @@ version |versionsuffix |toolchain ``3.0.0``|``-Python-3.6.3`` |``intel/2017b`` ``3.0.1``|``-Python-3.6.6`` |``intel/2018b`` ``3.0.2``|``-timed-pingpong`` |``gompi/2019a``, ``iimpi/2019a`` -``3.1.4``| |``gompi/2022b`` +``3.1.4``| |``gompi/2022b``, ``gompi/2023a`` ### MPICH @@ -22273,6 +22837,7 @@ version |versionsuffix |toolchain ``3.0-rc-20191217``|``-Python-3.7.4`` |``foss/2019b`` ``3.0.0`` |``-Python-3.8.2`` |``foss/2020a`` ``3.0.3`` | |``foss/2021a`` +``3.0.4`` | |``foss/2022b`` ``3.0_RC2`` |``-Python-2.7.13``|``foss/2017a`` ``3.0_RC3`` |``-Python-2.7.14``|``intel/2018a`` @@ -22366,8 +22931,8 @@ generate multiset combinations (n multichoose k). *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- -``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +---------|------------------------------------------------------------------------------------------------- +``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### MultilevelEstimators @@ -22462,6 +23027,7 @@ version |versionsuffix |toolchain ``5.4.1``|``-metis`` |``foss/2021b``, ``intel/2021b`` ``5.5.0``|``-metis`` |``foss/2021a`` ``5.5.1``|``-metis`` |``foss/2022a`` +``5.6.1``|``-metis`` |``foss/2022b``, ``foss/2023a`` ### muParser @@ -22607,6 +23173,7 @@ Flexible and Efficient Library for Deep Learning version |versionsuffix |toolchain ---------|--------------------------|-------------- ``0.9.3``|``-Python-2.7.12-R-3.3.3``|``foss/2016b`` +``1.9.1``| |``foss/2022a`` ### MyCC @@ -22710,7 +23277,7 @@ version |versionsuffix |toolchain ## N -[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanoflann](#nanoflann) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [NanoStat](#nanostat) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [NCO](#nco) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCII](#netmhcii) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [NEXUS-CL](#nexus-cl) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [nichenetr](#nichenetr) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) +[n2v](#n2v) - [NAG](#nag) - [NAGfor](#nagfor) - [NAMD](#namd) - [namedlist](#namedlist) - [nano](#nano) - [NanoCaller](#nanocaller) - [NanoComp](#nanocomp) - [nanocompore](#nanocompore) - [NanoFilt](#nanofilt) - [nanoflann](#nanoflann) - [nanoget](#nanoget) - [NanoLyse](#nanolyse) - [nanomath](#nanomath) - [nanomax-analysis-utils](#nanomax-analysis-utils) - [nanonet](#nanonet) - [NanoPlot](#nanoplot) - [nanopolish](#nanopolish) - [NanopolishComp](#nanopolishcomp) - [NanoStat](#nanostat) - [napari](#napari) - [NASM](#nasm) - [nauty](#nauty) - [nbclassic](#nbclassic) - [NBO](#nbo) - [NCBI-Toolkit](#ncbi-toolkit) - [ncbi-vdb](#ncbi-vdb) - [NCCL](#nccl) - [NCCL-tests](#nccl-tests) - [ncdf4](#ncdf4) - [ncdu](#ncdu) - [NCIPLOT](#nciplot) - [NCL](#ncl) - [NCO](#nco) - [ncolor](#ncolor) - [ncompress](#ncompress) - [ncurses](#ncurses) - [ncview](#ncview) - [nd2reader](#nd2reader) - [ne](#ne) - [NECI](#neci) - [NEdit](#nedit) - [Nek5000](#nek5000) - [Nektar++](#nektar++) - [neon](#neon) - [neptune-client](#neptune-client) - [Net-core](#net-core) - [netCDF](#netcdf) - [netCDF-C++](#netcdf-c++) - [netCDF-C++4](#netcdf-c++4) - [netCDF-Fortran](#netcdf-fortran) - [netcdf4-python](#netcdf4-python) - [netloc](#netloc) - [NetLogo](#netlogo) - [netMHC](#netmhc) - [netMHCII](#netmhcii) - [netMHCIIpan](#netmhciipan) - [netMHCpan](#netmhcpan) - [NetPIPE](#netpipe) - [NetPyNE](#netpyne) - [nettle](#nettle) - [networkTools](#networktools) - [networkx](#networkx) - [NeuroKit](#neurokit) - [NEURON](#neuron) - [NewHybrids](#newhybrids) - [Nextflow](#nextflow) - [NextGenMap](#nextgenmap) - [NEXUS-CL](#nexus-cl) - [nf-core-mag](#nf-core-mag) - [NFFT](#nfft) - [nghttp2](#nghttp2) - [nghttp3](#nghttp3) - [NGLess](#ngless) - [nglview](#nglview) - [NGS](#ngs) - [NGS-Python](#ngs-python) - [NGSadmix](#ngsadmix) - [NGSpeciesID](#ngspeciesid) - [ngspice](#ngspice) - [ngtcp2](#ngtcp2) - [NiBabel](#nibabel) - [nichenetr](#nichenetr) - [NIfTI](#nifti) - [nifti2dicom](#nifti2dicom) - [Nilearn](#nilearn) - [Nim](#nim) - [NIMBLE](#nimble) - [Ninja](#ninja) - [Nipype](#nipype) - [NLMpy](#nlmpy) - [nlohmann_json](#nlohmann_json) - [NLopt](#nlopt) - [NLTK](#nltk) - [nnU-Net](#nnu-net) - [Node-RED](#node-red) - [nodejs](#nodejs) - [Normaliz](#normaliz) - [nose-parameterized](#nose-parameterized) - [nose3](#nose3) - [novaSTA](#novasta) - [novoalign](#novoalign) - [NOVOPlasty](#novoplasty) - [npstat](#npstat) - [NRGLjubljana](#nrgljubljana) - [Nsight-Compute](#nsight-compute) - [Nsight-Systems](#nsight-systems) - [NSPR](#nspr) - [NSS](#nss) - [nsync](#nsync) - [ntCard](#ntcard) - [ntEdit](#ntedit) - [ntHits](#nthits) - [NTL](#ntl) - [NTPoly](#ntpoly) - [num2words](#num2words) - [numactl](#numactl) - [numba](#numba) - [numdiff](#numdiff) - [numexpr](#numexpr) - [numpy](#numpy) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [NVSHMEM](#nvshmem) - [nvtop](#nvtop) - [NWChem](#nwchem) - [NxTrim](#nxtrim) ### n2v @@ -22761,6 +23328,7 @@ version |versionsuffix |toolchain ``2.13``|``-mpi`` |``foss/2018b``, ``foss/2019b``, ``intel/2018b`` ``2.14``| |``fosscuda/2019b``, ``fosscuda/2020b`` ``2.14``|``-CUDA-11.3.1``|``foss/2021a`` +``2.14``|``-CUDA-11.7.0``|``foss/2022a`` ``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2022a``, ``intel/2020a`` ### namedlist @@ -22786,6 +23354,16 @@ version|toolchain ``7.1``|``GCCcore/12.2.0`` ``7.2``|``GCCcore/12.2.0`` +### NanoCaller + +NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data. + +*homepage*: + +version |toolchain +---------|-------------- +``3.4.1``|``foss/2022a`` + ### NanoComp Comparing runs of Oxford Nanopore sequencing data and alignments @@ -22941,6 +23519,7 @@ napari is a fast, interactive, multi-dimensional image viewer for Python. It's version |toolchain ----------|-------------- ``0.4.15``|``foss/2021b`` +``0.4.18``|``foss/2022a`` ### NASM @@ -22971,6 +23550,16 @@ version |toolchain ``2.7rc2``|``GCC/8.2.0-2.31.1`` ``2.7rc5``|``GCC/8.3.0`` +### nbclassic + +NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking. + +*homepage*: + +version |toolchain +---------|------------------ +``1.0.0``|``GCCcore/12.3.0`` + ### NBO The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. @@ -23079,6 +23668,7 @@ version |toolchain ``1.15.1``|``GCCcore/9.3.0`` ``1.16`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``1.17`` |``GCC/11.3.0`` +``1.18`` |``GCC/12.3.0`` ### NCIPLOT @@ -23128,6 +23718,16 @@ version |toolchain ``5.1.0``|``foss/2022a`` ``5.1.3``|``foss/2021a``, ``foss/2022a`` +### ncolor + +Fast remapping of instance labels 1,2,3,...,M to a smaller set of repeating, disjoint labels, 1,2,...,N. + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.1``|``foss/2022a`` + ### ncompress Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files. @@ -23151,7 +23751,7 @@ version|toolchain ``6.1``|``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2``|``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` ``6.3``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` -``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``6.4``|``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### ncview @@ -23162,7 +23762,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv version |toolchain ---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1.7``|``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8``|``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``2.1.8``|``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a`` ### nd2reader @@ -23282,6 +23882,7 @@ version |versionsuffix |toolchain ``4.8.0`` | |``gompi/2021a``, ``iimpi/2021a`` ``4.8.1`` | |``gompi/2021b``, ``iimpi/2021b`` ``4.9.0`` | |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a``, ``iimpi/2022b`` +``4.9.2`` | |``gompi/2023a``, ``iimpi/2023a`` ### netCDF-C++ @@ -23300,11 +23901,11 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: version |versionsuffix |toolchain ----------|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``4.3.0``| |``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0``|``-HDF5-1.8.18``|``intel/2017a`` ``4.3.0``|``-HDF5-1.8.19``|``intel/2017b`` -``4.3.1``| |``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a`` +``4.3.1``| |``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a`` ### netCDF-Fortran @@ -23324,6 +23925,7 @@ version |versionsuffix |toolchain ``4.5.2``| |``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``4.5.3``| |``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` ``4.6.0``| |``gompi/2022a``, ``gompi/2022b``, ``iimpi/2022a`` +``4.6.1``| |``gompi/2023a`` ### netcdf4-python @@ -23455,6 +24057,7 @@ version |toolchain ``3.7.3``|``GCCcore/11.2.0`` ``3.8`` |``GCCcore/11.3.0`` ``3.8.1``|``GCCcore/12.2.0`` +``3.9.1``|``GCCcore/12.3.0`` ### networkTools @@ -23494,6 +24097,7 @@ version |versionsuffix |toolchain ``2.8.4``| |``foss/2022a``, ``intel/2022a`` ``2.8.8``| |``gfbf/2022b`` ``3.0`` | |``gfbf/2022b`` +``3.1`` | |``gfbf/2023a`` ### NeuroKit @@ -23865,7 +24469,7 @@ version |toolchain ``2.6.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.2``|``GCCcore/10.2.0`` ``2.7.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.7.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2.7.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### NLTK @@ -23922,6 +24526,7 @@ version |toolchain ``14.17.6``|``GCCcore/11.2.0`` ``16.15.1``|``GCCcore/11.3.0`` ``18.12.1``|``GCCcore/12.2.0`` +``18.17.1``|``GCCcore/12.3.0`` ### Normaliz @@ -23948,6 +24553,26 @@ version |versionsuffix |toolchain ``0.5.0``|``-Python-3.5.2`` |``intel/2016b`` ``0.6.0``|``-Python-3.6.1`` |``intel/2017a`` +### nose3 + +Nose extends unittest to make testing easier. + +*homepage*: + +version |toolchain +---------|------------------ +``1.3.8``|``GCCcore/11.3.0`` + +### novaSTA + +C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse in terms of processing time (the code is not well optimized) and is thus not recommended for larger datasets. + +*homepage*: + +version|versionsuffix |toolchain +-------|----------------|-------------- +``1.1``|``-CUDA-11.7.0``|``foss/2022a`` + ### novoalign NovoCraft is a software bundle. NovoAlign: Market’s leading aligner with fully packed features designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, 454, and Color Spance NGS platforms. NovoAlignCS: Leading aligner packed with features designed to fully support reads from ABI SOLiD Color Space. NovoSort: Custom designed multi-threaded sort/merge tools for BAM files. NovoMethyl: It can analyse a set of alignments to identify methylated cytosine’s. WARNING! You can only use the sofware without a license (with some features disabled) if you are a non-profit organisation and use is for your own research or for use by students as part of their course. A license is required for use where these programs are part of a service where a third party is billed. @@ -24056,6 +24681,7 @@ version |toolchain ----------|------------------------------------------------------------------------------------------------ ``1.24.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.25.0``|``GCCcore/11.3.0`` +``1.26.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### ntCard @@ -24134,7 +24760,7 @@ version |toolchain ``2.0.12``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13``|``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``2.0.14``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``2.0.16``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.0.16``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### numba @@ -24237,6 +24863,7 @@ version |versionsuffix |toolchain ``22.9`` |``-CUDA-11.7.0``|``system`` ``22.11``|``-CUDA-11.7.0``|``system`` ``23.1`` |``-CUDA-12.0.0``|``system`` +``23.7`` |``-CUDA-12.1.1``|``system`` ### nvofbf @@ -24314,7 +24941,7 @@ version |toolchain ## O -[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxDNA](#oxdna) - [oxford_asl](#oxford_asl) +[Oases](#oases) - [OBITools](#obitools) - [OBITools3](#obitools3) - [OCaml](#ocaml) - [occt](#occt) - [oceanspy](#oceanspy) - [OCNet](#ocnet) - [Octave](#octave) - [Octopus-vcf](#octopus-vcf) - [OGDF](#ogdf) - [olaFlow](#olaflow) - [olego](#olego) - [OMA](#oma) - [OmegaFold](#omegafold) - [Omnipose](#omnipose) - [onedrive](#onedrive) - [ONNX](#onnx) - [ONNX-Runtime](#onnx-runtime) - [ont-fast5-api](#ont-fast5-api) - [ont-guppy](#ont-guppy) - [ont-remora](#ont-remora) - [OOMPA](#oompa) - [OPARI2](#opari2) - [Open-Data-Cube-Core](#open-data-cube-core) - [OpenAI-Gym](#openai-gym) - [OpenBabel](#openbabel) - [OpenBLAS](#openblas) - [openCARP](#opencarp) - [OpenCensus-python](#opencensus-python) - [OpenCoarrays](#opencoarrays) - [OpenColorIO](#opencolorio) - [OpenCV](#opencv) - [OpenEXR](#openexr) - [OpenFace](#openface) - [OpenFAST](#openfast) - [OpenFOAM](#openfoam) - [OpenFOAM-Extend](#openfoam-extend) - [OpenFold](#openfold) - [OpenForceField](#openforcefield) - [OpenImageIO](#openimageio) - [OpenJPEG](#openjpeg) - [OpenKIM-API](#openkim-api) - [openkim-models](#openkim-models) - [OpenMM](#openmm) - [OpenMM-PLUMED](#openmm-plumed) - [OpenMMTools](#openmmtools) - [OpenMolcas](#openmolcas) - [OpenMPI](#openmpi) - [OpenMS](#openms) - [OpenNLP](#opennlp) - [OpenPGM](#openpgm) - [OpenPIV](#openpiv) - [openpyxl](#openpyxl) - [OpenRefine](#openrefine) - [OpenSceneGraph](#openscenegraph) - [OpenSees](#opensees) - [OpenSlide](#openslide) - [openslide-python](#openslide-python) - [OpenSSL](#openssl) - [OpenStackClient](#openstackclient) - [OPERA](#opera) - [OPERA-MS](#opera-ms) - [OptaDOS](#optados) - [Optax](#optax) - [OptiType](#optitype) - [OptiX](#optix) - [Optuna](#optuna) - [OR-Tools](#or-tools) - [ORCA](#orca) - [ORFfinder](#orffinder) - [OrfM](#orfm) - [OrthoFinder](#orthofinder) - [OrthoMCL](#orthomcl) - [Osi](#osi) - [OSPRay](#ospray) - [OSU-Micro-Benchmarks](#osu-micro-benchmarks) - [OTF2](#otf2) - [OVITO](#ovito) - [ownCloud](#owncloud) - [oxDNA](#oxdna) - [oxford_asl](#oxford_asl) ### Oases @@ -24470,6 +25097,17 @@ version |versionsuffix |toolchain ---------|----------------|-------------- ``1.1.0``|``-CUDA-11.7.0``|``foss/2022a`` +### Omnipose + +Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.4.4``| |``foss/2022a`` +``0.4.4``|``-CUDA-11.7.0``|``foss/2022a`` + ### onedrive A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, OneDrive for Office365 and SharePoint. @@ -24514,7 +25152,7 @@ version |versionsuffix |toolchain ``3.3.0``|``-Python-3.7.4``|``foss/2019b`` ``4.0.0``| |``foss/2021a`` ``4.0.2``| |``foss/2021a``, ``foss/2021b`` -``4.1.1``| |``foss/2022b`` +``4.1.1``| |``foss/2022a``, ``foss/2022b`` ### ont-guppy @@ -24558,11 +25196,11 @@ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-sour *homepage*: version |toolchain ----------|------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``2.0`` |``foss/2016a`` ``2.0.5``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.6``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.0.7``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.7``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Open-Data-Cube-Core @@ -24584,6 +25222,7 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.17.1``|``-Python-3.7.4``|``foss/2019b`` ``0.21.0``| |``foss/2021b`` +``0.26.2``| |``foss/2022a`` ### OpenBabel @@ -24715,6 +25354,7 @@ version |versionsuffix |toolchain ``4.5.5`` |``-contrib`` |``foss/2021b`` ``4.6.0`` |``-CUDA-11.7.0-contrib`` |``foss/2022a`` ``4.6.0`` |``-contrib`` |``foss/2022a`` +``4.8.0`` |``-contrib`` |``foss/2022b`` ### OpenEXR @@ -24774,6 +25414,7 @@ version |versionsuffix|toolchain ``4.x-20170904``| |``intel/2016b`` ``5.0`` | |``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0-20180108``| |``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``5.0-20180606``| |``foss/2019b`` ``6`` | |``foss/2018b``, ``foss/2019b``, ``intel/2018a`` ``7`` | |``foss/2019b`` ``7`` |``-20200508``|``foss/2019b`` @@ -24782,6 +25423,7 @@ version |versionsuffix|toolchain ``9`` | |``foss/2021a``, ``intel/2021a`` ``10`` | |``foss/2022a`` ``10`` |``-20230119``|``foss/2022a`` +``11`` | |``foss/2022a`` ``v1606+`` | |``foss/2018b`` ``v1612+`` | |``foss/2018b`` ``v1712`` | |``foss/2017b``, ``intel/2017b`` @@ -24845,6 +25487,7 @@ version |toolchain ``2.0.12`` |``gompi/2019b``, ``iimpi/2019b`` ``2.1.12.0``|``gompi/2020a``, ``iimpi/2020a`` ``2.3.17.0``|``GCC/11.3.0`` +``2.4.14.0``|``GCC/12.3.0`` ### OpenJPEG @@ -24988,7 +25631,7 @@ version |versionsuffix |toolchain ``4.1.1`` | |``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ``4.1.2`` | |``GCC/10.2.0``, ``GCC/11.2.0`` ``4.1.4`` | |``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0`` -``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0`` +``4.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2023.1.0`` ``system``| |``GCC/system-2.29`` ### OpenMS @@ -25018,8 +25661,8 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: version |toolchain ------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +-----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``5.2.122``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ### OpenPIV @@ -25170,6 +25813,16 @@ version |toolchain -----------|-------------- ``1.2.380``|``GCC/11.3.0`` +### Optax + +Optax is a gradient processing and optimization library for JAX. + +*homepage*: + +version |toolchain +---------|-------------- +``0.1.7``|``foss/2022a`` + ### OptiType OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. @@ -25297,6 +25950,7 @@ version |toolchain ``0.108.5``|``GCCcore/7.3.0``, ``foss/2018b`` ``0.108.6``|``GCC/10.3.0``, ``GCCcore/10.2.0`` ``0.108.7``|``GCC/11.2.0`` +``0.108.8``|``GCC/12.2.0`` ### OSPRay @@ -25329,7 +25983,7 @@ version |versionsuffix |toolchain ``5.9`` |``-CUDA-11.7.0``|``gompi/2022a`` ``5.9`` |``-ROCm-4.5.0`` |``gompi/2021b`` ``6.2`` | |``gompi/2022.10``, ``gompi/2022b`` -``7.1-1``| |``gompi/2023a`` +``7.1-1``| |``gompi/2023a``, ``iimpi/2023a`` ### OTF2 @@ -25344,6 +25998,7 @@ version |toolchain ``2.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.0`` |``GCCcore/11.3.0`` ``3.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.0.3``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### OVITO @@ -25389,7 +26044,7 @@ version |versionsuffix |toolchain ## P -[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) +[p11-kit](#p11-kit) - [p4-phylogenetics](#p4-phylogenetics) - [p4est](#p4est) - [p4vasp](#p4vasp) - [p7zip](#p7zip) - [packmol](#packmol) - [pagmo](#pagmo) - [pairsnp](#pairsnp) - [PAL2NAL](#pal2nal) - [paladin](#paladin) - [PALEOMIX](#paleomix) - [PAML](#paml) - [panaroo](#panaroo) - [pandapower](#pandapower) - [pandas](#pandas) - [pandas-datareader](#pandas-datareader) - [PANDAseq](#pandaseq) - [Pandoc](#pandoc) - [Panedr](#panedr) - [Pango](#pango) - [pangolin](#pangolin) - [panito](#panito) - [PAPI](#papi) - [parallel](#parallel) - [parallel-fastq-dump](#parallel-fastq-dump) - [Parallel-Hashmap](#parallel-hashmap) - [ParallelIO](#parallelio) - [parameterized](#parameterized) - [paramiko](#paramiko) - [parasail](#parasail) - [Paraver](#paraver) - [ParaView](#paraview) - [Parcels](#parcels) - [PARI-GP](#pari-gp) - [ParmEd](#parmed) - [ParMETIS](#parmetis) - [ParMGridGen](#parmgridgen) - [Parsl](#parsl) - [PartitionFinder](#partitionfinder) - [pasta](#pasta) - [PaStiX](#pastix) - [pastml](#pastml) - [patch](#patch) - [patchelf](#patchelf) - [path.py](#path.py) - [PAUP](#paup) - [pauvre](#pauvre) - [pbbam](#pbbam) - [pbcopper](#pbcopper) - [pbdagcon](#pbdagcon) - [pbipa](#pbipa) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [pdsh](#pdsh) - [PDT](#pdt) - [peakdetect](#peakdetect) - [PEAR](#pear) - [PennCNV](#penncnv) - [PEPT](#pept) - [Percolator](#percolator) - [Perl](#perl) - [perl-app-cpanminus](#perl-app-cpanminus) - [Perl-bundle-CPAN](#perl-bundle-cpan) - [Perl4-CoreLibs](#perl4-corelibs) - [Perseus](#perseus) - [PEST++](#pest++) - [PETSc](#petsc) - [petsc4py](#petsc4py) - [PfamScan](#pfamscan) - [pfind](#pfind) - [pftoolsV3](#pftoolsv3) - [pFUnit](#pfunit) - [PGDSpider](#pgdspider) - [PGI](#pgi) - [PGPLOT](#pgplot) - [PHANOTATE](#phanotate) - [Phantompeakqualtools](#phantompeakqualtools) - [PHASE](#phase) - [PHAST](#phast) - [Phenoflow](#phenoflow) - [PheWAS](#phewas) - [PheWeb](#pheweb) - [PhiPack](#phipack) - [PHLAT](#phlat) - [phonemizer](#phonemizer) - [phono3py](#phono3py) - [phonopy](#phonopy) - [photontorch](#photontorch) - [phototonic](#phototonic) - [PHYLIP](#phylip) - [PhyloBayes-MPI](#phylobayes-mpi) - [phylokit](#phylokit) - [phylonaut](#phylonaut) - [PhyloPhlAn](#phylophlan) - [PhyML](#phyml) - [phyx](#phyx) - [picard](#picard) - [PICI-LIGGGHTS](#pici-liggghts) - [PICRUSt2](#picrust2) - [pigz](#pigz) - [PIL](#pil) - [PileOMeth](#pileometh) - [Pillow](#pillow) - [Pillow-SIMD](#pillow-simd) - [Pilon](#pilon) - [PIMS](#pims) - [Pindel](#pindel) - [Pingouin](#pingouin) - [Pint](#pint) - [pip](#pip) - [PIPITS](#pipits) - [PIRATE](#pirate) - [pIRS](#pirs) - [Pisces](#pisces) - [piSvM](#pisvm) - [piSvM-JSC](#pisvm-jsc) - [pixman](#pixman) - [pizzly](#pizzly) - [pkg-config](#pkg-config) - [pkgconf](#pkgconf) - [pkgconfig](#pkgconfig) - [PLAMS](#plams) - [plantcv](#plantcv) - [PlaScope](#plascope) - [PlasmaPy](#plasmapy) - [PLAST](#plast) - [Platanus](#platanus) - [Platypus](#platypus) - [Platypus-Opt](#platypus-opt) - [plc](#plc) - [PLINK](#plink) - [plinkliftover](#plinkliftover) - [plinkQC](#plinkqc) - [PLINKSEQ](#plinkseq) - [plot1cell](#plot1cell) - [Ploticus](#ploticus) - [plotly](#plotly) - [plotly-orca](#plotly-orca) - [plotly.py](#plotly.py) - [PLplot](#plplot) - [PLUMED](#plumed) - [PLY](#ply) - [PMIx](#pmix) - [pmt](#pmt) - [pmx](#pmx) - [PnetCDF](#pnetcdf) - [pocl](#pocl) - [pod5-file-format](#pod5-file-format) - [poetry](#poetry) - [polars](#polars) - [polymake](#polymake) - [pomkl](#pomkl) - [pompi](#pompi) - [poppler](#poppler) - [popscle](#popscle) - [popt](#popt) - [Porechop](#porechop) - [porefoam](#porefoam) - [poretools](#poretools) - [Portcullis](#portcullis) - [PortMidi](#portmidi) - [Postgres-XL](#postgres-xl) - [PostgreSQL](#postgresql) - [POT](#pot) - [POV-Ray](#pov-ray) - [powerlaw](#powerlaw) - [pp-sketchlib](#pp-sketchlib) - [PPanGGOLiN](#ppanggolin) - [PPfold](#ppfold) - [ppl](#ppl) - [pplacer](#pplacer) - [pplpy](#pplpy) - [PRANK](#prank) - [PRC](#prc) - [preCICE](#precice) - [PREQUAL](#prequal) - [preseq](#preseq) - [presto](#presto) - [pretty-yaml](#pretty-yaml) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [prodigal](#prodigal) - [ProFit](#profit) - [PROJ](#proj) - [ProjectQ](#projectq) - [prokka](#prokka) - [prompt-toolkit](#prompt-toolkit) - [proovread](#proovread) - [propy](#propy) - [Proteinortho](#proteinortho) - [ProtHint](#prothint) - [protobuf](#protobuf) - [protobuf-python](#protobuf-python) - [protozero](#protozero) - [PRSice](#prsice) - [pscom](#pscom) - [PSI](#psi) - [PSI4](#psi4) - [PsiCLASS](#psiclass) - [PSIPRED](#psipred) - [psmc](#psmc) - [psmpi](#psmpi) - [psmpi2](#psmpi2) - [PSolver](#psolver) - [PSORTb](#psortb) - [psrecord](#psrecord) - [pstoedit](#pstoedit) - [psutil](#psutil) - [psycopg2](#psycopg2) - [ptemcee](#ptemcee) - [PTESFinder](#ptesfinder) - [pubtcrs](#pubtcrs) - [pugixml](#pugixml) - [pullseq](#pullseq) - [PuLP](#pulp) - [purge_dups](#purge_dups) - [pv](#pv) - [py](#py) - [py-aiger](#py-aiger) - [py-aiger-bdd](#py-aiger-bdd) - [py-c3d](#py-c3d) - [py-cpuinfo](#py-cpuinfo) - [py3Dmol](#py3dmol) - [pyABC](#pyabc) - [PyAMG](#pyamg) - [PyAPS3](#pyaps3) - [pybedtools](#pybedtools) - [PyBerny](#pyberny) - [pyBigWig](#pybigwig) - [pybind11](#pybind11) - [pybinding](#pybinding) - [PyBioLib](#pybiolib) - [PyCairo](#pycairo) - [PyCalib](#pycalib) - [pyccel](#pyccel) - [PyCharm](#pycharm) - [PyCheMPS2](#pychemps2) - [Pychopper](#pychopper) - [PyCifRW](#pycifrw) - [PyClone](#pyclone) - [pycma](#pycma) - [pycocotools](#pycocotools) - [pycodestyle](#pycodestyle) - [PyCogent](#pycogent) - [pycoQC](#pycoqc) - [PyCUDA](#pycuda) - [PycURL](#pycurl) - [PyDamage](#pydamage) - [pydantic](#pydantic) - [PyDatastream](#pydatastream) - [pydicom](#pydicom) - [pydicom-seg](#pydicom-seg) - [pydlpoly](#pydlpoly) - [pydot](#pydot) - [pyEGA3](#pyega3) - [pyenchant](#pyenchant) - [PyEVTK](#pyevtk) - [pyFAI](#pyfai) - [pyfaidx](#pyfaidx) - [pyfasta](#pyfasta) - [PyFFmpeg](#pyffmpeg) - [pyFFTW](#pyfftw) - [pyfits](#pyfits) - [PyFMI](#pyfmi) - [PyFoam](#pyfoam) - [PyFR](#pyfr) - [PyFrag](#pyfrag) - [pygame](#pygame) - [pygccxml](#pygccxml) - [pyGenomeTracks](#pygenometracks) - [PyGEOS](#pygeos) - [pyGIMLi](#pygimli) - [Pygments](#pygments) - [pygmo](#pygmo) - [PyGObject](#pygobject) - [pygraphviz](#pygraphviz) - [pygrib](#pygrib) - [PyGTK](#pygtk) - [PyGTS](#pygts) - [PyGWAS](#pygwas) - [pyhdf](#pyhdf) - [PyImageJ](#pyimagej) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC3](#pymc3) - [pymca](#pymca) - [pymemcache](#pymemcache) - [PyMOL](#pymol) - [PyNAST](#pynast) - [pyobjcryst](#pyobjcryst) - [PyOD](#pyod) - [pyodbc](#pyodbc) - [Pyomo](#pyomo) - [PyOpenCL](#pyopencl) - [PyOpenGL](#pyopengl) - [pyparsing](#pyparsing) - [pyperf](#pyperf) - [pyplusplus](#pyplusplus) - [pypmt](#pypmt) - [PYPOWER](#pypower) - [pyproj](#pyproj) - [PyPSA](#pypsa) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt5](#pyqt5) - [PyQtGraph](#pyqtgraph) - [pyradiomics](#pyradiomics) - [PyRe](#pyre) - [PyRETIS](#pyretis) - [pyringe](#pyringe) - [pyro-api](#pyro-api) - [pyro-ppl](#pyro-ppl) - [Pyro4](#pyro4) - [PyRosetta](#pyrosetta) - [Pysam](#pysam) - [pysamstats](#pysamstats) - [PySAT](#pysat) - [pyScaf](#pyscaf) - [pySCENIC](#pyscenic) - [PySCF](#pyscf) - [pysheds](#pysheds) - [pyshp](#pyshp) - [PySide2](#pyside2) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [pytesseract](#pytesseract) - [pytest](#pytest) - [pytest-benchmark](#pytest-benchmark) - [pytest-cpp](#pytest-cpp) - [pytest-flakefinder](#pytest-flakefinder) - [pytest-rerunfailures](#pytest-rerunfailures) - [pytest-shard](#pytest-shard) - [pytest-xdist](#pytest-xdist) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-docx](#python-docx) - [python-hl7](#python-hl7) - [python-igraph](#python-igraph) - [python-irodsclient](#python-irodsclient) - [python-isal](#python-isal) - [python-Levenshtein](#python-levenshtein) - [python-libsbml](#python-libsbml) - [python-louvain](#python-louvain) - [python-mujoco](#python-mujoco) - [python-parasail](#python-parasail) - [python-telegram-bot](#python-telegram-bot) - [python-weka-wrapper3](#python-weka-wrapper3) - [python-xxhash](#python-xxhash) - [pythran](#pythran) - [PyTorch](#pytorch) - [PyTorch-bundle](#pytorch-bundle) - [pytorch-CycleGAN-pix2pix](#pytorch-cyclegan-pix2pix) - [PyTorch-Geometric](#pytorch-geometric) - [PyTorch-Ignite](#pytorch-ignite) - [PyTorch-Image-Models](#pytorch-image-models) - [PyTorch-Lightning](#pytorch-lightning) - [PyTorch3D](#pytorch3d) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -25638,6 +26293,7 @@ version |toolchain ``1.48.8`` |``GCCcore/11.2.0`` ``1.50.7`` |``GCCcore/11.3.0`` ``1.50.12``|``GCCcore/12.2.0`` +``1.50.14``|``GCCcore/12.3.0`` ### pangolin @@ -25676,6 +26332,7 @@ version |toolchain ``6.0.0`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.0.0.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``7.0.0`` |``GCCcore/11.3.0`` +``7.0.1`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### parallel @@ -25684,7 +26341,7 @@ parallel: Build and execute shell commands in parallel *homepage*: version |toolchain -------------|------------------------------- +------------|-------------------------------------- ``20141122``|``GCC/4.9.2`` ``20150322``|``GCC/4.9.2`` ``20150822``|``GCC/4.9.2`` @@ -25704,6 +26361,7 @@ version |toolchain ``20210622``|``GCCcore/10.3.0`` ``20210722``|``GCCcore/11.2.0`` ``20220722``|``GCCcore/11.3.0`` +``20230722``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### parallel-fastq-dump @@ -25748,6 +26406,16 @@ version |toolchain ---------|------------------ ``0.8.1``|``GCCcore/10.3.0`` +### paramiko + +Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files. + +*homepage*: + +version |toolchain +---------|------------------ +``3.2.0``|``GCCcore/12.3.0`` + ### parasail parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. @@ -25790,6 +26458,7 @@ version |versionsuffix |toolchain ``5.1.2`` |``-mpi`` |``foss/2016b``, ``intel/2016b`` ``5.2.0`` |``-mpi`` |``foss/2016b``, ``intel/2017a`` ``5.3.0`` |``-mpi`` |``foss/2016b`` +``5.4.1`` |``-Python-2.7.16-mpi``|``foss/2019b`` ``5.4.1`` |``-mpi`` |``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` |``-Python-2.7.15-mpi``|``foss/2018b`` ``5.6.2`` |``-Python-3.7.4-mpi`` |``foss/2019b``, ``intel/2019b`` @@ -25852,6 +26521,16 @@ version|toolchain -------|---------------------------------------------------------------------------------------------------------------------- ``1.0``|``gimkl/2.11.5``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2017a`` +### Parsl + +Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python's parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available. + +*homepage*: + +version |toolchain +-------------|------------------ +``2023.7.17``|``GCCcore/11.3.0`` + ### PartitionFinder PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. @@ -25861,6 +26540,7 @@ PartitionFinder 2 is a Python program for simultaneously choosing partitioning s version |versionsuffix |toolchain ---------|------------------|--------------- ``2.1.1``|``-Python-2.7.16``|``intel/2019b`` +``2.1.1``|``-Python-2.7.18``|``foss/2020b`` ### pasta @@ -25916,6 +26596,7 @@ version |toolchain ``0.12`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``0.13`` |``GCCcore/11.2.0`` ``0.15.0``|``GCCcore/11.3.0`` +``0.17.2``|``GCCcore/12.2.0`` ``0.18.0``|``GCCcore/12.3.0`` ### path.py @@ -26126,8 +26807,8 @@ A high performance, parallel remote shell utility *homepage*: version |toolchain ---------|-------------------------------------- -``2.34``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +--------|---------------------------------------------------------- +``2.34``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PDT @@ -26136,10 +26817,20 @@ Program Database Toolkit (PDT) is a framework for analyzing source code written *homepage*: version |toolchain -----------|----------------------------------------------------------------------------- +----------|--------------------------------------------------------------------------------------------------------------------- ``3.22`` |``foss/2016a`` ``3.25`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.25.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``3.25.1``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` + +### peakdetect + +Simple peak detection library for Python based on Billauer's work and this gist. + +*homepage*: + +version|toolchain +-------|-------------- +``1.2``|``foss/2022a`` ### PEAR @@ -26221,6 +26912,7 @@ version |versionsuffix|toolchain ``5.36.0``| |``GCCcore/12.1.0``, ``GCCcore/12.2.0`` ``5.36.0``|``-minimal`` |``GCCcore/12.2.0`` ``5.36.1``| |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``5.38.0``| |``GCCcore/13.2.0`` ### perl-app-cpanminus @@ -26350,6 +27042,7 @@ version |toolchain ---------|--------------- ``3.2.9``|``gompi/2018b`` ``4.2.0``|``gompi/2020b`` +``4.7.3``|``gompi/2022a`` ### PGDSpider @@ -26676,6 +27369,16 @@ version |toolchain ---------|-------------- ``3.8.1``|``foss/2022a`` +### PICRUSt2 + +PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.2``|``foss/2022b`` + ### pigz pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. @@ -26720,36 +27423,37 @@ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Py *homepage*: -version |versionsuffix |toolchain ----------|---------------------------------|--------------------------------------------------- -``3.2.0``|``-Python-2.7.11`` |``intel/2016a`` -``3.2.0``|``-Python-2.7.11-freetype-2.6.3``|``foss/2016a``, ``intel/2016a`` -``3.4.2``|``-Python-2.7.12`` |``intel/2016b`` -``3.4.2``|``-Python-3.5.2`` |``foss/2016b``, ``intel/2016b`` -``3.4.2``|``-Python-3.5.2-freetype-2.6.5`` |``intel/2016b`` -``4.1.0``|``-Python-2.7.13`` |``intel/2017a`` -``4.1.1``|``-Python-3.6.1`` |``intel/2017a`` -``4.2.1``|``-Python-3.6.1`` |``intel/2017a`` -``4.3.0``|``-Python-2.7.13`` |``intel/2017a`` -``4.3.0``|``-Python-2.7.14`` |``intel/2017b`` -``4.3.0``|``-Python-3.6.3`` |``foss/2017b`` -``5.0.0``|``-Python-2.7.14`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.0.0``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` -``5.0.0``|``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` -``5.3.0``|``-Python-2.7.15`` |``foss/2018b`` -``5.3.0``|``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``6.0.0``| |``GCCcore/8.2.0`` -``6.2.1``| |``GCCcore/8.3.0`` -``6.2.2``|``-Python-2.7.18`` |``foss/2020b`` -``7.0.0``|``-Python-3.8.2`` |``GCCcore/9.3.0`` -``8.0.1``| |``GCCcore/10.2.0`` -``8.2.0``| |``GCCcore/10.3.0`` -``8.3.1``| |``GCCcore/11.2.0`` -``8.3.2``| |``GCCcore/11.2.0`` -``9.1.0``| |``GCCcore/10.3.0`` -``9.1.1``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``9.2.0``| |``GCCcore/10.2.0`` -``9.4.0``| |``GCCcore/12.2.0`` +version |versionsuffix |toolchain +----------|---------------------------------|--------------------------------------------------- +``3.2.0`` |``-Python-2.7.11`` |``intel/2016a`` +``3.2.0`` |``-Python-2.7.11-freetype-2.6.3``|``foss/2016a``, ``intel/2016a`` +``3.4.2`` |``-Python-2.7.12`` |``intel/2016b`` +``3.4.2`` |``-Python-3.5.2`` |``foss/2016b``, ``intel/2016b`` +``3.4.2`` |``-Python-3.5.2-freetype-2.6.5`` |``intel/2016b`` +``4.1.0`` |``-Python-2.7.13`` |``intel/2017a`` +``4.1.1`` |``-Python-3.6.1`` |``intel/2017a`` +``4.2.1`` |``-Python-3.6.1`` |``intel/2017a`` +``4.3.0`` |``-Python-2.7.13`` |``intel/2017a`` +``4.3.0`` |``-Python-2.7.14`` |``intel/2017b`` +``4.3.0`` |``-Python-3.6.3`` |``foss/2017b`` +``5.0.0`` |``-Python-2.7.14`` |``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.0.0`` |``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` +``5.0.0`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` +``5.3.0`` |``-Python-2.7.15`` |``foss/2018b`` +``5.3.0`` |``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``6.0.0`` | |``GCCcore/8.2.0`` +``6.2.1`` | |``GCCcore/8.3.0`` +``6.2.2`` |``-Python-2.7.18`` |``foss/2020b`` +``7.0.0`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` +``8.0.1`` | |``GCCcore/10.2.0`` +``8.2.0`` | |``GCCcore/10.3.0`` +``8.3.1`` | |``GCCcore/11.2.0`` +``8.3.2`` | |``GCCcore/11.2.0`` +``9.1.0`` | |``GCCcore/10.3.0`` +``9.1.1`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``9.2.0`` | |``GCCcore/10.2.0`` +``9.4.0`` | |``GCCcore/12.2.0`` +``10.0.0``| |``GCCcore/12.3.0`` ### Pillow-SIMD @@ -26768,6 +27472,7 @@ version |versionsuffix |toolchain ``8.3.1`` | |``GCCcore/11.2.0`` ``8.3.2`` | |``GCCcore/11.2.0`` ``9.2.0`` | |``GCCcore/11.3.0`` +``9.5.0`` | |``GCCcore/12.3.0`` ### Pilon @@ -26824,6 +27529,7 @@ version |versionsuffix |toolchain ``0.14`` |``-Python-3.7.4``|``GCCcore/8.3.0`` ``0.19.2``| |``GCCcore/11.2.0`` ``0.20.1``| |``GCCcore/10.3.0`` +``0.22`` | |``GCCcore/11.3.0`` ### pip @@ -26911,7 +27617,7 @@ version |toolchain ``0.38.0``|``GCCcore/8.2.0`` ``0.38.4``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.40.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``0.42.2``|``GCCcore/12.2.0`` +``0.42.2``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### pizzly @@ -26948,6 +27654,7 @@ version |toolchain ``1.9.3``|``GCCcore/12.2.0`` ``1.9.4``|``GCCcore/13.1.0`` ``1.9.5``|``GCCcore/12.3.0`` +``2.0.3``|``GCCcore/13.2.0`` ### pkgconfig @@ -26956,7 +27663,7 @@ pkgconfig is a Python module to interface with the pkg-config command line tool *homepage*: version |versionsuffix |toolchain ----------|------------------|---------------------------------------------------------- +---------|------------------|------------------------------------------------------------------------------ ``1.1.0``|``-Python-2.7.11``|``foss/2016a``, ``intel/2016a`` ``1.1.0``|``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` ``1.1.0``|``-Python-3.5.1`` |``foss/2016a`` @@ -26973,7 +27680,7 @@ version |versionsuffix |toolchain ``1.5.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``1.5.1``|``-python`` |``GCCcore/10.2.0``, ``GCCcore/8.2.0`` ``1.5.4``|``-python`` |``GCCcore/10.3.0`` -``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PLAMS @@ -27046,6 +27753,16 @@ version |versionsuffix |toolchain ---------|------------------|--------------- ``0.8.1``|``-Python-2.7.11``|``intel/2016a`` +### Platypus-Opt + +Platypus is a framework for evolutionary computing in Python with a focus on multiobjective evolutionary algorithms (MOEAs). + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2022a`` + ### plc plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). @@ -27168,6 +27885,7 @@ version |toolchain ``5.4.0`` |``GCCcore/11.2.0`` ``5.12.0``|``GCCcore/11.3.0`` ``5.13.1``|``GCCcore/12.2.0`` +``5.16.0``|``GCCcore/12.3.0`` ### PLplot @@ -27211,6 +27929,7 @@ version |versionsuffix |toolchain ``2.7.3``| |``foss/2021b`` ``2.8.0``| |``foss/2021b`` ``2.8.1``| |``foss/2022a`` +``2.9.0``| |``foss/2022b`` ### PLY @@ -27219,7 +27938,8 @@ PLY is yet another implementation of lex and yacc for Python. *homepage*: version |versionsuffix |toolchain ---------|-----------------|----------------- +--------|-----------------|------------------ +``3.11``| |``GCCcore/12.2.0`` ``3.11``|``-Python-3.6.4``|``foss/2018a`` ``3.11``|``-Python-3.7.4``|``GCCcore/8.3.0`` @@ -27279,11 +27999,11 @@ version |toolchain ``1.10.0``|``foss/2018b``, ``intel/2018b`` ``1.12.1``|``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` ``1.12.2``|``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` -``1.12.3``|``gompi/2021b``, ``gompi/2022a``, ``iimpi/2022a`` +``1.12.3``|``gompi/2021b``, ``gompi/2022a``, ``gompi/2023a``, ``iimpi/2022a`` ### pocl -Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard +PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported). *homepage*: @@ -27295,6 +28015,7 @@ version|toolchain ``1.5``|``GCC/9.3.0`` ``1.6``|``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` ``1.8``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``4.0``|``GCC/12.3.0`` ### pod5-file-format @@ -27316,6 +28037,7 @@ version |versionsuffix |toolchain ---------|-----------------|------------------ ``1.0.9``|``-Python-3.8.2``|``GCCcore/9.3.0`` ``1.2.2``| |``GCCcore/11.3.0`` +``1.5.1``| |``GCCcore/12.3.0`` ### polars @@ -27441,6 +28163,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``1.2.2``|``-Python-3.7.4``|``foss/2019b`` +### PortMidi + +PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA). + +*homepage*: + +version |toolchain +---------|------------------ +``2.0.4``|``GCCcore/11.3.0`` + ### Postgres-XL Postgres-XL is a horizontally scalable open source SQL database cluster, flexible enough to handle varying database workloads: @@ -27736,6 +28468,7 @@ version |toolchain ``5.0.0``|``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``6.0.0``|``GCCcore/8.2.0`` ``6.2.1``|``GCCcore/8.3.0`` +``6.3.1``|``GCCcore/10.3.0`` ``7.0.0``|``GCCcore/9.3.0`` ``7.2.1``|``GCCcore/10.2.0`` ``8.0.1``|``GCCcore/10.3.0`` @@ -27761,12 +28494,12 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: version |versionsuffix |toolchain -----------|------------------|---------------------------------------------------------------------------------------------------- +----------|------------------|--------------------------------------------------------------------------------------------------------------------- ``1.11`` |``-BioPerl-1.7.0``|``foss/2016b`` ``1.13`` |``-BioPerl-1.7.2``|``intel/2018a`` ``1.13.4``| |``foss/2018b`` ``1.13.7``| |``gompi/2019a`` -``1.14.5``| |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``1.14.5``| |``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b`` ### prompt-toolkit @@ -27850,6 +28583,7 @@ version |toolchain ``3.19.4`` |``GCCcore/11.3.0`` ``3.21.9`` |``GCCcore/10.3.0`` ``23.0`` |``GCCcore/12.2.0`` +``24.0`` |``GCCcore/12.3.0`` ### protobuf-python @@ -27878,6 +28612,7 @@ version |versionsuffix |toolchain ``3.17.3``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.19.4``| |``GCCcore/11.3.0`` ``4.23.0``| |``GCCcore/12.2.0`` +``4.24.0``| |``GCCcore/12.3.0`` ### protozero @@ -28055,6 +28790,7 @@ version |versionsuffix |toolchain ``5.6.3``| |``GCCcore/8.2.0`` ``5.9.3``| |``GCCcore/10.2.0``, ``GCCcore/11.3.0`` ``5.9.4``| |``GCCcore/11.2.0`` +``5.9.5``| |``GCCcore/12.2.0`` ### psycopg2 @@ -28130,6 +28866,7 @@ PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and c version |toolchain ---------|-------------- ``2.5.1``|``foss/2021a`` +``2.7.0``|``foss/2022b`` ### purge_dups @@ -28141,6 +28878,16 @@ version |toolchain ---------|-------------- ``1.2.5``|``foss/2021b`` +### pv + +Pipe Viewer - monitor the progress of data through a pipe + +*homepage*: + +version |toolchain +----------|------------------ +``1.7.24``|``GCCcore/12.3.0`` + ### py library with cross-python path, ini-parsing, io, code, log facilities @@ -28173,6 +28920,16 @@ version |versionsuffix |toolchain ---------|-----------------|-------------- ``3.0.0``|``-Python-3.8.2``|``foss/2020a`` +### py-c3d + +This is a small library for reading and writing C3D binary files. C3D files are a standard format for recording 3-dimensional time sequence data, especially data recorded by a 3D motion tracking apparatus. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.2``|``foss/2022a`` + ### py-cpuinfo py-cpuinfo gets CPU info with pure Python. @@ -28241,7 +28998,7 @@ version |versionsuffix |toolchain ``0.8.1`` | |``foss/2019b`` ``0.8.2`` | |``GCC/10.2.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` ``0.8.2`` |``-Python-2.7.18``|``GCC/10.2.0`` -``0.9.0`` | |``GCC/11.3.0`` +``0.9.0`` | |``GCC/11.3.0``, ``GCC/12.2.0`` ### PyBerny @@ -28265,6 +29022,7 @@ version |versionsuffix |toolchain ``0.3.13``|``-Python-3.6.6``|``foss/2018b`` ``0.3.17``| |``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ``0.3.18``| |``GCCcore/10.2.0``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``0.3.22``| |``foss/2022b`` ### pybind11 @@ -28284,6 +29042,7 @@ version |versionsuffix |toolchain ``2.7.1`` |``-Python-2.7.18``|``GCCcore/11.2.0`` ``2.9.2`` | |``GCCcore/11.3.0`` ``2.10.3``| |``GCCcore/12.2.0`` +``2.11.1``| |``GCCcore/12.3.0`` ### pybinding @@ -28324,6 +29083,7 @@ version |versionsuffix |toolchain ``1.20.0``| |``GCCcore/10.2.0`` ``1.20.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.21.0``| |``GCCcore/11.3.0`` +``1.24.0``| |``GCCcore/12.2.0`` ### PyCalib @@ -28478,9 +29238,9 @@ PycURL is a Python interface to libcurl. PycURL can be used to fetch objects ide *homepage*: version |versionsuffix |toolchain -------------|-----------------|------------------ +------------|-----------------|---------------------------------------------------------- ``7.43.0.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` -``7.45.2`` | |``GCCcore/11.3.0`` +``7.45.2`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### PyDamage @@ -28708,6 +29468,16 @@ version |versionsuffix|toolchain -----------------|-------------|--------------- ``2019-20220216``|``-ASA`` |``intel/2020b`` +### pygame + +Pygame is a set of Python modules designed for writing video games. Pygame adds functionality on top of the excellent SDL library. This allows you to create fully featured games and multimedia programs in the python language. + +*homepage*: + +version |toolchain +---------|------------------ +``2.1.0``|``GCCcore/11.3.0`` + ### pygccxml Python package for easy C++ declarations navigation. @@ -28792,6 +29562,7 @@ version |versionsuffix |toolchain ``3.34.0``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``3.34.0``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``3.42.1``| |``GCCcore/11.3.0`` +``3.44.1``| |``GCCcore/12.2.0`` ### pygraphviz @@ -28912,12 +29683,13 @@ Pylint is a tool that checks for errors in Python code, tries to enforce a codi *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------------------------ -``1.9.3``|``-Python-2.7.15``|``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.5``|``-Python-2.7.15``|``GCCcore/8.2.0`` -``1.9.5``|``-Python-2.7.16``|``GCCcore/8.3.0`` -``2.7.4``| |``GCCcore/10.2.0`` +version |versionsuffix |toolchain +----------|------------------|------------------------------------------------ +``1.9.3`` |``-Python-2.7.15``|``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.5`` |``-Python-2.7.15``|``GCCcore/8.2.0`` +``1.9.5`` |``-Python-2.7.16``|``GCCcore/8.3.0`` +``2.7.4`` | |``GCCcore/10.2.0`` +``2.17.4``| |``GCCcore/12.2.0`` ### pyMannKendall @@ -29042,6 +29814,16 @@ version |toolchain ---------|------------------------------- ``0.8.7``|``foss/2020b``, ``intel/2020b`` +### pyodbc + +pyodbc is an open source Python module that makes accessing ODBC databases simple. It implements the DB API 2.0 specification but is packed with even more Pythonic convenience. + +*homepage*: + +version |toolchain +----------|-------------- +``4.0.39``|``foss/2022b`` + ### Pyomo Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. @@ -29126,8 +29908,8 @@ PMT is a high-level software library capable of collecting power consumptio *homepage*: version |toolchain ----------|-------------- -``1.1.0``|``foss/2022a`` +---------|------------------------------ +``1.1.0``|``foss/2022a``, ``gfbf/2023a`` ### PYPOWER @@ -29155,6 +29937,7 @@ version |versionsuffix |toolchain ``3.3.1`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``3.4.0`` | |``GCCcore/11.3.0`` ``3.5.0`` | |``GCCcore/12.2.0`` +``3.6.0`` | |``GCCcore/12.3.0`` ### PyPSA @@ -29292,6 +30075,7 @@ Pyro is a flexible, scalable deep probabilistic programming library built on PyT version |toolchain ---------|------------------ ``1.5.2``|``fosscuda/2020b`` +``1.8.4``|``foss/2022a`` ### Pyro4 @@ -29675,7 +30459,7 @@ version |versionsuffix |toolchain ``2.7.15``|``-bare`` |``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.7.16``| |``GCCcore/8.3.0`` ``2.7.16``|``-bare`` |``GCCcore/8.3.0`` -``2.7.18``| |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.7.18``| |``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ``2.7.18``|``-bare`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` ``3.5.1`` | |``foss/2016a``, ``intel/2016a`` ``3.5.2`` | |``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` @@ -29711,6 +30495,16 @@ version |toolchain ----------|-------------- ``3.10.4``|``foss/2022a`` +### Python-bundle-PyPI + +Bundle of Python packages from PyPI + +*homepage*: + +version |toolchain +-----------|------------------ +``2023.06``|``GCCcore/12.3.0`` + ### python-docx python-docx is a Python library for creating and updating Microsoft Word (.docx) files @@ -29746,6 +30540,7 @@ version |versionsuffix |toolchain ``0.9.6`` | |``foss/2021a`` ``0.9.8`` | |``foss/2021b`` ``0.10.3`` | |``foss/2022a`` +``0.10.6`` | |``foss/2022b`` ### python-irodsclient @@ -30090,11 +30885,12 @@ version |versionsuffix |toolchain ``18.1.1``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``22.3.0``| |``GCCcore/10.3.0`` ``24.0.1``| |``GCCcore/11.3.0`` +``25.1.1``| |``GCCcore/12.3.0`` ## Q -[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) +[Q6](#q6) - [QCA](#qca) - [qcat](#qcat) - [QCG-PilotJob](#qcg-pilotjob) - [qcint](#qcint) - [QCxMS](#qcxms) - [QD](#qd) - [QDD](#qdd) - [QEMU](#qemu) - [qforce](#qforce) - [QGIS](#qgis) - [Qhull](#qhull) - [QIIME](#qiime) - [QIIME2](#qiime2) - [Qiskit](#qiskit) - [QJson](#qjson) - [QML](#qml) - [qnorm](#qnorm) - [qpth](#qpth) - [qrupdate](#qrupdate) - [QScintilla](#qscintilla) - [Qt](#qt) - [Qt5](#qt5) - [Qt5Webkit](#qt5webkit) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) ### Q6 @@ -30193,6 +30989,16 @@ version |toolchain ----------|--------------- ``2.10.1``|``intel/2017b`` +### qforce + +Quantum Mechanically augmented molecular force fields. Q-Force is a software package for deriving all-atom force fields from quantum mechanical calculations in an automated manner. + +*homepage*: + +version |toolchain +----------|-------------- +``0.6.11``|``foss/2022a`` + ### QGIS QGIS is a user friendly Open Source Geographic Information System (GIS) @@ -30216,7 +31022,7 @@ version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2015.2``|``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2019.1``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2020.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``2020.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### QIIME @@ -30230,21 +31036,22 @@ version |toolchain ### QIIME2 -QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. +QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, open source, and community developed. -*homepage*: +*homepage*: -version |toolchain ------------|---------- -``2017.10``|``system`` -``2018.2`` |``system`` -``2019.4`` |``system`` -``2019.7`` |``system`` -``2020.8`` |``system`` -``2020.11``|``system`` -``2021.8`` |``system`` -``2022.8`` |``system`` -``2022.11``|``system`` +version |toolchain +------------|-------------- +``2017.10`` |``system`` +``2018.2`` |``system`` +``2019.4`` |``system`` +``2019.7`` |``system`` +``2020.8`` |``system`` +``2020.11`` |``system`` +``2021.8`` |``system`` +``2022.8`` |``system`` +``2022.11`` |``system`` +``2023.5.1``|``foss/2022a`` ### Qiskit @@ -30340,23 +31147,24 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: -version |toolchain -----------|------------------------------------------------------------------------------------ -``5.6.0`` |``foss/2016a``, ``intel/2016a`` -``5.7.0`` |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.7.1`` |``intel/2016b`` -``5.8.0`` |``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``5.9.3`` |``foss/2017b`` -``5.9.8`` |``fosscuda/2018b`` -``5.10.1``|``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``5.11.2``|``foss/2018b`` -``5.12.3``|``GCCcore/8.2.0`` -``5.13.1``|``GCCcore/8.3.0`` -``5.14.1``|``GCCcore/9.3.0`` -``5.14.2``|``GCCcore/10.2.0`` -``5.15.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.15.5``|``GCCcore/11.3.0`` -``5.15.7``|``GCCcore/12.2.0`` +version |toolchain +-----------|------------------------------------------------------------------------------------ +``5.6.0`` |``foss/2016a``, ``intel/2016a`` +``5.7.0`` |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``5.7.1`` |``intel/2016b`` +``5.8.0`` |``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``5.9.3`` |``foss/2017b`` +``5.9.8`` |``fosscuda/2018b`` +``5.10.1`` |``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` +``5.11.2`` |``foss/2018b`` +``5.12.3`` |``GCCcore/8.2.0`` +``5.13.1`` |``GCCcore/8.3.0`` +``5.14.1`` |``GCCcore/9.3.0`` +``5.14.2`` |``GCCcore/10.2.0`` +``5.15.2`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.15.5`` |``GCCcore/11.3.0`` +``5.15.7`` |``GCCcore/12.2.0`` +``5.15.10``|``GCCcore/12.3.0`` ### Qt5Webkit @@ -30474,6 +31282,7 @@ version |versionsuffix|toolchain ``6.8`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``7.0`` | |``foss/2021b``, ``intel/2021b`` ``7.1`` | |``foss/2022a``, ``intel/2022a`` +``7.2`` | |``foss/2022b``, ``intel/2022b`` ### QUAST @@ -30584,7 +31393,7 @@ version |toolchain ## R -[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [Rust](#rust) - [rustworkx](#rustworkx) +[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-INLA](#r-inla) - [R-keras](#r-keras) - [R-MXM](#r-mxm) - [R-opencv](#r-opencv) - [R-tesseract](#r-tesseract) - [R-transport](#r-transport) - [R2jags](#r2jags) - [Racon](#racon) - [radeontop](#radeontop) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Rascaf](#rascaf) - [RASPA2](#raspa2) - [rasterio](#rasterio) - [rasterstats](#rasterstats) - [Ratatosk](#ratatosk) - [Raven](#raven) - [RAxML](#raxml) - [RAxML-NG](#raxml-ng) - [Ray-assembler](#ray-assembler) - [Ray-project](#ray-project) - [Raysect](#raysect) - [RBFOpt](#rbfopt) - [rclone](#rclone) - [Rcorrector](#rcorrector) - [RcppGSL](#rcppgsl) - [rCUDA](#rcuda) - [RDFlib](#rdflib) - [RDKit](#rdkit) - [RDP-Classifier](#rdp-classifier) - [RE2](#re2) - [re2c](#re2c) - [Reads2snp](#reads2snp) - [Reapr](#reapr) - [ReaxFF](#reaxff) - [RECON](#recon) - [Red](#red) - [Redis](#redis) - [redis-py](#redis-py) - [Redundans](#redundans) - [ReFrame](#reframe) - [regionmask](#regionmask) - [RegTools](#regtools) - [Relate](#relate) - [RELION](#relion) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [resolos](#resolos) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [RFdiffusion](#rfdiffusion) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RheoTool](#rheotool) - [Rhodium](#rhodium) - [rickflow](#rickflow) - [RInChI](#rinchi) - [rioxarray](#rioxarray) - [ripunzip](#ripunzip) - [rising](#rising) - [Rivet](#rivet) - [rjags](#rjags) - [RLCard](#rlcard) - [rmarkdown](#rmarkdown) - [Rmath](#rmath) - [rMATS-turbo](#rmats-turbo) - [RMBlast](#rmblast) - [RNA-Bloom](#rna-bloom) - [RNA-SeQC](#rna-seqc) - [RNAclust](#rnaclust) - [RNAcode](#rnacode) - [RNAIndel](#rnaindel) - [RNAmmer](#rnammer) - [rnaQUAST](#rnaquast) - [RNAz](#rnaz) - [RnBeads](#rnbeads) - [Roary](#roary) - [ROCm](#rocm) - [rocm-cmake](#rocm-cmake) - [ROCm-CompilerSupport](#rocm-compilersupport) - [rocm-smi](#rocm-smi) - [rocminfo](#rocminfo) - [ROCR-Runtime](#rocr-runtime) - [ROCT-Thunk-Interface](#roct-thunk-interface) - [ROI_PAC](#roi_pac) - [ROME](#rome) - [ROOT](#root) - [root_numpy](#root_numpy) - [rootpy](#rootpy) - [Rosetta](#rosetta) - [rpmrebuild](#rpmrebuild) - [RPostgreSQL](#rpostgresql) - [rpy2](#rpy2) - [RQGIS3](#rqgis3) - [RSEM](#rsem) - [RSeQC](#rseqc) - [RStan](#rstan) - [rstanarm](#rstanarm) - [RStudio-Server](#rstudio-server) - [RTG-Tools](#rtg-tools) - [Rtree](#rtree) - [ruamel.yaml](#ruamel.yaml) - [Ruby](#ruby) - [Ruby-Tk](#ruby-tk) - [ruffus](#ruffus) - [ruptures](#ruptures) - [Rust](#rust) - [rustworkx](#rustworkx) ### R @@ -30736,7 +31545,7 @@ version |toolchain ``1.4.10``|``GCC/7.3.0-2.30`` ``1.4.13``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.21``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.5.0`` |``GCCcore/11.2.0`` +``1.5.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ### radeontop @@ -31006,7 +31815,7 @@ version |versionsuffix |toolchain Rclone is a command line program to sync files and directories to and from a variety of online storage services -*homepage*: +*homepage*: version |versionsuffix|toolchain ----------|-------------|---------- @@ -31014,6 +31823,7 @@ version |versionsuffix|toolchain ``1.54.1``|``-amd64`` |``system`` ``1.56.0``|``-amd64`` |``system`` ``1.57.0``| |``system`` +``1.63.1``|``-amd64`` |``system`` ### Rcorrector @@ -31100,6 +31910,7 @@ version |toolchain ``2022-02-01``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2022-06-01``|``GCCcore/11.3.0`` ``2023-03-01``|``GCCcore/12.2.0`` +``2023-08-01``|``GCCcore/12.3.0`` ### re2c @@ -31116,6 +31927,7 @@ version |toolchain ``2.1.1``|``GCCcore/10.3.0`` ``2.2`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``3.0`` |``GCCcore/12.2.0`` +``3.1`` |``GCCcore/12.3.0`` ### Reads2snp @@ -31256,6 +32068,7 @@ version |toolchain ---------|------------------------------ ``0.4.2``|``foss/2020b`` ``0.5.2``|``foss/2020b``, ``foss/2021b`` +``1.0.0``|``foss/2022b`` ### Relate @@ -31425,6 +32238,16 @@ version |toolchain ``1.1.1``|``GCC/10.2.0``, ``GCC/11.2.0`` ``1.2.1``|``gompi/2022a`` +### RFdiffusion + +RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.0``|``foss/2022a`` + ### rgdal Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. @@ -31487,6 +32310,16 @@ version|toolchain -------|-------------- ``5.0``|``foss/2019b`` +### Rhodium + +Rhodium is an open source Python library for robust decision making (RDM) and multiobjective robust decision making (MORDM), and exploratory modelling (EM). + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.0``|``foss/2022a`` + ### rickflow Running and Analyzing OpenMM Jobs @@ -31574,6 +32407,7 @@ version |versionsuffix|toolchain ``4-10``|``-R-4.1.0`` |``foss/2021a`` ``4-12``|``-R-4.1.2`` |``foss/2021b`` ``4-13``|``-R-4.2.1`` |``foss/2022a`` +``4-13``|``-R-4.2.2`` |``foss/2022b`` ### RLCard @@ -31724,9 +32558,10 @@ RnBeads is an R package for comprehensive analysis of DNA methylation data obtai *homepage*: -version |versionsuffix|toolchain ----------|-------------|-------------- -``2.6.0``|``-R-4.0.0`` |``foss/2020a`` +version |versionsuffix|toolchain +----------|-------------|-------------- +``2.6.0`` |``-R-4.0.0`` |``foss/2020a`` +``2.14.0``|``-R-4.2.1`` |``foss/2022a`` ### Roary @@ -32001,9 +32836,10 @@ RTG Tools contains utilities to easily manipulate and accurately compare multipl *homepage*: -version |versionsuffix|toolchain ----------|-------------|---------- -``3.9.1``|``-Java-1.8``|``system`` +version |versionsuffix|toolchain +----------|-------------|---------- +``3.9.1`` |``-Java-1.8``|``system`` +``3.12.1``|``-Java-11`` |``system`` ### Rtree @@ -32070,6 +32906,16 @@ version |toolchain ---------|---------------------------------- ``2.8.4``|``GCCcore/11.3.0``, ``foss/2021b`` +### ruptures + +ruptures is a Python library for off-line change point detection. This package provides methods for the analysis and segmentation of non-stationary signals. Implemented algorithms include exact and approximate detection for various parametric and non-parametric models. ruptures focuses on ease of use by providing a well-documented and consistent interface. In addition, thanks to its modular structure, different algorithms and models can be connected and extended within this package. + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.8``|``foss/2022a`` + ### Rust Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. @@ -32109,7 +32955,7 @@ version |toolchain ## S -[S-Lang](#s-lang) - [S4](#s4) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [S4](#s4) - [Sabre](#sabre) - [Safetensors](#safetensors) - [SAGE](#sage) - [Sailfish](#sailfish) - [SALib](#salib) - [Salmon](#salmon) - [SALMON-TDDFT](#salmon-tddft) - [Sambamba](#sambamba) - [samblaster](#samblaster) - [Samcef](#samcef) - [samclip](#samclip) - [samplot](#samplot) - [SAMtools](#samtools) - [sansa](#sansa) - [SAP](#sap) - [SAS](#sas) - [Satsuma2](#satsuma2) - [savvy](#savvy) - [Saxon-HE](#saxon-he) - [SBCL](#sbcl) - [sbt](#sbt) - [ScaFaCoS](#scafacos) - [ScaLAPACK](#scalapack) - [Scalasca](#scalasca) - [SCALCE](#scalce) - [Scalene](#scalene) - [scanpy](#scanpy) - [scArches](#scarches) - [sceasy](#sceasy) - [SCENIC](#scenic) - [scGeneFit](#scgenefit) - [SCGid](#scgid) - [scGSVA](#scgsva) - [scHiCExplorer](#schicexplorer) - [Schrodinger](#schrodinger) - [scib](#scib) - [scib-metrics](#scib-metrics) - [sciClone](#sciclone) - [ScientificPython](#scientificpython) - [scikit-allel](#scikit-allel) - [scikit-bio](#scikit-bio) - [scikit-build](#scikit-build) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-misc](#scikit-misc) - [scikit-multilearn](#scikit-multilearn) - [scikit-optimize](#scikit-optimize) - [scikit-plot](#scikit-plot) - [scikit-uplift](#scikit-uplift) - [SCIP](#scip) - [SCIPhI](#sciphi) - [scipy](#scipy) - [SciPy-bundle](#scipy-bundle) - [SCnorm](#scnorm) - [Scoary](#scoary) - [SCons](#scons) - [SCOOP](#scoop) - [SCopeLoomR](#scopeloomr) - [Score-P](#score-p) - [SCOTCH](#scotch) - [scp](#scp) - [scPred](#scpred) - [Scrappie](#scrappie) - [scVelo](#scvelo) - [scvi-tools](#scvi-tools) - [Scythe](#scythe) - [SDCC](#sdcc) - [SDL](#sdl) - [SDL2](#sdl2) - [SDL2_image](#sdl2_image) - [SDL2_mixer](#sdl2_mixer) - [SDL2_ttf](#sdl2_ttf) - [SDL_image](#sdl_image) - [SDSL](#sdsl) - [Seaborn](#seaborn) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SentencePiece](#sentencepiece) - [sentinelsat](#sentinelsat) - [sep](#sep) - [SEPP](#sepp) - [Seq-Gen](#seq-gen) - [seq2HLA](#seq2hla) - [SeqAn](#seqan) - [SeqAn3](#seqan3) - [SeqKit](#seqkit) - [SeqLib](#seqlib) - [Seqmagick](#seqmagick) - [SeqPrep](#seqprep) - [seqtk](#seqtk) - [Serf](#serf) - [setuptools](#setuptools) - [setuptools-rust](#setuptools-rust) - [Seurat](#seurat) - [SeuratData](#seuratdata) - [SeuratDisk](#seuratdisk) - [SeuratWrappers](#seuratwrappers) - [sf](#sf) - [sfftk](#sfftk) - [Shannon](#shannon) - [SHAP](#shap) - [shapAAR](#shapaar) - [SHAPEIT](#shapeit) - [SHAPEIT4](#shapeit4) - [Shapely](#shapely) - [sharutils](#sharutils) - [Shasta](#shasta) - [ShengBTE](#shengbte) - [shift](#shift) - [SHORE](#shore) - [Short-Pair](#short-pair) - [shovill](#shovill) - [shrinkwrap](#shrinkwrap) - [SHTns](#shtns) - [Sibelia](#sibelia) - [SICER2](#sicer2) - [sickle](#sickle) - [Siesta](#siesta) - [SignalP](#signalp) - [silhouetteRank](#silhouetterank) - [silx](#silx) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [SiNVICT](#sinvict) - [SIONlib](#sionlib) - [SIP](#sip) - [siscone](#siscone) - [SISSO](#sisso) - [SISSO++](#sisso++) - [SKESA](#skesa) - [sketchmap](#sketchmap) - [skewer](#skewer) - [sklearn-pandas](#sklearn-pandas) - [sklearn-som](#sklearn-som) - [skorch](#skorch) - [SlamDunk](#slamdunk) - [SLATEC](#slatec) - [SLEPc](#slepc) - [slepc4py](#slepc4py) - [sleuth](#sleuth) - [slidingwindow](#slidingwindow) - [SLiM](#slim) - [slow5tools](#slow5tools) - [slurm-drmaa](#slurm-drmaa) - [smafa](#smafa) - [smallgenomeutilities](#smallgenomeutilities) - [SMAP](#smap) - [SMARTdenovo](#smartdenovo) - [SMC++](#smc++) - [smfishHmrf](#smfishhmrf) - [smithwaterman](#smithwaterman) - [Smoldyn](#smoldyn) - [smooth-topk](#smooth-topk) - [SMRT-Link](#smrt-link) - [SMV](#smv) - [snakemake](#snakemake) - [SNAP](#snap) - [SNAP-HMM](#snap-hmm) - [SNAPE-pooled](#snape-pooled) - [snaphu](#snaphu) - [snappy](#snappy) - [Sniffles](#sniffles) - [snippy](#snippy) - [snp-sites](#snp-sites) - [snpEff](#snpeff) - [SNPhylo](#snphylo) - [SNPomatic](#snpomatic) - [SOAPaligner](#soapaligner) - [SOAPdenovo-Trans](#soapdenovo-trans) - [SOAPdenovo2](#soapdenovo2) - [SOAPfuse](#soapfuse) - [socat](#socat) - [SOCI](#soci) - [SolexaQA++](#solexaqa++) - [sonic](#sonic) - [SoPlex](#soplex) - [SoQt](#soqt) - [SortMeRNA](#sortmerna) - [SoupX](#soupx) - [SoX](#sox) - [SoXt](#soxt) - [SpaceRanger](#spaceranger) - [Spack](#spack) - [spaCy](#spacy) - [SPAdes](#spades) - [spaln](#spaln) - [Spark](#spark) - [sparse-neighbors-search](#sparse-neighbors-search) - [sparsehash](#sparsehash) - [SpatialDE](#spatialde) - [spatialreg](#spatialreg) - [spdlog](#spdlog) - [SpectrA](#spectra) - [spectral.methods](#spectral.methods) - [speech_tools](#speech_tools) - [spektral](#spektral) - [spglib](#spglib) - [spglib-python](#spglib-python) - [Sphinx](#sphinx) - [Sphinx-RTD-Theme](#sphinx-rtd-theme) - [SpiceyPy](#spiceypy) - [SpiecEasi](#spieceasi) - [SplAdder](#spladder) - [SPLASH](#splash) - [SpliceMap](#splicemap) - [split-seq](#split-seq) - [splitRef](#splitref) - [SPM](#spm) - [spoa](#spoa) - [SPOOLES](#spooles) - [SPOTPY](#spotpy) - [SPRNG](#sprng) - [Spyder](#spyder) - [SQLite](#sqlite) - [SqueezeMeta](#squeezemeta) - [Squidpy](#squidpy) - [SRA-Toolkit](#sra-toolkit) - [sradownloader](#sradownloader) - [SRPRISM](#srprism) - [SRST2](#srst2) - [SSAHA2](#ssaha2) - [SSN](#ssn) - [SSPACE_Basic](#sspace_basic) - [SSW](#ssw) - [STACEY](#stacey) - [Stack](#stack) - [Stacks](#stacks) - [STAMP](#stamp) - [StaMPS](#stamps) - [Stampy](#stampy) - [STAR](#star) - [STAR-CCM+](#star-ccm+) - [STAR-Fusion](#star-fusion) - [stardist](#stardist) - [stars](#stars) - [Stata](#stata) - [Statistics-R](#statistics-r) - [statsmodels](#statsmodels) - [STEAK](#steak) - [STIR](#stir) - [stpipeline](#stpipeline) - [strace](#strace) - [Strainberry](#strainberry) - [STREAM](#stream) - [strelka](#strelka) - [StringTie](#stringtie) - [stripy](#stripy) - [STRique](#strique) - [Structure](#structure) - [Structure_threader](#structure_threader) - [STRUMPACK](#strumpack) - [suave](#suave) - [SuAVE-biomat](#suave-biomat) - [Subread](#subread) - [subset-bam](#subset-bam) - [Subversion](#subversion) - [suds](#suds) - [SuiteSparse](#suitesparse) - [SUMACLUST](#sumaclust) - [SUMATRA](#sumatra) - [SUMO](#sumo) - [SUNDIALS](#sundials) - [SunPy](#sunpy) - [SuperLU](#superlu) - [SuperLU_DIST](#superlu_dist) - [supermagic](#supermagic) - [supernova](#supernova) - [SURVIVOR](#survivor) - [SVclone](#svclone) - [SVDetect](#svdetect) - [SVDquest](#svdquest) - [SVG](#svg) - [SVIM](#svim) - [svist4get](#svist4get) - [swarm](#swarm) - [SWASH](#swash) - [SWAT+](#swat+) - [swifter](#swifter) - [SWIG](#swig) - [SWIPE](#swipe) - [swissknife](#swissknife) - [SymEngine](#symengine) - [SymEngine-python](#symengine-python) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -32132,6 +32978,16 @@ version |toolchain ------------------|-------------- ``1.1.1-20180610``|``foss/2017b`` +### Sabre + +Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). + +*homepage*: + +version |toolchain +--------------|-------------- +``2013-09-28``|``GCC/12.2.0`` + ### Safetensors Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast. @@ -32292,6 +33148,7 @@ version |versionsuffix |toolchain ``1.15.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` ``1.16.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` ``1.17`` | |``GCC/12.2.0`` +``1.18`` | |``GCC/12.3.0`` ### sansa @@ -32447,6 +33304,7 @@ Scalene is a high-performance CPU, GPU and memory profiler for Python that does version |toolchain ----------|------------------ ``1.5.13``|``GCCcore/11.2.0`` +``1.5.26``|``GCCcore/12.3.0`` ### scanpy @@ -32512,6 +33370,16 @@ version |toolchain ---------|-------------- ``0.9b0``|``foss/2021b`` +### scGSVA + +scGSVA provides wrap functions to do GSVA analysis for single cell data. And scGSVA includes functions to build annotation for almost all species. scGSVA also provides function to generate figures based on the GSVA results. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``0.0.14``|``-R-4.2.1`` |``foss/2022a`` + ### scHiCExplorer The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data. @@ -32547,6 +33415,16 @@ version |toolchain ``1.1.1``|``foss/2022a`` ``1.1.3``|``foss/2021a`` +### scib-metrics + +Accelerated and Python-only metrics for benchmarking single-cell integration outputs + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.3``|``foss/2021a`` + ### sciClone An R package for inferring the subclonal architecture of tumors @@ -32604,6 +33482,7 @@ version |versionsuffix |toolchain ``0.11.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``0.15.0``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``0.17.2``| |``GCCcore/12.2.0`` +``0.17.6``| |``GCCcore/12.3.0`` ### scikit-cuda @@ -32641,6 +33520,7 @@ version |versionsuffix |toolchain ``0.18.3``| |``foss/2021a`` ``0.19.1``| |``foss/2021b`` ``0.19.3``| |``foss/2022a`` +``0.21.0``| |``foss/2022b`` ### scikit-learn @@ -32716,6 +33596,16 @@ version |versionsuffix |toolchain ``0.8.1``|``-Python-3.8.2``|``foss/2020a`` ``0.9.0``| |``foss/2021a`` +### scikit-plot + +Scikit-plot is the result of an unartistic data scientist's dreadful realization that *visualization is one of the most crucial components in the data science process, not just a mere afterthought*. + +*homepage*: + +version |toolchain +---------|-------------- +``0.3.7``|``foss/2022b`` + ### scikit-uplift scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. Uplift prediction aims to estimate the causal impact of a treatment at the individual level. @@ -32780,6 +33670,7 @@ version |versionsuffix |toolchain ``2021.10``|``-Python-2.7.18``|``foss/2021b`` ``2022.05``| |``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` ``2023.02``| |``gfbf/2022b`` +``2023.07``| |``gfbf/2023a`` ### SCnorm @@ -32870,6 +33761,8 @@ version |versionsuffix |toolchain ``8.0`` | |``gompi/2021b``, ``gompi/2022a`` ``8.0`` |``-CUDA-11.4.1``|``gompi/2021b`` ``8.0`` |``-CUDA-11.7.0``|``gompi/2022a`` +``8.1`` | |``gompi/2022b``, ``gompi/2023a`` +``8.1`` |``-CUDA-12.0.0``|``gompi/2022b`` ### SCOTCH @@ -32887,6 +33780,7 @@ version |versionsuffix|toolchain ``6.1.0`` | |``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b``, ``iimpi/2021a`` ``6.1.2`` | |``gompi/2021b``, ``iimpi/2021b`` ``7.0.1`` | |``gompi/2022a``, ``iimpi/2022a`` +``7.0.3`` | |``gompi/2022b``, ``gompi/2023a`` ### scp @@ -32988,16 +33882,38 @@ version |toolchain ``2.0.20``|``GCCcore/11.2.0`` ``2.0.22``|``GCCcore/11.3.0`` ``2.26.3``|``GCCcore/12.2.0`` +``2.28.2``|``GCCcore/12.3.0`` ### SDL2_image -SDL_image is an image file loading library. +This is a simple library to load images of various formats as SDL surfaces. It can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP images, depending on build options (see the note below for details.) -*homepage*: +*homepage*: version |toolchain ----------|----------------- +---------|------------------ ``2.0.3``|``GCCcore/6.4.0`` +``2.6.3``|``GCCcore/11.3.0`` + +### SDL2_mixer + +Due to popular demand, here is a simple multi-channel audio mixer. It supports 8 channels of 16 bit stereo audio, plus a single channel of music. It can load FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus audio, depending on build options (see the note below for details.) + +*homepage*: + +version |toolchain +---------|------------------ +``2.6.3``|``GCCcore/11.3.0`` + +### SDL2_ttf + +This library is a wrapper around the FreeType and Harfbuzz libraries, allowing you to use TrueType fonts to render text in SDL applications. + +*homepage*: + +version |toolchain +----------|------------------ +``2.20.2``|``GCCcore/11.3.0`` ### SDL_image @@ -33097,6 +34013,16 @@ version |toolchain ``0.2.0``|``foss/2016b``, ``intel/2017b``, ``intel/2018a`` ``0.3.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2020.4.304`` +### segment-anything + +The Segment Anything Model (SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image. It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot performance on a variety of segmentation tasks. + +*homepage*: + +version|toolchain +-------|-------------- +``1.0``|``foss/2022a`` + ### segmentation-models Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. @@ -33150,6 +34076,16 @@ version |versionsuffix |toolchain ``0.1.96``| |``GCC/10.2.0``, ``GCC/10.3.0`` ``0.1.97``| |``GCC/11.3.0`` +### sentinelsat + +Sentinelsat makes searching, downloading and retrieving the metadata of Sentinel satellite images from the Copernicus Open Access Hub easy. + +*homepage*: + +version |toolchain +---------|------------------ +``1.2.1``|``GCCcore/11.3.0`` + ### sep Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only) @@ -33291,9 +34227,20 @@ Easily download, build, install, upgrade, and uninstall Python packages *homepage*: version |versionsuffix|toolchain -----------|-------------|---------- +----------|-------------|------------------ ``1.4.2`` | |``system`` ``41.0.1``|``-py3`` |``system`` +``64.0.3``| |``GCCcore/12.2.0`` + +### setuptools-rust + +setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython. + +*homepage*: + +version |toolchain +---------|------------------ +``1.6.0``|``GCCcore/12.3.0`` ### Seurat @@ -33310,6 +34257,7 @@ version |versionsuffix|toolchain ``3.1.5`` |``-R-4.0.0`` |``foss/2020a`` ``4.0.1`` |``-R-4.0.3`` |``foss/2020b`` ``4.0.3`` |``-R-4.0.3`` |``foss/2020b`` +``4.1.0`` |``-R-4.1.0`` |``foss/2021a`` ``4.2.0`` |``-R-4.2.1`` |``foss/2022a`` ``4.3.0`` |``-R-4.1.2`` |``foss/2021b`` ``4.3.0`` |``-R-4.2.1`` |``foss/2022a`` @@ -33343,6 +34291,7 @@ SeuratWrappers is a collection of community-provided methods and extensions for version |versionsuffix|toolchain ------------|-------------|-------------- ``20210528``|``-R-4.0.3`` |``foss/2020b`` +``20221022``|``-R-4.2.1`` |``foss/2022a`` ### sf @@ -33432,7 +34381,7 @@ version |versionsuffix |toolchain ``1.8.1.post1``| |``GCC/11.2.0`` ``1.8.2`` | |``foss/2021b``, ``foss/2022a`` ``1.8a1`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -``2.0.1`` | |``foss/2022b`` +``2.0.1`` | |``foss/2022b``, ``gfbf/2023a`` ### sharutils @@ -33751,14 +34700,14 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: version |versionsuffix|toolchain ----------|-------------|---------------------------------------------------------------------------- +---------|-------------|------------------------------------------------------------------------------ ``1.6.1``| |``foss/2016a`` ``1.6.1``|``-tools`` |``foss/2016a`` ``1.7.1``| |``foss/2017a`` ``1.7.1``|``-tools`` |``foss/2017a`` ``1.7.4``|``-tools`` |``GCCcore/8.2.0`` ``1.7.6``|``-tools`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.7.7``|``-tools`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.7.7``|``-tools`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SIP @@ -33966,6 +34915,16 @@ version |toolchain ---------|--------------- ``0.4.0``|``gompi/2021b`` +### slurm-drmaa + +DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. + +*homepage*: + +version |toolchain +---------|------------------ +``1.1.3``|``GCCcore/12.2.0`` + ### smafa Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. @@ -34033,8 +34992,8 @@ smith-waterman-gotoh alignment algorithm. *homepage*: version |toolchain -------------|----------------------------------------------------------------------------- -``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +------------|------------------------------------------------------------------------------------------------- +``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ### Smoldyn @@ -34095,6 +35054,7 @@ version |versionsuffix |toolchain ``6.10.0``| |``foss/2021b`` ``7.18.2``| |``foss/2021b`` ``7.22.0``| |``foss/2022a`` +``7.32.3``| |``foss/2022b`` ### SNAP @@ -34376,13 +35336,14 @@ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``1.1.0``|``GCC/9.3.0`` ``1.2.2``|``GCC/9.3.0`` ``1.3.0``|``GCC/10.3.0`` ``1.3.1``|``GCC/11.2.0`` ``2.0.0``|``GCC/11.2.0`` ``2.0.1``|``GCC/11.3.0`` +``2.1.0``|``GCC/11.3.0``, ``GCC/12.2.0`` ### Spack @@ -34527,6 +35488,7 @@ Very fast, header-only/compiled, C++ logging library. version |toolchain ----------|-------------------------------------- ``1.9.2`` |``GCCcore/10.3.0`` +``1.10.0``|``GCCcore/11.2.0`` ``1.11.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SpectrA @@ -34578,12 +35540,12 @@ Spglib is a C library for finding and handling crystal symmetries. *homepage*: version |toolchain -----------|------------------------- +----------|-------------------------------------- ``1.9.2`` |``intel/2016.02-GCC-4.9`` ``1.9.9`` |``intel/2017b`` ``1.16.1``|``GCCcore/10.2.0`` ``1.16.2``|``GCCcore/10.3.0`` -``2.0.2`` |``GCCcore/11.3.0`` +``2.0.2`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### spglib-python @@ -34656,6 +35618,7 @@ Sparse InversE Covariance estimation for Ecological Association and Statistical version |versionsuffix|toolchain ------------|-------------|--------------- ``1.0.0`` |``-R-3.4.4`` |``intel/2018a`` +``1.1.1`` |``-R-4.2.1`` |``foss/2022a`` ``20160830``|``-R-3.3.1`` |``intel/2016b`` ### SplAdder @@ -34739,8 +35702,8 @@ SPOOLES is a library for solving sparse real and complex linear systems of equa *homepage*: version|toolchain --------|--------------- -``2.2``|``gompi/2021a`` +-------|-------------------------------- +``2.2``|``gompi/2021a``, ``gompi/2022b`` ### SPOTPY @@ -34945,9 +35908,10 @@ Stack is a cross-platform program for developing Haskell projects. It is intende *homepage*: -version |versionsuffix|toolchain ----------|-------------|---------- -``2.3.3``|``-x86_64`` |``system`` +version |versionsuffix|toolchain +----------|-------------|---------- +``2.3.3`` |``-x86_64`` |``system`` +``2.11.1``|``-x86_64`` |``system`` ### Stacks @@ -35039,6 +36003,7 @@ version |toolchain ``2.7.9a`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``2.7.10a_alpha_220601``|``GCC/10.3.0`` ``2.7.10b`` |``GCC/11.3.0``, ``GCC/12.2.0`` +``2.7.11a`` |``GCC/12.3.0`` ### STAR-CCM+ @@ -35258,8 +36223,8 @@ The program structure is a free software package for using multi-locus genotype *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------- -``2.3.4``|``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` +---------|--------------------------------------------------------------------------------------------------------------------- +``2.3.4``|``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` ### Structure_threader @@ -35291,6 +36256,16 @@ version |toolchain ------------|-------------- ``20160529``|``foss/2020b`` +### SuAVE-biomat + +Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape + +*homepage*: + +version |toolchain +------------------|--------------- +``2.0.0-20230815``|``intel/2023a`` + ### Subread High performance read alignment, quantification and mutation discovery @@ -35416,6 +36391,7 @@ version |toolchain ``6.2.0``|``foss/2020b``, ``intel/2020b`` ``6.3.0``|``foss/2021b``, ``foss/2022a`` ``6.5.1``|``foss/2022a`` +``6.6.0``|``foss/2022b`` ### SunPy @@ -35451,6 +36427,7 @@ version |versionsuffix |toolchain ``5.4.0``|``-trisolve-merge``|``intel/2020a`` ``6.4.0``| |``foss/2020a``, ``intel/2020a`` ``8.1.0``| |``foss/2022a`` +``8.1.2``| |``foss/2022b`` ### supermagic @@ -35612,6 +36589,7 @@ version |versionsuffix |toolchain ``3.0.12``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``4.0.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.0.2`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.1.1`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### SWIPE @@ -35683,9 +36661,10 @@ version |versionsuffix |toolchain ``1.6.2`` |``-Python-3.8.2`` |``foss/2020a`` ``1.7.1`` | |``foss/2020b``, ``intel/2020b`` ``1.8`` | |``foss/2021a`` -``1.9`` | |``foss/2021b`` +``1.9`` | |``foss/2021b``, ``intel/2021b`` ``1.10.1``| |``foss/2022a``, ``intel/2022a`` ``1.11.1``| |``foss/2022a``, ``intel/2022a`` +``1.12`` | |``gfbf/2023a`` ### synthcity @@ -35731,8 +36710,19 @@ version |toolchain ## T -[tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [Tapenade](#tapenade) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [TensorFlow-Datasets](#tensorflow-datasets) - [TensorFlow-Graphics](#tensorflow-graphics) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [toil](#toil) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [TOPAS](#topas) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvision](#torchvision) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [Trinotate](#trinotate) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [typing-extensions](#typing-extensions) +[T-Coffee](#t-coffee) - [tabix](#tabix) - [tabixpp](#tabixpp) - [taco](#taco) - [TagDust](#tagdust) - [TagLib](#taglib) - [Taiyaki](#taiyaki) - [TALON](#talon) - [TALYS](#talys) - [TAMkin](#tamkin) - [tantan](#tantan) - [Tapenade](#tapenade) - [task-spooler](#task-spooler) - [taxator-tk](#taxator-tk) - [TBA](#tba) - [tbb](#tbb) - [tbl2asn](#tbl2asn) - [TCC](#tcc) - [Tcl](#tcl) - [TCLAP](#tclap) - [tcsh](#tcsh) - [tecplot360ex](#tecplot360ex) - [TELEMAC-MASCARET](#telemac-mascaret) - [Telescope](#telescope) - [Teneto](#teneto) - [tensorboard](#tensorboard) - [tensorboardX](#tensorboardx) - [TensorFlow](#tensorflow) - [tensorflow-compression](#tensorflow-compression) - [TensorFlow-Datasets](#tensorflow-datasets) - [TensorFlow-Graphics](#tensorflow-graphics) - [tensorflow-probability](#tensorflow-probability) - [TensorRT](#tensorrt) - [terastructure](#terastructure) - [termcolor](#termcolor) - [Tesla-Deployment-Kit](#tesla-deployment-kit) - [tesseract](#tesseract) - [testpath](#testpath) - [TetGen](#tetgen) - [TEToolkit](#tetoolkit) - [TEtranscripts](#tetranscripts) - [texinfo](#texinfo) - [texlive](#texlive) - [Text-CSV](#text-csv) - [TFEA](#tfea) - [Theano](#theano) - [ThemisPy](#themispy) - [THetA](#theta) - [thirdorder](#thirdorder) - [thurstonianIRT](#thurstonianirt) - [TiCCutils](#ticcutils) - [tidybayes](#tidybayes) - [tidymodels](#tidymodels) - [Tika](#tika) - [TiMBL](#timbl) - [time](#time) - [timm](#timm) - [TINKER](#tinker) - [TinyDB](#tinydb) - [TinyXML](#tinyxml) - [Tk](#tk) - [Tkinter](#tkinter) - [TM-align](#tm-align) - [tMAE](#tmae) - [tmap](#tmap) - [tmux](#tmux) - [TN93](#tn93) - [TOBIAS](#tobias) - [ToFu](#tofu) - [Togl](#togl) - [toil](#toil) - [tokenizers](#tokenizers) - [Tombo](#tombo) - [TOML-Fortran](#toml-fortran) - [TOPAS](#topas) - [topaz](#topaz) - [TopHat](#tophat) - [torchaudio](#torchaudio) - [torchdata](#torchdata) - [torchinfo](#torchinfo) - [torchsampler](#torchsampler) - [torchtext](#torchtext) - [torchvf](#torchvf) - [torchvision](#torchvision) - [tornado](#tornado) - [TotalView](#totalview) - [tqdm](#tqdm) - [Tracer](#tracer) - [TranscriptClean](#transcriptclean) - [TransDecoder](#transdecoder) - [Transformers](#transformers) - [Transrate](#transrate) - [travis](#travis) - [TRAVIS-Analyzer](#travis-analyzer) - [treatSens](#treatsens) - [TreeMix](#treemix) - [TreeShrink](#treeshrink) - [TRF](#trf) - [Triangle](#triangle) - [Trilinos](#trilinos) - [Trim_Galore](#trim_galore) - [trimAl](#trimal) - [trimesh](#trimesh) - [Trimmomatic](#trimmomatic) - [Trinity](#trinity) - [Trinotate](#trinotate) - [Triplexator](#triplexator) - [TRIQS](#triqs) - [TRIQS-cthyb](#triqs-cthyb) - [TRIQS-dft_tools](#triqs-dft_tools) - [TRIQS-tprf](#triqs-tprf) - [tRNAscan-SE](#trnascan-se) - [TRUST](#trust) - [TRUST4](#trust4) - [Trycycler](#trycycler) - [tseriesEntropy](#tseriesentropy) - [tsne](#tsne) - [turbinesFoam](#turbinesfoam) - [TurboVNC](#turbovnc) - [TVB](#tvb) - [tvb-data](#tvb-data) - [TVB-deps](#tvb-deps) - [tvb-framework](#tvb-framework) - [tvb-library](#tvb-library) - [TWL-NINJA](#twl-ninja) - [TXR](#txr) - [typing-extensions](#typing-extensions) + +### T-Coffee + +A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures + +*homepage*: + +version |toolchain +--------------------|---------- +``13.45.61.3c310a9``|``system`` +``13.46.0.919e8c6b``|``system`` ### tabix @@ -35753,6 +36743,7 @@ C++ wrapper to tabix indexer version |toolchain ---------|------------------------------------------------------------- ``1.1.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +``1.1.2``|``GCC/11.3.0`` ### taco @@ -35905,6 +36896,7 @@ version |toolchain ``2020.3`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2021.4.0`` |``GCCcore/11.2.0`` ``2021.5.0`` |``GCCcore/11.3.0`` +``2021.10.0`` |``GCCcore/12.2.0`` ### tbl2asn @@ -35918,6 +36910,7 @@ version |versionsuffix|toolchain ``20180227``|``-linux64`` |``system`` ``20200302``|``-linux64`` |``system`` ``20220427``|``-linux64`` |``system`` +``20230713``|``-linux64`` |``system`` ### TCC @@ -35977,6 +36970,7 @@ version |toolchain ``6.22.04``|``GCCcore/10.3.0`` ``6.24.01``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``6.24.07``|``GCCcore/12.2.0`` +``6.24.10``|``GCCcore/12.3.0`` ### tecplot360ex @@ -36112,6 +37106,17 @@ version |versionsuffix |toolchain ``2.9.1`` |``-CUDA-11.7.0`` |``foss/2022a`` ``2.11.0``| |``foss/2022a`` ``2.11.0``|``-CUDA-11.7.0`` |``foss/2022a`` +``2.13.0``| |``foss/2022b``, ``foss/2023a`` + +### tensorflow-compression + +TensorFlow Compression (TFC) contains data compression tools for TensorFlow. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``2.11.0``|``-CUDA-11.7.0``|``foss/2022a`` ### TensorFlow-Datasets @@ -36145,6 +37150,7 @@ version |versionsuffix |toolchain ``0.9.0`` |``-Python-3.7.4``|``foss/2019b`` ``0.12.1``| |``foss/2020b``, ``fosscuda/2020b`` ``0.16.0``| |``foss/2021b`` +``0.19.0``|``-CUDA-11.7.0`` |``foss/2022a`` ### TensorRT @@ -36419,9 +37425,9 @@ The `time' command runs another program, then displays information about the res *homepage*: version|toolchain --------|----------------------------------------------------------------------------------------------------------------------------------------------------------- +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.7``|``system`` -``1.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### timm @@ -36485,6 +37491,7 @@ version |versionsuffix |toolchain ``8.6.10``| |``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``8.6.12``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``8.6.13``| |``GCCcore/12.3.0`` ### Tkinter @@ -36513,6 +37520,7 @@ version |versionsuffix |toolchain ``3.9.6`` | |``GCCcore/11.2.0`` ``3.10.4``| |``GCCcore/11.3.0`` ``3.10.8``| |``GCCcore/12.2.0`` +``3.11.3``| |``GCCcore/12.3.0`` ### TM-align @@ -36742,6 +37750,17 @@ version |versionsuffix |toolchain ``0.10.0``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` ``0.14.1``|``-PyTorch-1.12.0`` |``foss/2022a`` +### torchvf + +TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.1.3``| |``foss/2022a`` +``0.1.3``|``-CUDA-11.7.0``|``foss/2022a`` + ### torchvision Datasets, Transforms and Models specific to Computer Vision @@ -36772,6 +37791,16 @@ version |versionsuffix |toolchain ``0.13.1``| |``foss/2022a`` ``0.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` +### tornado + +Tornado is a Python web framework and asynchronous networking library. + +*homepage*: + +version |toolchain +---------|------------------ +``6.3.2``|``GCCcore/12.3.0`` + ### TotalView TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors. @@ -36807,6 +37836,7 @@ version |versionsuffix |toolchain ``4.62.3``| |``GCCcore/11.2.0`` ``4.64.0``| |``GCCcore/11.3.0`` ``4.64.1``| |``GCCcore/12.2.0`` +``4.66.1``| |``GCCcore/12.3.0`` ### Tracer @@ -37145,6 +38175,16 @@ version |versionsuffix |toolchain ``0.5.2``| |``foss/2021a`` ``0.5.3``| |``foss/2021b`` +### tseriesEntropy + +Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``0.6-0``|``-R-4.2.1`` |``foss/2022a`` + ### tsne Python library containing T-SNE algorithms. @@ -37241,6 +38281,16 @@ version |toolchain ``0.97-cluster_only``|``GCC/10.2.0`` ``0.98-cluster_only``|``GCC/11.3.0`` +### TXR + +TXR is a pragmatic, convenient tool ready to take on your daily hacking challenges with its dual personality: its whole-document pattern matching and extraction language for scraping information from arbitrary text sources, and its powerful data-processing language to slice through problems like a hot knife through butter. Many tasks can be accomplished with TXR "one liners" directly from your system prompt. + +*homepage*: + +version|toolchain +-------|------------------ +``291``|``GCCcore/12.2.0`` + ### typing-extensions Typing Extensions - Backported and Experimental Type Hints for Python @@ -37260,7 +38310,7 @@ version |versionsuffix |toolchain ## U -[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) +[UCC](#ucc) - [UCC-CUDA](#ucc-cuda) - [UCLUST](#uclust) - [UCX](#ucx) - [UCX-CUDA](#ucx-cuda) - [ucx-py](#ucx-py) - [UCX-ROCm](#ucx-rocm) - [udocker](#udocker) - [UDUNITS](#udunits) - [UFL](#ufl) - [Ultralytics](#ultralytics) - [umap-learn](#umap-learn) - [UMI-tools](#umi-tools) - [umi4cPackage](#umi4cpackage) - [umis](#umis) - [UNAFold](#unafold) - [uncertainty-calibration](#uncertainty-calibration) - [unicore-uftp](#unicore-uftp) - [Unicycler](#unicycler) - [Unidecode](#unidecode) - [unifdef](#unifdef) - [UniFrac](#unifrac) - [unimap](#unimap) - [units](#units) - [unixODBC](#unixodbc) - [unrar](#unrar) - [UnZip](#unzip) - [UQTk](#uqtk) - [USEARCH](#usearch) - [UShER](#usher) - [USPEX](#uspex) - [utf8proc](#utf8proc) - [util-linux](#util-linux) ### UCC @@ -37502,6 +38552,26 @@ version |versionsuffix |toolchain ``1.1.1``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``1.3.6``| |``GCCcore/11.3.0`` +### unifdef + +unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone. + +*homepage*: + +version |toolchain +--------|------------------ +``2.12``|``GCCcore/11.3.0`` + +### UniFrac + +UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. + +*homepage*: + +version |toolchain +---------|-------------- +``1.3.2``|``foss/2022a`` + ### unimap Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. @@ -37528,9 +38598,10 @@ unixODBC provides a uniform interface between application and database driver *homepage*: -version |toolchain ----------|-------------- -``2.3.7``|``foss/2018b`` +version |toolchain +----------|-------------- +``2.3.7`` |``foss/2018b`` +``2.3.11``|``foss/2022b`` ### unrar @@ -37644,7 +38715,7 @@ version |toolchain ## V -[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [vConTACT2](#vcontact2) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirSorter2](#virsorter2) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [visdom](#visdom) - [vispr](#vispr) - [VisPy](#vispy) - [vitessce-python](#vitessce-python) - [vitessceR](#vitesscer) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) +[V8](#v8) - [Vala](#vala) - [Valgrind](#valgrind) - [Vampir](#vampir) - [Vampire](#vampire) - [VarDict](#vardict) - [variant_tools](#variant_tools) - [VariantMetaCaller](#variantmetacaller) - [VarScan](#varscan) - [vartools](#vartools) - [VASP](#vasp) - [VAtools](#vatools) - [vawk](#vawk) - [VBZ-Compression](#vbz-compression) - [VCF-kit](#vcf-kit) - [vcflib](#vcflib) - [vcfnp](#vcfnp) - [VCFtools](#vcftools) - [vConTACT2](#vcontact2) - [VEGAS](#vegas) - [velocyto](#velocyto) - [Velvet](#velvet) - [VEP](#vep) - [verifyBamID](#verifybamid) - [VERSE](#verse) - [VESTA](#vesta) - [ViennaRNA](#viennarna) - [Vim](#vim) - [VirSorter](#virsorter) - [VirSorter2](#virsorter2) - [virtualenv](#virtualenv) - [VirtualGL](#virtualgl) - [Virtuoso-opensource](#virtuoso-opensource) - [visdom](#visdom) - [vispr](#vispr) - [VisPy](#vispy) - [vitessce-python](#vitessce-python) - [vitessceR](#vitesscer) - [VMD](#vmd) - [VMTK](#vmtk) - [voltools](#voltools) - [vorbis-tools](#vorbis-tools) - [Voro++](#voro++) - [vsc-base](#vsc-base) - [vsc-install](#vsc-install) - [vsc-mympirun](#vsc-mympirun) - [vsc-mympirun-scoop](#vsc-mympirun-scoop) - [vsc-processcontrol](#vsc-processcontrol) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) ### V8 @@ -37686,6 +38757,7 @@ version |toolchain ``3.18.1``|``gompi/2021b``, ``iimpi/2021b`` ``3.19.0``|``gompi/2022a`` ``3.20.0``|``gompi/2022a`` +``3.21.0``|``gompi/2022b``, ``gompi/2023a`` ### Vampir @@ -37824,6 +38896,7 @@ version |versionsuffix |toolchain ``1.0.2``|``-Python-3.8.2``|``GCC/9.3.0`` ``1.0.3``|``-R-4.1.0`` |``foss/2021a`` ``1.0.3``|``-R-4.1.2`` |``foss/2021b`` +``1.0.9``|``-R-4.2.1`` |``foss/2022a`` ### vcfnp @@ -37990,6 +39063,16 @@ version |toolchain ---------|-------------- ``2.2.4``|``foss/2022a`` +### virtualenv + +A tool for creating isolated virtual python environments. + +*homepage*: + +version |toolchain +-----------|------------------ +``20.23.1``|``GCCcore/12.3.0`` + ### VirtualGL VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration. @@ -38001,6 +39084,7 @@ version |toolchain ``2.6.1``|``foss/2018b`` ``2.6.2``|``GCCcore/9.3.0`` ``3.0`` |``GCC/11.2.0`` +``3.1`` |``GCC/12.3.0`` ### Virtuoso-opensource @@ -38038,9 +39122,10 @@ VisPy is a high-performance interactive 2D/3D data visualization library levera *homepage*: -version |toolchain ----------|------------------------------- -``0.6.6``|``foss/2020b``, ``intel/2020b`` +version |toolchain +----------|------------------------------- +``0.6.6`` |``foss/2020b``, ``intel/2020b`` +``0.12.2``|``foss/2022a`` ### vitessce-python @@ -38262,6 +39347,7 @@ version |versionsuffix |toolchain ``8.1.1`` |``-Python-3.6.6`` |``foss/2018b``, ``fosscuda/2018b`` ``8.2.0`` | |``foss/2021a`` ``8.2.0`` |``-Python-2.7.15``|``foss/2019a`` +``8.2.0`` |``-Python-2.7.16``|``foss/2019b`` ``8.2.0`` |``-Python-3.7.2`` |``foss/2019a``, ``intel/2019a`` ``8.2.0`` |``-Python-3.7.4`` |``foss/2019b`` ``8.2.0`` |``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` @@ -38326,7 +39412,7 @@ version |toolchain ## W -[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) +[wandb](#wandb) - [Wannier90](#wannier90) - [WannierTools](#wanniertools) - [Wayland](#wayland) - [Waylandpp](#waylandpp) - [WCSLIB](#wcslib) - [WCT](#wct) - [wcwidth](#wcwidth) - [webin-cli](#webin-cli) - [WebKitGTK+](#webkitgtk+) - [WebSocket++](#websocket++) - [WEKA](#weka) - [WFA2](#wfa2) - [wget](#wget) - [wgsim](#wgsim) - [WHAM](#wham) - [WhatsHap](#whatshap) - [wheel](#wheel) - [WIEN2k](#wien2k) - [WildMagic](#wildmagic) - [Winnowmap](#winnowmap) - [WisecondorX](#wisecondorx) - [WISExome](#wisexome) - [wkhtmltopdf](#wkhtmltopdf) - [worker](#worker) - [wpebackend-fdo](#wpebackend-fdo) - [WPS](#wps) - [wrapt](#wrapt) - [WRF](#wrf) - [WRF-Fire](#wrf-fire) - [wrf-python](#wrf-python) - [wtdbg2](#wtdbg2) - [wxPropertyGrid](#wxpropertygrid) - [wxPython](#wxpython) - [wxWidgets](#wxwidgets) ### wandb @@ -38377,6 +39463,7 @@ version |toolchain ----------|-------------------------------------- ``1.20.0``|``GCCcore/11.3.0`` ``1.21.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.22.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Waylandpp @@ -38442,6 +39529,7 @@ version |toolchain ``2.24.1``|``GCC/8.2.0-2.31.1`` ``2.27.4``|``GCC/10.3.0``, ``GCC/8.3.0`` ``2.37.1``|``GCC/11.2.0`` +``2.40.4``|``GCC/11.3.0`` ### WebSocket++ @@ -38464,6 +39552,16 @@ version |versionsuffix |toolchain ``3.6.12``|``-Java-1.7.0_80``|``system`` ``3.7.0`` |``-Java-1.7.0_80``|``system`` +### WFA2 + +The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. + +*homepage*: + +version |toolchain +---------|------------------ +``2.3.3``|``GCCcore/11.3.0`` + ### wget GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. @@ -38619,13 +39717,14 @@ version |versionsuffix |toolchain ### wpebackend-fdo -WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. +WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. *homepage*: version |toolchain ----------|------------------ ``1.13.1``|``GCCcore/11.2.0`` +``1.14.1``|``GCCcore/11.3.0`` ### WPS @@ -38651,8 +39750,8 @@ The aim of the wrapt module is to provide a transparent object proxy for Python, *homepage*: version |toolchain -----------|------------------------------- -``1.15.0``|``foss/2022a``, ``intel/2022a`` +----------|----------------------------------------------- +``1.15.0``|``foss/2022a``, ``gfbf/2022b``, ``intel/2022a`` ### WRF @@ -38733,6 +39832,7 @@ version |versionsuffix |toolchain ``4.0.7.post2``|``-Python-3.7.4`` |``GCC/8.3.0`` ``4.1.1`` | |``foss/2021a`` ``4.2.0`` | |``foss/2021b`` +``4.2.1`` | |``foss/2022a`` ### wxWidgets @@ -38749,7 +39849,7 @@ version |toolchain ``3.1.5`` |``GCC/10.3.0``, ``GCC/11.2.0`` ``3.2.0`` |``GCC/11.2.0`` ``3.2.1`` |``GCC/11.3.0`` -``3.2.2.1``|``GCCcore/12.2.0`` +``3.2.2.1``|``GCC/12.2.0``, ``GCC/12.3.0`` ## X @@ -38798,7 +39898,7 @@ x264 is a free software library and application for encoding video streams into *homepage*: version |toolchain -------------|--------------------------------- +------------|-------------------------------------- ``20160114``|``gimkl/2.11.5``, ``intel/2016a`` ``20160430``|``foss/2016a``, ``intel/2016a`` ``20160614``|``foss/2016b``, ``intel/2016b`` @@ -38816,7 +39916,7 @@ version |toolchain ``20210414``|``GCCcore/10.3.0`` ``20210613``|``GCCcore/11.2.0`` ``20220620``|``GCCcore/11.3.0`` -``20230226``|``GCCcore/12.2.0`` +``20230226``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### x265 @@ -38825,7 +39925,7 @@ x265 is a free software library and application for encoding video streams into *homepage*: version|toolchain --------|------------------------------------------------------------------------------ +-------|-------------------------------------------------------------------------------------------------- ``2.4``|``foss/2016b`` ``2.5``|``intel/2017a`` ``2.6``|``GCCcore/6.4.0``, ``intel/2017b`` @@ -38834,7 +39934,7 @@ version|toolchain ``3.0``|``GCCcore/8.2.0`` ``3.2``|``GCCcore/8.3.0`` ``3.3``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``3.5``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### XALT @@ -39242,7 +40342,7 @@ version |toolchain ``1.19.1``|``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2``|``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``1.19.3``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``1.20.0``|``GCCcore/12.3.0`` +``1.20.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### XPLOR-NIH @@ -39266,7 +40366,7 @@ version |versionsuffix |toolchain ``1.2.2``|``-X11-20180131``|``GCCcore/6.4.0`` ``1.2.3``| |``GCCcore/7.3.0`` ``1.2.4``| |``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.5``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### xproto @@ -39348,6 +40448,7 @@ version |toolchain ``1.20.13``|``GCCcore/11.2.0`` ``21.1.3`` |``GCCcore/11.3.0`` ``21.1.6`` |``GCCcore/12.2.0`` +``21.1.8`` |``GCCcore/12.3.0`` ### xxd @@ -39358,6 +40459,7 @@ xxd is part of the VIM package and this will only install xxd, not vim! xxd conv version |toolchain ------------|------------------------------------------------------------------------------ ``8.2.4220``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``9.0.1696``|``GCCcore/12.2.0`` ### xxHash @@ -39387,6 +40489,7 @@ version |versionsuffix |toolchain ``5.2.5``| |``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ``5.2.7``| |``GCCcore/12.2.0`` ``5.4.2``| |``GCCcore/12.3.0``, ``GCCcore/13.1.0`` +``5.4.4``| |``GCCcore/13.2.0`` ## Y @@ -39448,6 +40551,7 @@ version |toolchain ---------|------------------------- ``3.4.2``|``intel/2016.02-GCC-4.9`` ``5.0.4``|``intel/2021a`` +``5.1.2``|``intel/2021b`` ### yaml-cpp @@ -39539,14 +40643,20 @@ Z3 is a theorem prover from Microsoft Research. *homepage*: -version |toolchain -----------|------------------------------------ -``4.8.9`` |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.8.10``|``GCCcore/10.2.0`` -``4.8.11``|``GCCcore/10.3.0`` -``4.8.12``|``GCCcore/11.2.0`` -``4.8.16``|``GCCcore/11.3.0`` -``4.10.2``|``GCCcore/11.3.0`` +version |versionsuffix |toolchain +----------|------------------|-------------------------------------- +``4.8.9`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.8.10``| |``GCCcore/10.2.0`` +``4.8.10``|``-Python-3.8.6`` |``GCCcore/10.2.0`` +``4.8.11``| |``GCCcore/10.3.0`` +``4.8.11``|``-Python-3.9.5`` |``GCCcore/10.3.0`` +``4.8.12``| |``GCCcore/11.2.0`` +``4.8.12``|``-Python-3.9.6`` |``GCCcore/11.2.0`` +``4.8.16``| |``GCCcore/11.3.0`` +``4.8.16``|``-Python-3.10.4``|``GCCcore/11.3.0`` +``4.10.2``| |``GCCcore/11.3.0`` +``4.10.2``|``-Python-3.10.4``|``GCCcore/11.3.0`` +``4.12.2``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### zarr @@ -39561,6 +40671,7 @@ version |versionsuffix |toolchain ``2.8.1`` | |``foss/2020b`` ``2.10.1``| |``foss/2021a`` ``2.13.3``| |``foss/2021b``, ``foss/2022a`` +``2.16.0``| |``foss/2022b`` ### ZeroMQ @@ -39577,7 +40688,7 @@ version |toolchain ``4.2.5``|``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3``|``GCCcore/10.2.0`` -``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``4.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### zfp @@ -39643,7 +40754,7 @@ version |toolchain ``1.2.10``|``system`` ``1.2.11``|``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ``1.2.12``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` -``1.2.13``|``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``system`` +``1.2.13``|``GCCcore/11.4.0``, ``GCCcore/12.3.0``, ``GCCcore/13.1.0``, ``GCCcore/13.2.0``, ``system`` ### zlib-ng diff --git a/docs/version-specific/toolchain-opts.md b/docs/version-specific/toolchain-opts.md index c5514657b..52afd923a 100644 --- a/docs/version-specific/toolchain-opts.md +++ b/docs/version-specific/toolchain-opts.md @@ -2,7 +2,7 @@ *(see also* ``eb --avail-toolchain-opts `` *)* -[cgmpich](#cgmpich) - [cgmpolf](#cgmpolf) - [cgmvapich2](#cgmvapich2) - [cgmvolf](#cgmvolf) - [cgompi](#cgompi) - [cgoolf](#cgoolf) - [ClangGCC](#clanggcc) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [FCC](#fcc) - [ffmpi](#ffmpi) - [foss](#foss) - [fosscuda](#fosscuda) - [Fujitsu](#fujitsu) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gfbf](#gfbf) - [gimkl](#gimkl) - [gimpi](#gimpi) - [gimpic](#gimpic) - [giolf](#giolf) - [giolfc](#giolfc) - [gmacml](#gmacml) - [gmkl](#gmkl) - [gmklc](#gmklc) - [gmpich2](#gmpich2) - [gmpich](#gmpich) - [gmpit](#gmpit) - [gmpolf](#gmpolf) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [goalf](#goalf) - [gobff](#gobff) - [goblf](#goblf) - [gofbf](#gofbf) - [golf](#golf) - [golfc](#golfc) - [gomkl](#gomkl) - [gomklc](#gomklc) - [gompi](#gompi) - [gompic](#gompic) - [goolf](#goolf) - [goolfc](#goolfc) - [gpsmpi](#gpsmpi) - [gpsolf](#gpsolf) - [gqacml](#gqacml) - [gsmpi](#gsmpi) - [gsolf](#gsolf) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ictce](#ictce) - [iibff](#iibff) - [iimkl](#iimkl) - [iimklc](#iimklc) - [iimpi](#iimpi) - [iimpic](#iimpic) - [iiqmpi](#iiqmpi) - [impich](#impich) - [impmkl](#impmkl) - [intel-compilers](#intel-compilers) - [intel-para](#intel-para) - [intel](#intel) - [intelcuda](#intelcuda) - [iomkl](#iomkl) - [iomklc](#iomklc) - [iompi](#iompi) - [iompic](#iompic) - [ipsmpi](#ipsmpi) - [iqacml](#iqacml) - [ismkl](#ismkl) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [nvompic](#nvompic) - [nvpsmpi](#nvpsmpi) - [nvpsmpic](#nvpsmpic) - [PGI](#pgi) - [pmkl](#pmkl) - [pomkl](#pomkl) - [pompi](#pompi) - [system](#system) - [xlcxlf](#xlcxlf) - [xlmpich2](#xlmpich2) - [xlmpich](#xlmpich) - [xlmvapich2](#xlmvapich2) - [xlompi](#xlompi) +[cgmpich](#cgmpich) - [cgmpolf](#cgmpolf) - [cgmvapich2](#cgmvapich2) - [cgmvolf](#cgmvolf) - [cgompi](#cgompi) - [cgoolf](#cgoolf) - [ClangGCC](#clanggcc) - [CrayCCE](#craycce) - [CrayGNU](#craygnu) - [CrayIntel](#crayintel) - [CrayPGI](#craypgi) - [FCC](#fcc) - [ffmpi](#ffmpi) - [foss](#foss) - [fosscuda](#fosscuda) - [Fujitsu](#fujitsu) - [GCC](#gcc) - [GCCcore](#gcccore) - [gcccuda](#gcccuda) - [gfbf](#gfbf) - [gimkl](#gimkl) - [gimpi](#gimpi) - [gimpic](#gimpic) - [giolf](#giolf) - [giolfc](#giolfc) - [gmacml](#gmacml) - [gmkl](#gmkl) - [gmklc](#gmklc) - [gmpich2](#gmpich2) - [gmpich](#gmpich) - [gmpit](#gmpit) - [gmpolf](#gmpolf) - [gmvapich2](#gmvapich2) - [gmvolf](#gmvolf) - [GNU](#gnu) - [goalf](#goalf) - [gobff](#gobff) - [goblf](#goblf) - [gofbf](#gofbf) - [golf](#golf) - [golfc](#golfc) - [gomkl](#gomkl) - [gomklc](#gomklc) - [gompi](#gompi) - [gompic](#gompic) - [goolf](#goolf) - [goolfc](#goolfc) - [gpsmpi](#gpsmpi) - [gpsolf](#gpsolf) - [gqacml](#gqacml) - [gsmpi](#gsmpi) - [gsolf](#gsolf) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [ictce](#ictce) - [ifbf](#ifbf) - [iibff](#iibff) - [iimkl](#iimkl) - [iimklc](#iimklc) - [iimpi](#iimpi) - [iimpic](#iimpic) - [iiqmpi](#iiqmpi) - [impich](#impich) - [impmkl](#impmkl) - [intel-compilers](#intel-compilers) - [intel-para](#intel-para) - [intel](#intel) - [intelcuda](#intelcuda) - [iofbf](#iofbf) - [iomkl](#iomkl) - [iomklc](#iomklc) - [iompi](#iompi) - [iompic](#iompic) - [ipsmpi](#ipsmpi) - [iqacml](#iqacml) - [ismkl](#ismkl) - [NVHPC](#nvhpc) - [nvofbf](#nvofbf) - [nvompi](#nvompi) - [nvompic](#nvompic) - [nvpsmpi](#nvpsmpi) - [nvpsmpic](#nvpsmpic) - [PGI](#pgi) - [pmkl](#pmkl) - [pomkl](#pomkl) - [pompi](#pompi) - [system](#system) - [xlcxlf](#xlcxlf) - [xlmpich2](#xlmpich2) - [xlmpich](#xlmpich) - [xlmvapich2](#xlmvapich2) - [xlompi](#xlompi) ## cgmpich @@ -2284,6 +2284,50 @@ option |description ``verbose`` |Verbose output |``False`` ``veryloose`` |Very loose precision |``False`` +## ifbf + +### Available options for ifbf toolchain + +option |description |default +-------------------------|------------------------------------------------------------------------------------------------------------------------------------------|--------- +``32bit`` |Compile 32bit target |``False`` +``cciscxx`` |Use CC as CXX |``False`` +``cstd`` |Specify C standard |``None`` +``debug`` |Enable debug |``False`` +``defaultopt`` |Default compiler optimizations |``False`` +``defaultprec`` |Default precision |``False`` +``error-unknown-option`` |Error instead of warning for unknown options |``False`` +``extra_cflags`` |Specify extra CFLAGS options. |``None`` +``extra_cxxflags`` |Specify extra CXXFLAGS options. |``None`` +``extra_f90flags`` |Specify extra F90FLAGS options. |``None`` +``extra_fcflags`` |Specify extra FCFLAGS options. |``None`` +``extra_fflags`` |Specify extra FFLAGS options. |``None`` +``i8`` |Integers are 8 byte integers |``False`` +``ieee`` |Adhere to IEEE-754 rules |``False`` +``intel-static`` |Link Intel provided libraries statically |``False`` +``loose`` |Loose precision |``False`` +``lowopt`` |Low compiler optimizations |``False`` +``no-icc`` |Don't set Intel specific macros |``False`` +``noopt`` |Disable compiler optimizations |``False`` +``oneapi`` |Use oneAPI compilers icx/icpx/ifx instead of classic compilers |``None`` +``oneapi_c_cxx`` |Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer)|``None`` +``oneapi_fortran`` |Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler |``False`` +``openmp`` |Enable OpenMP |``False`` +``opt`` |High compiler optimizations |``False`` +``optarch`` |Enable architecture optimizations |``True`` +``packed-linker-options``|Pack the linker options as comma separated list |``False`` +``pic`` |Use PIC |``False`` +``precise`` |High precision |``False`` +``r8`` |Real is 8 byte real |``False`` +``rpath`` |Use RPATH wrappers when --rpath is enabled in EasyBuild configuration |``True`` +``shared`` |Build shared library |``False`` +``static`` |Build static library |``False`` +``strict`` |Strict (highest) precision |``False`` +``unroll`` |Unroll loops |``False`` +``vectorize`` |Enable compiler auto-vectorization, default except for noopt and lowopt |``None`` +``verbose`` |Verbose output |``False`` +``veryloose`` |Very loose precision |``False`` + ## iibff ### Available options for iibff toolchain @@ -2803,6 +2847,51 @@ option |description ``verbose`` |Verbose output |``False`` ``veryloose`` |Very loose precision |``False`` +## iofbf + +### Available options for iofbf toolchain + +option |description |default +-------------------------|------------------------------------------------------------------------------------------------------------------------------------------|--------- +``32bit`` |Compile 32bit target |``False`` +``cciscxx`` |Use CC as CXX |``False`` +``cstd`` |Specify C standard |``None`` +``debug`` |Enable debug |``False`` +``defaultopt`` |Default compiler optimizations |``False`` +``defaultprec`` |Default precision |``False`` +``error-unknown-option`` |Error instead of warning for unknown options |``False`` +``extra_cflags`` |Specify extra CFLAGS options. |``None`` +``extra_cxxflags`` |Specify extra CXXFLAGS options. |``None`` +``extra_f90flags`` |Specify extra F90FLAGS options. |``None`` +``extra_fcflags`` |Specify extra FCFLAGS options. |``None`` +``extra_fflags`` |Specify extra FFLAGS options. |``None`` +``i8`` |Integers are 8 byte integers |``False`` +``ieee`` |Adhere to IEEE-754 rules |``False`` +``intel-static`` |Link Intel provided libraries statically |``False`` +``loose`` |Loose precision |``False`` +``lowopt`` |Low compiler optimizations |``False`` +``no-icc`` |Don't set Intel specific macros |``False`` +``noopt`` |Disable compiler optimizations |``False`` +``oneapi`` |Use oneAPI compilers icx/icpx/ifx instead of classic compilers |``None`` +``oneapi_c_cxx`` |Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer)|``None`` +``oneapi_fortran`` |Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler |``False`` +``openmp`` |Enable OpenMP |``False`` +``opt`` |High compiler optimizations |``False`` +``optarch`` |Enable architecture optimizations |``True`` +``packed-linker-options``|Pack the linker options as comma separated list |``False`` +``pic`` |Use PIC |``False`` +``precise`` |High precision |``False`` +``r8`` |Real is 8 byte real |``False`` +``rpath`` |Use RPATH wrappers when --rpath is enabled in EasyBuild configuration |``True`` +``shared`` |Build shared library |``False`` +``static`` |Build static library |``False`` +``strict`` |Strict (highest) precision |``False`` +``unroll`` |Unroll loops |``False`` +``usempi`` |Use MPI compiler as default compiler |``False`` +``vectorize`` |Enable compiler auto-vectorization, default except for noopt and lowopt |``None`` +``verbose`` |Verbose output |``False`` +``veryloose`` |Very loose precision |``False`` + ## iomkl ### Available options for iomkl toolchain diff --git a/docs/version-specific/toolchains.md b/docs/version-specific/toolchains.md index 649b4960d..ae399fd0e 100644 --- a/docs/version-specific/toolchains.md +++ b/docs/version-specific/toolchains.md @@ -57,6 +57,7 @@ Name |Compiler(s) |MPI |Linear algebra |FFT **iccifort** |icc, ifort |*(none)* |*(none)* |*(none)* **iccifortcuda** |icc, ifort, CUDA|*(none)* |*(none)* |*(none)* **ictce** |icc, ifort |impi |imkl |imkl +**ifbf** |intel-compilers |*(none)* |FlexiBLAS |FFTW **iibff** |icc, ifort |impi |BLIS, libFLAME, ScaLAPACK|FFTW **iimkl** |icc, ifort |*(none)* |imkl |imkl **iimklc** |icc, ifort |*(none)* |imkl |imkl @@ -69,6 +70,7 @@ Name |Compiler(s) |MPI |Linear algebra |FFT **intel-compilers**|intel-compilers |*(none)* |*(none)* |*(none)* **intel-para** |icc, ifort |psmpi |imkl |imkl **intelcuda** |icc, ifort, CUDA|impi |imkl |imkl +**iofbf** |icc, ifort |OpenMPI |FlexiBLAS, ScaLAPACK |FFTW **iomkl** |icc, ifort |OpenMPI |imkl |imkl **iomklc** |icc, ifort, CUDA|OpenMPI |imkl |imkl **iompi** |icc, ifort |OpenMPI |*(none)* |*(none)* From 51e8f9a3bf7f987164601ee6aa7eb787dc9b6273 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 13:58:01 +0200 Subject: [PATCH 40/41] add release notes for EasyBuild v4.8.1 --- docs/changelog-docs.md | 3 + docs/release-notes.md | 170 ++++++++++++++++++++++++++++++++++++++++- 2 files changed, 169 insertions(+), 4 deletions(-) diff --git a/docs/changelog-docs.md b/docs/changelog-docs.md index c1871a195..9d8db8912 100644 --- a/docs/changelog-docs.md +++ b/docs/changelog-docs.md @@ -7,6 +7,9 @@ search: (for EasyBuild release notes, see [EasyBuild release notes][release_notes]) +- **release 20230911.01** (*9 Sept 2023*): update + release notes for EasyBuild v4.8.1 (see + [EasyBuild v4.8.1 (11 Sept 2023)][release_notes_eb481]) - **release 20230707.01** (*7 July 2023*): update release notes for EasyBuild v4.8.0 (see [EasyBuild v4.8.0 (7 July 2023)][release_notes_eb480]) diff --git a/docs/release-notes.md b/docs/release-notes.md index b507cb89a..727136a70 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -6,10 +6,172 @@ search: # EasyBuild release notes {: #release_notes } The latest version of EasyBuild provides support for building and -installing [**3,161** different software packages](../version-specific/supported-software), -including 39 different (compiler) toolchains. -It contains 249 software-specific easyblocks and 42 generic easyblocks, -alongside 17,511 easyconfig files. +installing [**3,244** different software packages](../version-specific/supported-software), +including 40 different (compiler) toolchains. +It contains 251 software-specific easyblocks and 42 generic easyblocks, +alongside 18,021 easyconfig files. + + +## EasyBuild v4.8.1 (11 Sept 2023) {: #release_notes_eb481 } + +bugix/update release + +**framework** + +- various enhancements, including: + - add end-to-end test for running EasyBuild in different Linux distros using containers ([#3968](https://github.com/easybuilders/easybuild-framework/pull/3968)) + - suggest default title in `--review-pr` ([#4287](https://github.com/easybuilders/easybuild-framework/pull/4287)) + - add `build_and_install_loop` hooks to run before and after the install loop for individual easyconfigs ([#4304](https://github.com/easybuilders/easybuild-framework/pull/4304)) + - implement support for `cancel_hook` and `fail_hook` ([#4315](https://github.com/easybuilders/easybuild-framework/pull/4315), [#4325](https://github.com/easybuilders/easybuild-framework/pull/4325)) + - add postiter hook to the list of steps so the corresponding hook can be used ([#4316](https://github.com/easybuilders/easybuild-framework/pull/4316)) + - add `run_shell_cmd` hook ([#4323](https://github.com/easybuilders/easybuild-framework/pull/4323)) + - add `build_info_msg` easyconfig parameter to print message during installation of an easyconfig ([#4324](https://github.com/easybuilders/easybuild-framework/pull/4324)) + - add `--silence-hook-trigger` configuration option to supress printing of debug message every time a hook is triggered ([#4329](https://github.com/easybuilders/easybuild-framework/pull/4329)) + - add support for using fine grained Github tokens ([#4332](https://github.com/easybuilders/easybuild-framework/pull/4332)) + - add definitions for `ifbf` and `iofbf` toolchain ([#4337](https://github.com/easybuilders/easybuild-framework/pull/4337)) + - add support for submodule filtering and specifying extra Git configuration in `git_config` ([#4338](https://github.com/easybuilders/easybuild-framework/pull/4338), [#4339](https://github.com/easybuilders/easybuild-framework/pull/4339)) +- various bug fixes, including: + - improve error when checksum dict has no entry for a file ([#4150](https://github.com/easybuilders/easybuild-framework/pull/4150)) + - avoid error being logged when `checksums.json` is not found ([#4261](https://github.com/easybuilders/easybuild-framework/pull/4261)) + - don't fail in `mkdir` if path gets created while processing it ([#4300](https://github.com/easybuilders/easybuild-framework/pull/4300), [#4328](https://github.com/easybuilders/easybuild-framework/pull/4328)) + - ignore request for external module (meta)data when no modules tool is active ([#4308](https://github.com/easybuilders/easybuild-framework/pull/4308)) + - use `sys.executable` to obtain path to `python` command in tests, rather than assuming that `python` command is available in `$PATH` ([#4309](https://github.com/easybuilders/easybuild-framework/pull/4309)) + - fix `test_add_and_remove_module_path` by replacing string comparison of paths by checking whether they point to the same path (since symlinks may cause trouble) ([#4312](https://github.com/easybuilders/easybuild-framework/pull/4312)) + - enhance `Toolchain.get_flag` to handle lists ([#4319](https://github.com/easybuilders/easybuild-framework/pull/4319)) + - only add extensions in module file if there are extensions ([#4331](https://github.com/easybuilders/easybuild-framework/pull/4331)) + +**easyblocks** + +- new custom easyblock for sympy ([#2949](https://github.com/easybuilders/easybuild-easyblocks/pull/2949)) and tensorflow-compression ([#2990](https://github.com/easybuilders/easybuild-easyblocks/pull/2990)) +- minor enhancements and updates, including: + - drop unnecessary CUDA stub libraries from `$LIBRARY_PATH` ([#2793](https://github.com/easybuilders/easybuild-easyblocks/pull/2793)) + - update Score-P easyblock to use `--with-nocross-compiler-suite=nvhpc` for recent software versions ([#2928](https://github.com/easybuilders/easybuild-easyblocks/pull/2928)) + - unset `$CPPFLAGS`, `$LDFLAGS`, `$LIB` which may interfere with Score-P configure magic ([#2928](https://github.com/easybuilders/easybuild-easyblocks/pull/2928)) + - update Clang easyblock for versions >= 16 + run tests only for final stage of bootstrap build ([#2929](https://github.com/easybuilders/easybuild-easyblocks/pull/2929)) + - handle new directory structure for Intel Advisor ([#2942](https://github.com/easybuilders/easybuild-easyblocks/pull/2942)) + - use `DCPU_BASELINE=DETECT` for OpenCV when default optarch compiler option is used ([#2954](https://github.com/easybuilders/easybuild-easyblocks/pull/2954)) + - update MXNet easyblock + don't try to install R extension by default for MXNet >= 1.0 ([#2955](https://github.com/easybuilders/easybuild-easyblocks/pull/2955)) + - use `checkMCR.sh` to determine if we have the correct MCR for FreeSurfer ([#2962](https://github.com/easybuilders/easybuild-easyblocks/pull/2962)) + - add options to `MesonNinja` easyblock to customize `build_cmd`, `install_cmd`, `builddir` ([#2963](https://github.com/easybuilders/easybuild-easyblocks/pull/2963), [#2993](https://github.com/easybuilders/easybuild-easyblocks/pull/2993)) + - add support for building CP2K with libvori support ([#2967](https://github.com/easybuilders/easybuild-easyblocks/pull/2967)) + - enable system `pybind11` for PyTorch 1.10+ to make sure `pybind11` provided as dependency is used ([#2968](https://github.com/easybuilders/easybuild-easyblocks/pull/2968)) + - update LLVM easyblock for LLVM v16: symlink `third-party` to `third-party-.src` ([#2970](https://github.com/easybuilders/easybuild-easyblocks/pull/2970), [#2994](https://github.com/easybuilders/easybuild-easyblocks/pull/2994)) + - update scipy easyblock for scipy >= 1.11.0 ([#2971](https://github.com/easybuilders/easybuild-easyblocks/pull/2971), [#2980](https://github.com/easybuilders/easybuild-easyblocks/pull/2980)) + - update sanity check for Mesa >= 22.3 ([#2973](https://github.com/easybuilders/easybuild-easyblocks/pull/2973)) + - update sanity check for OpenFOAM 11 ([#2978](https://github.com/easybuilders/easybuild-easyblocks/pull/2978)) + - add support to `PerlModule` easyblock to customize prefix option used in installation command ([#2979](https://github.com/easybuilders/easybuild-easyblocks/pull/2979)) + - update TensorFlow easyblock for v2.13 since LMDB is no longer a dependency ([#2982](https://github.com/easybuilders/easybuild-easyblocks/pull/2982)) + - enhance PyTorch easyblock to print individual failed tests ([#2983](https://github.com/easybuilders/easybuild-easyblocks/pull/2983)) + - enhance PETSc easyblock to support using custom `$PETSC_ARCH` ([#2987](https://github.com/easybuilders/easybuild-easyblocks/pull/2987)) +- various bug fixes, including: + - correctly determine path to active binutils in TensorFlow easyblock ([#2218](https://github.com/easybuilders/easybuild-easyblocks/pull/2218)) + - patch Java binaries/libraries when using alternate sysroot to ensure correct glibc & co are picked up + add custom sanity check ([#2557](https://github.com/easybuilders/easybuild-easyblocks/pull/2557), [#2995](https://github.com/easybuilders/easybuild-easyblocks/pull/2995)) + - update OpenMPI easyblock to fix sanity check for Clang-based compilers ([#2774](https://github.com/easybuilders/easybuild-easyblocks/pull/2774)) + - improve depot management in `JuliaPackage` easyblock ([#2935](https://github.com/easybuilders/easybuild-easyblocks/pull/2935)) + - disable disk space check in STAR-CCM+ installer ([#2956](https://github.com/easybuilders/easybuild-easyblocks/pull/2956)) + - fix type check for `optarch` value in `Cargo` easyblock ([#2969](https://github.com/easybuilders/easybuild-easyblocks/pull/2969)) + - conditionally add `-Wno-unused-command-line-argument` to `$CFLAGS` to fix error when installing `imkl-FFTW` with RPATH ([#2975](https://github.com/easybuilders/easybuild-easyblocks/pull/2975)) + - enhance `PythonPackage` easyblock to deal with `posix_local` installation scheme used by Python in recent Debian/Ubuntu versions ([#2977](https://github.com/easybuilders/easybuild-easyblocks/pull/2977), [#2988](https://github.com/easybuilders/easybuild-easyblocks/pull/2988)) + - don't add MATLAB libraries to `$LD_LIBRARY_PATH` ([#2981](https://github.com/easybuilders/easybuild-easyblocks/pull/2981)) + - enhance Mesa easyblock to append EGL vendor library directory path to `$__EGL_VENDOR_LIBRARY_DIRS` ([#2985](https://github.com/easybuilders/easybuild-easyblocks/pull/2985)) + - fix typo in TensorFlow easyblock when finding libdir of OpenSSL ([#2989](https://github.com/easybuilders/easybuild-easyblocks/pull/2989)) + +**easyconfigs** + +- added example easyconfig files for 83 new software packages: + - ALAMODE ([#18733](https://github.com/easybuilders/easybuild-easyconfigs/pull/18733)), AMRFinderPlus ([#18559](https://github.com/easybuilders/easybuild-easyconfigs/pull/18559)), Ax (#68), bcrypt ([#18208](https://github.com/easybuilders/easybuild-easyconfigs/pull/18208)), bench ([#18656](https://github.com/easybuilders/easybuild-easyconfigs/pull/18656)), BgeeDB ([#18743](https://github.com/easybuilders/easybuild-easyconfigs/pull/18743)), + Boost.Python-NumPy ([#18505](https://github.com/easybuilders/easybuild-easyconfigs/pull/18505)), CatBoost ([#18591](https://github.com/easybuilders/easybuild-easyconfigs/pull/18591)), centerline ([#18273](https://github.com/easybuilders/easybuild-easyconfigs/pull/18273)), cffi (#7105), ChIPseeker ([#18662](https://github.com/easybuilders/easybuild-easyconfigs/pull/18662)), + connected-components-3d ([#18289](https://github.com/easybuilders/easybuild-easyconfigs/pull/18289)), cryptography (#8495), CVglasso ([#18657](https://github.com/easybuilders/easybuild-easyconfigs/pull/18657)), DiffBind ([#18663](https://github.com/easybuilders/easybuild-easyconfigs/pull/18663)), drmaa-python ([#18614](https://github.com/easybuilders/easybuild-easyconfigs/pull/18614)), + e3nn ([#18304](https://github.com/easybuilders/easybuild-easyconfigs/pull/18304)), flit ([#18208](https://github.com/easybuilders/easybuild-easyconfigs/pull/18208)), GAPPadder ([#18692](https://github.com/easybuilders/easybuild-easyconfigs/pull/18692)), GenerativeModels ([#18451](https://github.com/easybuilders/easybuild-easyconfigs/pull/18451)), geosphere ([#18659](https://github.com/easybuilders/easybuild-easyconfigs/pull/18659)), gffutils ([#18331](https://github.com/easybuilders/easybuild-easyconfigs/pull/18331)), + gkmSVM ([#18660](https://github.com/easybuilders/easybuild-easyconfigs/pull/18660)), hampel ([#18409](https://github.com/easybuilders/easybuild-easyconfigs/pull/18409)), hatchling ([#18208](https://github.com/easybuilders/easybuild-easyconfigs/pull/18208)), HDF-EOS2 ([#18297](https://github.com/easybuilders/easybuild-easyconfigs/pull/18297)), Hybpiper ([#18414](https://github.com/easybuilders/easybuild-easyconfigs/pull/18414)), inih ([#18516](https://github.com/easybuilders/easybuild-easyconfigs/pull/18516)), + IsoformSwitchAnalyzeR ([#18664](https://github.com/easybuilders/easybuild-easyconfigs/pull/18664)), IsoQuant ([#18331](https://github.com/easybuilders/easybuild-easyconfigs/pull/18331)), Jupyter-bundle ([#18634](https://github.com/easybuilders/easybuild-easyconfigs/pull/18634)), JupyterNotebook ([#18735](https://github.com/easybuilders/easybuild-easyconfigs/pull/18735), [#18735](https://github.com/easybuilders/easybuild-easyconfigs/pull/18735)), + leafcutter ([#18615](https://github.com/easybuilders/easybuild-easyconfigs/pull/18615)), libleidenalg ([#18548](https://github.com/easybuilders/easybuild-easyconfigs/pull/18548)), LIBSVM-Python ([#18455](https://github.com/easybuilders/easybuild-easyconfigs/pull/18455)), libvori ([#18379](https://github.com/easybuilders/easybuild-easyconfigs/pull/18379)), maturin ([#18405](https://github.com/easybuilders/easybuild-easyconfigs/pull/18405)), + meboot ([#18658](https://github.com/easybuilders/easybuild-easyconfigs/pull/18658)), mgen ([#18402](https://github.com/easybuilders/easybuild-easyconfigs/pull/18402)), Mikado ([#18614](https://github.com/easybuilders/easybuild-easyconfigs/pull/18614)), NanoCaller ([#18726](https://github.com/easybuilders/easybuild-easyconfigs/pull/18726)), nbclassic ([#18617](https://github.com/easybuilders/easybuild-easyconfigs/pull/18617)), ncolor (#7146), + nose3 ([#18234](https://github.com/easybuilders/easybuild-easyconfigs/pull/18234)), novaSTA ([#18601](https://github.com/easybuilders/easybuild-easyconfigs/pull/18601)), Omnipose ([#18402](https://github.com/easybuilders/easybuild-easyconfigs/pull/18402)), Optax ([#18610](https://github.com/easybuilders/easybuild-easyconfigs/pull/18610)), paramiko (#1504), Parsl ([#18408](https://github.com/easybuilders/easybuild-easyconfigs/pull/18408)), + peakdetect ([#18402](https://github.com/easybuilders/easybuild-easyconfigs/pull/18402)), PICRUSt2 ([#18333](https://github.com/easybuilders/easybuild-easyconfigs/pull/18333), [#18459](https://github.com/easybuilders/easybuild-easyconfigs/pull/18459)), Platypus-Opt ([#18291](https://github.com/easybuilders/easybuild-easyconfigs/pull/18291)), PortMidi ([#18252](https://github.com/easybuilders/easybuild-easyconfigs/pull/18252)), pv ([#16439](https://github.com/easybuilders/easybuild-easyconfigs/pull/16439)), + py-c3d ([#18409](https://github.com/easybuilders/easybuild-easyconfigs/pull/18409)), pygame ([#18252](https://github.com/easybuilders/easybuild-easyconfigs/pull/18252)), pyodbc ([#18334](https://github.com/easybuilders/easybuild-easyconfigs/pull/18334)), Python-bundle-PyPI ([#18208](https://github.com/easybuilders/easybuild-easyconfigs/pull/18208)), qforce ([#18456](https://github.com/easybuilders/easybuild-easyconfigs/pull/18456)), + RFdiffusion ([#18304](https://github.com/easybuilders/easybuild-easyconfigs/pull/18304)), Rhodium ([#18291](https://github.com/easybuilders/easybuild-easyconfigs/pull/18291)), ruptures ([#18306](https://github.com/easybuilders/easybuild-easyconfigs/pull/18306)), Sabre ([#18342](https://github.com/easybuilders/easybuild-easyconfigs/pull/18342)), scGSVA ([#18401](https://github.com/easybuilders/easybuild-easyconfigs/pull/18401)), scib-metrics ([#18734](https://github.com/easybuilders/easybuild-easyconfigs/pull/18734)), + scikit-plot ([#18377](https://github.com/easybuilders/easybuild-easyconfigs/pull/18377)), SDL2_mixer ([#18252](https://github.com/easybuilders/easybuild-easyconfigs/pull/18252)), SDL2_ttf ([#18252](https://github.com/easybuilders/easybuild-easyconfigs/pull/18252)), segment-anything ([#18290](https://github.com/easybuilders/easybuild-easyconfigs/pull/18290)), sentinelsat ([#18367](https://github.com/easybuilders/easybuild-easyconfigs/pull/18367)), + setuptools-rust ([#18208](https://github.com/easybuilders/easybuild-easyconfigs/pull/18208)), slurm-drmaa ([#18614](https://github.com/easybuilders/easybuild-easyconfigs/pull/18614)), SuAVE-biomat ([#18678](https://github.com/easybuilders/easybuild-easyconfigs/pull/18678)), T-Coffee ([#17916](https://github.com/easybuilders/easybuild-easyconfigs/pull/17916)), + tensorflow-compression ([#18676](https://github.com/easybuilders/easybuild-easyconfigs/pull/18676)), torchvf ([#18637](https://github.com/easybuilders/easybuild-easyconfigs/pull/18637)), tornado ([#18511](https://github.com/easybuilders/easybuild-easyconfigs/pull/18511)), tseriesEntropy ([#18661](https://github.com/easybuilders/easybuild-easyconfigs/pull/18661)), TXR ([#18665](https://github.com/easybuilders/easybuild-easyconfigs/pull/18665)), + unifdef ([#18427](https://github.com/easybuilders/easybuild-easyconfigs/pull/18427)), UniFrac ([#18407](https://github.com/easybuilders/easybuild-easyconfigs/pull/18407)), virtualenv (#2660), WFA2 ([#18636](https://github.com/easybuilders/easybuild-easyconfigs/pull/18636)) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.10.3, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07-2, anndata 0.9.2, + APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng 3.9.0, + assimp 5.2.5, BAGEL 1.2.2, bam-readcount 1.0.1, Bazel 6.3.1, BCFtools 1.18, BeautifulSoup 4.12.2, BEDTools 2.31.0, + biom-format 2.1.15, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, c-ares 1.19.1, ccache 4.8.3, CDO 2.2.2, CFITSIO 4.3.0, + Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CoinUtils 2.11.9, + conan 1.60.2, configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, CubeLib 4.8.1, CubeWriter 4.8.1, + CUDA 12.2.2, dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, dill 0.3.7, ecBuild 3.8.0, ecCodes 2.31.0, + ELPA 2023.05.001, exiv2 0.28.0, expecttest 0.1.5, fastparquet 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0, + flatbuffers 23.5.26, flatbuffers-python 23.5.26, FreeSurfer 7.4.1, fsom 20151117, gc 8.2.4, GCC 13.2.0, GDB 13.2, + GEOS 3.12.0, gettext 0.22, GHC 9.2.2, Ghostscript 10.01.2, GLib 2.77.1, gmpy2 2.1.5, gnuplot 5.4.8, + GObject-Introspection 1.76.1, gperftools 2.12, Graphviz 8.1.0, gRPC 1.57.0, GST-plugins-base 1.22.5, + GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, hiredis 1.2.0, + Horovod 0.28.1, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2, + igraph 0.10.6, iimkl/2023a, imageio 2.31.1, ImageMagick 7.1.1-15, inferCNV 1.14.2, IPython 8.14.0, ISL 0.26, + Julia 1.9.3, JupyterLab 4.0.5, jupyter-resource-usage 1.0.0, kma 1.4.12a, KMC 3.2.2, leidenalg 0.10.1, + libdrm 2.4.115, libdwarf 0.7.0, libfabric 1.19.0, libgit2 1.7.1, libGLU 9.0.3, libsndfile 1.2.2, libwpe 1.14.1, + libxml2 2.11.5, LittleCMS 2.15, LLVM 16.0.6, Lua 5.4.6, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3, + Mamba 23.1.0, matplotlib 3.7.2, medaka 1.8.1 + 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2, + Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, MRtrix 3.0.4, MUMPS 5.6.1, MXNet 1.9.1, napari 0.4.18, ncdu 1.18, + netCDF 4.9.2, netCDF-Fortran 4.6.1, nettle 3.9.1, networkx 3.1, nodejs 18.17.1, nsync 1.26.0, NVHPC 23.7, + OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenImageIO 2.4.14.0, Osi 0.108.8, OTF2 3.0.3, Pango 1.50.14, + PAPI 7.0.1, parallel 20230722, Perl 5.38.0, Pillow 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pkgconf 2.0.3, + plotly.py 5.16.0, PLUMED 2.9.0, pocl 4.0, poetry 1.5.1, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5, + PuLP 2.7.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PyGObject 3.44.1, Pylint 2.17.4, pyproj 3.6.0, + pyro-ppl 1.8.4, python-igraph 0.10.6, PyZMQ 25.1.1, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2, + rclone 1.63.1, RE2 2023-08-01, re2c 3.1, RegTools 1.0.0, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18, + Scalene 1.5.26, scikit-build 0.17.6, scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3, + SDL2 2.28.2, SDL2_image 2.6.3, setuptools 64.0.3, SeuratWrappers 20221022, snakemake 7.32.3, SpaceRanger 2.1.0, + SpiecEasi 1.1.1, Stack 2.11.1, STAR 2.7.11a, SUNDIALS 6.6.0, SWIG 4.1.1, sympy 1.12, tabixpp 1.1.2, tbb 2021.10.0, + tbl2asn 20230713, tcsh 6.24.10, TensorFlow 2.13.0, tensorflow-probability 0.19.0, Tk 8.6.13, Tkinter 3.11.3, + tqdm 4.66.1, unixODBC 2.3.11, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, Wayland 1.22.0, + WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wxPython 4.2.1, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2, + Z3 4.12.2, zarr 2.16.0 +- minor enhancements, including: + - add extensions to recent R-bundle-Bioconductors easyconfigs: UCell ([#18281](https://github.com/easybuilders/easybuild-easyconfigs/pull/18281)), decoupleR ([#18399](https://github.com/easybuilders/easybuild-easyconfigs/pull/18399), [#18552](https://github.com/easybuilders/easybuild-easyconfigs/pull/18552)), RnBeads ([#18682](https://github.com/easybuilders/easybuild-easyconfigs/pull/18682)) + - add extensions to recent R easyconfigs: tabletools ([#18510](https://github.com/easybuilders/easybuild-easyconfigs/pull/18510)), flextables ([#18719](https://github.com/easybuilders/easybuild-easyconfigs/pull/18719)) + - add test for easyconfig file permissions ([#18647](https://github.com/easybuilders/easybuild-easyconfigs/pull/18647)) + - simplify build and install options for Ghostscript ([#18750](https://github.com/easybuilders/easybuild-easyconfigs/pull/18750)) +- various bug fixes, including: + - set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value ([#17976](https://github.com/easybuilders/easybuild-easyconfigs/pull/17976)) + - remove superflous dependencies from Horovod easyconfig on top of PyTorch ([#18262](https://github.com/easybuilders/easybuild-easyconfigs/pull/18262)) + - disable building documentation for libsigc++ 2.10.x ([#18301](https://github.com/easybuilders/easybuild-easyconfigs/pull/18301)) + - use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 ([#18303](https://github.com/easybuilders/easybuild-easyconfigs/pull/18303)) + - add `hpctestlib` to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig ([#18320](https://github.com/easybuilders/easybuild-easyconfigs/pull/18320)) + - fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command ([#18348](https://github.com/easybuilders/easybuild-easyconfigs/pull/18348), [#18432](https://github.com/easybuilders/easybuild-easyconfigs/pull/18432), [#18440](https://github.com/easybuilders/easybuild-easyconfigs/pull/18440), [#18441](https://github.com/easybuilders/easybuild-easyconfigs/pull/18441)) + - add/fix patches for PyTorch 1.13.1 w/ foss/2022a ([#18371](https://github.com/easybuilders/easybuild-easyconfigs/pull/18371)) + - add missing nbclassic extension to jupyter-server 1.21.0 ([#18389](https://github.com/easybuilders/easybuild-easyconfigs/pull/18389)) + - fix batchspawner for JupyterHub 3.0 ([#18390](https://github.com/easybuilders/easybuild-easyconfigs/pull/18390)) + - fix compiler flags and toolchain options for ScaLAPACK 2.1.0 + 2.2.0 ([#18396](https://github.com/easybuilders/easybuild-easyconfigs/pull/18396), [#18397](https://github.com/easybuilders/easybuild-easyconfigs/pull/18397)) + - add patch to fix CUDA race condition problem for Score-P v8.0 ([#18411](https://github.com/easybuilders/easybuild-easyconfigs/pull/18411)) + - add `-DABSL_PROPAGATE_CXX_STD=ON` to recent Abseil easyconfigs (required for PyTorch) ([#18413](https://github.com/easybuilders/easybuild-easyconfigs/pull/18413)) + - add missing patches for PyTorch 1.12.0 w/ foss/2022a ([#18430](https://github.com/easybuilders/easybuild-easyconfigs/pull/18430)) + - fix regression in GCC 12.1 + 12.2 with wrong warnings ([#18434](https://github.com/easybuilders/easybuild-easyconfigs/pull/18434)) + - add patch for LIBSVM 3.30 to pass `$CFLAGS` + `$LDFLAGS` and run tests ([#18454](https://github.com/easybuilders/easybuild-easyconfigs/pull/18454)) + - add patch for Automake 1.16.5 to fix help2man error ([#18468](https://github.com/easybuilders/easybuild-easyconfigs/pull/18468)) + - consistently use ON/OFF for -DBUILD_SHARED_LIBS ([#18484](https://github.com/easybuilders/easybuild-easyconfigs/pull/18484)) + - add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 ([#18491](https://github.com/easybuilders/easybuild-easyconfigs/pull/18491)) + - add patches to fix PyTorch 1.12.1 + 1.13.1 on POWER on POWER ([#18489](https://github.com/easybuilders/easybuild-easyconfigs/pull/18489), [#18490](https://github.com/easybuilders/easybuild-easyconfigs/pull/18490), [#18492](https://github.com/easybuilders/easybuild-easyconfigs/pull/18492), [#18493](https://github.com/easybuilders/easybuild-easyconfigs/pull/18493), [#18494](https://github.com/easybuilders/easybuild-easyconfigs/pull/18494), [#18500](https://github.com/easybuilders/easybuild-easyconfigs/pull/18500)) + - add patch to fix flaky `test_jit_legacy` test for PyTorch 1.13.1 ([#18500](https://github.com/easybuilders/easybuild-easyconfigs/pull/18500)) + - add alternative checksum for Extrae v4.0.4 ([#18564](https://github.com/easybuilders/easybuild-easyconfigs/pull/18564)) + - remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it ([#18630](https://github.com/easybuilders/easybuild-easyconfigs/pull/18630)) + - correct `dirs` in `sanity_check_paths` in template easyconfig ([#18635](https://github.com/easybuilders/easybuild-easyconfigs/pull/18635)) + - set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` ([#18641](https://github.com/easybuilders/easybuild-easyconfigs/pull/18641)) + - fix sanity check for ccache by setting `LC_ALL=C` ([#18677](https://github.com/easybuilders/easybuild-easyconfigs/pull/18677)) + - make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency ([#18680](https://github.com/easybuilders/easybuild-easyconfigs/pull/18680)) + - strip out hardcoded `-march=native` used by RapidJSON 1.1.0 ([#18725](https://github.com/easybuilders/easybuild-easyconfigs/pull/18725)) + - disable detection of Dbus broker for `at-spi2-core` ([#18727](https://github.com/easybuilders/easybuild-easyconfigs/pull/18727)) + - make sure that `moduleclass` is set in all easyconfig files (and is not set to default `base` module class) ([#18739](https://github.com/easybuilders/easybuild-easyconfigs/pull/18739)) + - add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 ([#18746](https://github.com/easybuilders/easybuild-easyconfigs/pull/18746)) + - add patch for PMIx 4.x to use `lchown` so links are not followed ([#18755](https://github.com/easybuilders/easybuild-easyconfigs/pull/18755)) +- other changes: + - update `Java/11` wrapper to Java/11.0.20 ([#18435](https://github.com/easybuilders/easybuild-easyconfigs/pull/18435)) + - use custom easyblock for recent sympy easyconfigs to prevent test failures ([#18428](https://github.com/easybuilders/easybuild-easyconfigs/pull/18428)) + - use `GCC/12.2.0` toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with `GCCcore/12.2.0` ([#18501](https://github.com/easybuilders/easybuild-easyconfigs/pull/18501)) + - disable wx support in gnuplot 5.4.6 ([#18648](https://github.com/easybuilders/easybuild-easyconfigs/pull/18648), [#18691](https://github.com/easybuilders/easybuild-easyconfigs/pull/18691)) + - filter out template + archived easyconfigs when determining changed easyconfigs in PRs ([#18753](https://github.com/easybuilders/easybuild-easyconfigs/pull/18753)) ## EasyBuild v4.8.0 (7 July 2023) {: #release_notes_eb480 } From 4381857dc2e6b7ea3cf858ec1ad09d6e59719290 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 13:58:36 +0200 Subject: [PATCH 41/41] fix typo in help message for --silence-hook-trigger --- docs/version-specific/eb-help.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index 95f4daa4a..228b571e6 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -298,7 +298,7 @@ Option flag |Option ``--set-gid-bit`` |Set group ID bit on newly created directories (default: False) ``--show-progress-bar`` |Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` |Silence specified deprecation warnings out of (python2, Lmod6, easyconfig, toolchain) (type comma-separated list) -``--silence-hook-trigger`` |Supress printing of debug message every time a hook is triggered (default: False) +``--silence-hook-trigger`` |Suppress printing of debug message every time a hook is triggered (default: False) ``--skip-extensions`` |Skip installation of extensions (default: False) ``-t, --skip-test-cases`` |Skip running test cases (default: False) ``--skip-test-step`` |Skip running the test step (e.g. unit tests) (default: False)