diff --git a/docs/common-toolchains.md b/docs/common-toolchains.md index 121286875..267bd860e 100644 --- a/docs/common-toolchains.md +++ b/docs/common-toolchains.md @@ -51,8 +51,8 @@ graph LR A --> |binutils| C[intel-compilers]; B --> |OpenMPI| E[gompi]; C --> |impi| F[iimpi]; - B --> |FlexiBLAS + FFTW + ScaLAPACK| D[gfbf]; - D --> |OpenMPI| G[foss]; + B --> |FlexiBLAS (incl. LAPACK) + FFTW| D[gfbf]; + D --> |OpenMPI + ScaLAPACK| G[foss]; E --> |FlexiBLAS + FFTW + ScaLAPACK| G[foss]; F --> |imkl| Z[intel]; C --> |imkl| H[iimkl]; diff --git a/docs/configuration.md b/docs/configuration.md index d8dcc3d41..c93f0062b 100644 --- a/docs/configuration.md +++ b/docs/configuration.md @@ -620,7 +620,9 @@ output of `type -f module` (in a `bash` shell), or `alias module` (in a `tcsh` s The actual module command (i.e., `modulecmd`, `modulecmd.tcl`, `lmod`, ...) must be available via `$PATH` (which is not standard), except when using Lmod -(in that case the `lmod` binary can also be located via `$LMOD_CMD`). +(in that case the `lmod` binary can also be located via `$LMOD_CMD`) or when using +Environment Modules (in that case the `modulecmd.tcl` binary can also be located via +`$MODULES_CMD`). For example, to indicate that EasyBuild should be using `Lmod` as modules tool: diff --git a/docs/easybuild-v5/changes-in-default-configuration.md b/docs/easybuild-v5/changes-in-default-configuration.md new file mode 100644 index 000000000..e71551c20 --- /dev/null +++ b/docs/easybuild-v5/changes-in-default-configuration.md @@ -0,0 +1,52 @@ +# Changes in default configuration in EasyBuild v5.0 + +*(for a full overview of changes in EasyBuild v5.0, see [here](overview-of-changes.md))* + +Various changes in default configuration included in EasyBuild v5.0, including: + +* [Enable RPATH linking by default][rpath] +* [Enable `--trace` by default][trace] + +--- + +## Enable RPATH linking by default {: #rpath } + +[RPATH linking][rpath_support] is enabled by default in EasyBuild v5.0 (see [easybuild-framework PR #4448](https://github.com/easybuilders/easybuild-framework/pull/4448)). + +The benefits for enabling RPATH are explained in [Why RPATH?][rpath_support_why]. + +This enhancement **does not** add any filtering of environment variables. This means `$LD_LIBRARY_PATH` +will continue to be appended by the environment module files EasyBuild generates, +unless it is configured to filter these variables (via `--filter-env-vars`, +see also [Relation to `$LD_LIBRARY_PATH`][rpath_support_LD_LIBRARY_PATH]). + +To disable RPATH linking, either: + +* Use the `--disable-rpath` command line option; +* Set the `$EASYBUILD_DISABLE_RPATH` environment variable; +* Disable RPATH linking in an EasyBuild [configuration file](../configuration.md#configuration_file): + + ``` ini + [override] + rpath=0 + ``` + + +--- + +## Enable `--trace` by default {: #trace } + +The [`--trace` option](../tracing-progress.md) is enabled by default (see [easybuild-framework PR #4250](https://github.com/easybuilders/easybuild-framework/pull/4250)). + +This makes the output produced by the `eb` command more informative, by providing more information about what's going on in the background. + +To disable trace output, either: + +* Use the `--disable-trace` command line option; +* Set the `$EASYBUILD_DISABLE_TRACE` environment variable; +* Disable trace mode in a [configuration file](../configuration.md#configuration_file): + + ``` ini + [override] + trace=0 + ``` diff --git a/docs/easybuild-v5/enhancements.md b/docs/easybuild-v5/enhancements.md index 16660f6c5..33b3543dd 100644 --- a/docs/easybuild-v5/enhancements.md +++ b/docs/easybuild-v5/enhancements.md @@ -5,7 +5,6 @@ Various significant enhancements are included in EasyBuild v5.0, including: * [`run_shell_cmd` function][run_shell_cmd] -* [Enable `--trace` by default][trace] --- @@ -13,21 +12,3 @@ Various significant enhancements are included in EasyBuild v5.0, including: See dedicated page on the new [`run_shell_cmd` function](run_shell_cmd.md). ---- - -## Enable `--trace` by default {: #trace } - -The [`--trace` option](../tracing-progress.md) is enabled by default (see [easybuild-framework PR #4250](https://github.com/easybuilders/easybuild-framework/pull/4250)). - -This makes the output produced by the `eb` command more informative, by providing more information about what's going on in the background. - -To disable trace output, either: - -* Use the `--disable-trace` command line option; -* Set the `$EASYBUILD_DISABLE_TRACE` environment variable; -* Disable trace mode in a [configuration file](../configuration.md#configuration_file): - - ``` ini - [override] - trace=0 - ``` diff --git a/docs/easybuild-v5/index.md b/docs/easybuild-v5/index.md index f6578511c..b1002acff 100644 --- a/docs/easybuild-v5/index.md +++ b/docs/easybuild-v5/index.md @@ -2,6 +2,7 @@ - [Overview of changes](overview-of-changes.md) - [Backwards-incompatible changes](backwards-incompatible-changes.md) + - [Changes in default configuration](changes-in-default-configuration.md) - [Enhancements](enhancements.md) - [`run_shell_cmd` function](run_shell_cmd.md) - [Deprecated functionality](deprecated-functionality.md) diff --git a/docs/easybuild-v5/overview-of-changes.md b/docs/easybuild-v5/overview-of-changes.md index 3eec0ff9f..9ab66bda3 100644 --- a/docs/easybuild-v5/overview-of-changes.md +++ b/docs/easybuild-v5/overview-of-changes.md @@ -3,16 +3,15 @@ !!! 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 section of the documentation regularly as the planned changes are being implemented, - and when there are [proposed changes](proposed-changes.md) where we are requesting community feedback. + We intend to update this section of the documentation regularly as the planned changes are being implemented. This page provides a concise overview of the most prominent changes in EasyBuild version 5.0, which can be categorized as: * [Enhancements](enhancements.md) +* [Changes in default configuration](changes-in-default-configuration.md) * [Backward-incompatible changes](backwards-incompatible-changes.md) * [Deprecated functionality](deprecated-functionality.md) -* [Proposed changes](proposed-changes.md) * [Policies](policies.md) For in-depth details on a particular change, see the pull requests that are linked diff --git a/docs/easybuild-v5/proposed-changes.md b/docs/easybuild-v5/proposed-changes.md deleted file mode 100644 index d7af4c5df..000000000 --- a/docs/easybuild-v5/proposed-changes.md +++ /dev/null @@ -1,9 +0,0 @@ -# Proposed changes for EasyBuild v5.0 - -*(for a full overview of changes in EasyBuild v5.0, see [here](overview-of-changes.md))* - -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](https://github.com/easybuilders/easybuild/issues/871) -* [Toolchain support policy](https://github.com/easybuilders/easybuild/issues/872) diff --git a/docs/installation.md b/docs/installation.md index 246bd2758..0d2b5bd4b 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -69,11 +69,11 @@ This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example.lo ``` !!! tip - The Tcl-based or Lmod implementations of environment modules do their default sorting differently. - The former will normally sort in the lexicographic order, while Lmod follows - an approach that is closer to Python's construct `LooseVersion` way of ordering. Such aspects - may make a big difference, if you have installed both versions 1.9.0 and 1.15.2, - with respect to what is the version being loaded by default. + The Tcl/C Environment Modules (version <= 3.2.10) does its default sorting differently than + newer versions of Environment Modules and Lmod. The former will normally sort in the + lexicographic order, while the latters follow an approach that is closer to Python's construct + `LooseVersion` way of ordering. Such aspects may make a big difference, if you have installed + both versions 1.9.0 and 1.15.2, with respect to what is the version being loaded by default. You can also run `eb --show-system-info` to see system information relevant to EasyBuild, or run`eb --show-config` to see the default EasyBuild configuration (see also [Configuring EasyBuild][configuring_easybuild]). @@ -356,12 +356,16 @@ Supported module tools: the `module` function; for example, using `type module` or `type -f module`. !!! note - For Lmod specifically, EasyBuild will try to fall back to finding the `lmod` binary via the `$LMOD_CMD` + For Lmod, EasyBuild will try to fall back to finding the `lmod` binary via the `$LMOD_CMD` environment variable, in case `lmod` is not available in `$PATH`. In EasyBuild versions *prior* to 2.1.1, the path specified by `$LMOD_CMD` was (erroneously) preferred over the (first) `lmod` binary available via `$PATH`. + For modern Tcl-only environment modules (version >= 4.0.0), EasyBuild will try to fall back to finding the + `modulecmd.tcl` binary via the `$MODULES_CMD` environment variable, in case `modulecmd.tcl` is not available + in `$PATH`. + Additional notes: diff --git a/docs/manipulating-dependencies.md b/docs/manipulating-dependencies.md index 174072713..be64621f6 100644 --- a/docs/manipulating-dependencies.md +++ b/docs/manipulating-dependencies.md @@ -85,8 +85,8 @@ $ eb HDF5-1.8.13-intel-2015a.eb --hide-deps=zlib,Szip -D ``` !!! note - Using Lmod (version >= 5.7.5), hidden modules can be made visible in the output of '`module avail`' using the - `--show-hidden` option. + Using Lmod (version >= 5.7.5) or Environment Modules (version >= 4.6.0), hidden modules can be made + visible in the output of '`module avail`' using respectively the `--show-hidden` or `--all` option. For example: diff --git a/docs/release-notes.md b/docs/release-notes.md index 6ea900a50..37f9e64fd 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -12,6 +12,273 @@ It contains 254 software-specific easyblocks and 43 generic easyblocks, alongside 18,752 easyconfig files. +## EasyBuild v4.9.1 (5 April 2024) {: #release_notes_eb491 } + +bugix/update release + +**framework** + +- various enhancements, including: + - make `is_rpath_wrapper` faster by only checking file contents if file is not located in subdirectory of RPATH wrapper subdirectory ([#4406](https://github.com/easybuilders/easybuild-framework/pull/4406)) + - add terse support to `--missing-modules` ([#4407](https://github.com/easybuilders/easybuild-framework/pull/4407)) + - adapt version pattern for `EnvironmentModules` to allow using development version ([#4416](https://github.com/easybuilders/easybuild-framework/pull/4416)) + - use `--all` option with `EnvironmentModules` v4.6+ to get available hidden modules ([#4417](https://github.com/easybuilders/easybuild-framework/pull/4417)) + - add support for appending to path environment variables via `modextrapaths_append` + add corresponding `allow_append_abs_path` ([#4436](https://github.com/easybuilders/easybuild-framework/pull/4436)) + - improve output produced by `--check-github` ([#4437](https://github.com/easybuilders/easybuild-framework/pull/4437)) + - add script for updating local git repos with `develop` branch ([#4438](https://github.com/easybuilders/easybuild-framework/pull/4438)) + - show error when multiple PR options are passed ([#4440](https://github.com/easybuilders/easybuild-framework/pull/4440)) + - improve `findPythonDeps` script to recognize non-canonical package names ([#4445](https://github.com/easybuilders/easybuild-framework/pull/4445)) + - add support for `--from-commit` and `--include-easyblocks-from-commit` ([#4468](https://github.com/easybuilders/easybuild-framework/pull/4468)) + - improve logging & handling of (empty) `--optarch` values ([#4481](https://github.com/easybuilders/easybuild-framework/pull/4481)) + - add `--short` option to `findUpdatedEcs` script ([#4488](https://github.com/easybuilders/easybuild-framework/pull/4488)) + - add generic GCC and Clang compiler flags for RISC-V ([#4489](https://github.com/easybuilders/easybuild-framework/pull/4489)) +- various bug fixes, including: + - clean up log file of `EasyBlock` instance in `check_sha256_checksums` ([#4452](https://github.com/easybuilders/easybuild-framework/pull/4452)) + - fix description of `backup-modules` configuration option ([#4456](https://github.com/easybuilders/easybuild-framework/pull/4456)) + - replace `'` with `"` for `printf` in CI workflow for running test suite to have bash replace a variable ([#4461](https://github.com/easybuilders/easybuild-framework/pull/4461)) + - use `cp -dR` instead of `cp -a` for shell script "extraction" ([#4465](https://github.com/easybuilders/easybuild-framework/pull/4465)) + - fix link to documentation in `close_pr` message ([#4466](https://github.com/easybuilders/easybuild-framework/pull/4466)) + - fix `test_github_merge_pr` by using more recent easyconfigs PR ([#4470](https://github.com/easybuilders/easybuild-framework/pull/4470)) + - add workaround for 404 error when installing packages in CI workflow for testing Apptainer integration ([#4472](https://github.com/easybuilders/easybuild-framework/pull/4472)) +- other changes: + - clean up & speed up environment checks ([#4409](https://github.com/easybuilders/easybuild-framework/pull/4409)) + - use more performant and concise dict construction by using dict comprehensions ([#4410](https://github.com/easybuilders/easybuild-framework/pull/4410)) + - remove superflous string formatting ([#4411](https://github.com/easybuilders/easybuild-framework/pull/4411)) + - clean up uses of `getattr` and `hasattr` ([#4412](https://github.com/easybuilders/easybuild-framework/pull/4412)) + - update copyright lines to 2024 ([#4494](https://github.com/easybuilders/easybuild-framework/pull/4494)) + +**easyblocks** + +- 1 new software-specific easyblock: DualSPHysics ([#3050](https://github.com/easybuilders/easybuild-easyblocks/pull/3050)) +- minor enhancements and updates, including: + - use proxy in sanity check of custom easyblock to install OpenSSL wrapper ([#2922](https://github.com/easybuilders/easybuild-easyblocks/pull/2922)) + - update Clang-AOMP easyblock for ROCm 5.6 ([#2958](https://github.com/easybuilders/easybuild-easyblocks/pull/2958)) + - consider both `$EBROOTGCC` and `$EBROOTGCCCORE` in Clang-AOMP easyblock to specify `-DGCC_INSTALL_PREFIX` ([#2958](https://github.com/easybuilders/easybuild-easyblocks/pull/2958)) + - update WIEN2k easyblock for v23.2 ([#3035](https://github.com/easybuilders/easybuild-easyblocks/pull/3035)) + - enhance LAMMPS easyblock to dynamically add `ARMV81` and `A64FX` to Kokkos CPU mapping based on LAMMPS version ([#3036](https://github.com/easybuilders/easybuild-easyblocks/pull/3036)) + - add `pip_verbose` option to PythonPackage and set it to True in PyTorch easyblock, to show build output when using pip ([#3065](https://github.com/easybuilders/easybuild-easyblocks/pull/3065)) + - also support OpenSSL 3 in OpenSSL wrapper easyblock ([#3081](https://github.com/easybuilders/easybuild-easyblocks/pull/3081)) + - improve error checking in PyTorch easyblock ([#3085](https://github.com/easybuilders/easybuild-easyblocks/pull/3085)) + - update MCR easyblock for compatibility with versions >= R2022b ([#3119](https://github.com/easybuilders/easybuild-easyblocks/pull/3119)) + - add `species` easyconfig parameter to VEP easyblock ([#3121](https://github.com/easybuilders/easybuild-easyblocks/pull/3121)) + - only install Gurobi Python bindings via `setup.py` for Gurobi v10.x and older ([#3225](https://github.com/easybuilders/easybuild-easyblocks/pull/3225)) + - consistently honor `pretestopts` & `testopts` in `PerlModule` ([#3231](https://github.com/easybuilders/easybuild-easyblocks/pull/3231)) + - fix OCaml easyblock for recent versions ([#3235](https://github.com/easybuilders/easybuild-easyblocks/pull/3235)) + - improve QuantumESPRESSO easyblock by cleaning up and extending configure step + running test suite ([#3241](https://github.com/easybuilders/easybuild-easyblocks/pull/3241), [#3258](https://github.com/easybuilders/easybuild-easyblocks/pull/3258)) + - allow overriding `testinstall` in PyTorch easyconfigs ([#3250](https://github.com/easybuilders/easybuild-easyblocks/pull/3250)) + - enhance GCC easyblock to set `$LIBRARY_PATH` and disable building of NVPTX offload support on RISC-V systems ([#3256](https://github.com/easybuilders/easybuild-easyblocks/pull/3256)) + - add support for conda provided by Miniforge ([#3260](https://github.com/easybuilders/easybuild-easyblocks/pull/3260)) + - set `$GOPATH` in configure step of `GoPackage` easyblock to avoid polluting `$HOME/go` ([#3262](https://github.com/easybuilders/easybuild-easyblocks/pull/3262)) +- various bug fixes, including: + - set `$BGW_TEST_MPI_NPROCS` in BerkeleyGW test step ([#2950](https://github.com/easybuilders/easybuild-easyblocks/pull/2950)) + - fix installation of Python bindings for LAMMPS >= 2Aug2023 + fix sanity check by doing `MPI_Finalize` ([#3036](https://github.com/easybuilders/easybuild-easyblocks/pull/3036)) + - fix ELPA preprocessor flag for QuantumESPRESSO >= 7 ([#3063](https://github.com/easybuilders/easybuild-easyblocks/pull/3063)) + - fix link order in PETSc easyblock for SCOTCH >= 7.x ([#3069](https://github.com/easybuilders/easybuild-easyblocks/pull/3069)) + - update PyTorch easyblock to avoid configure warnings by disabling some options ([#3070](https://github.com/easybuilders/easybuild-easyblocks/pull/3070)) + - pick Tcl/Tk lib directory correctly in R easyblock, may be either `lib` or `lib64` ([#3072](https://github.com/easybuilders/easybuild-easyblocks/pull/3072)) + - use `(=|:=)` in regex because OpenFOAM rule files use `:=` instead of `=` since v2212 ([#3073](https://github.com/easybuilders/easybuild-easyblocks/pull/3073)) + - add Clang `opt` binary to RPATH wrapper dir ([#3076](https://github.com/easybuilders/easybuild-easyblocks/pull/3076)) + - improve `generate_crate_list` + parsing of crates in `Cargo` easyblock ([#3084](https://github.com/easybuilders/easybuild-easyblocks/pull/3084)) + - remove trailing slash in `PETSC_DIR` set by custom easyblock for PETSc ([#3086](https://github.com/easybuilders/easybuild-easyblocks/pull/3086)) + - use correct TCL configure options for Python 3.11+ ([#3087](https://github.com/easybuilders/easybuild-easyblocks/pull/3087)) + - tweak `CMakeMake` easyblock to apply CMake policy to select `python` based on `$PATH` order, instead of highest version ([#3088](https://github.com/easybuilders/easybuild-easyblocks/pull/3088)) + - update `Cargo` easyblock to extract crates into a vendor subdir and overwrite git repo URLs with local paths ([#3118](https://github.com/easybuilders/easybuild-easyblocks/pull/3118)) + - only add `--with-ucc` for OpenMPI 4.1.4+ ([#3223](https://github.com/easybuilders/easybuild-easyblocks/pull/3223)) + - remove trailing slash in `SLEPC_DIR` in configure step of custom easyblock for SLEPc ([#3229](https://github.com/easybuilders/easybuild-easyblocks/pull/3229)) + - fix OpenFOAM easyblock to fix `motorBike` example in sanity check for versions >=11 ([#3232](https://github.com/easybuilders/easybuild-easyblocks/pull/3232)) + - only run CUDA sanity check command for torchvision if GPU is present ([#3236](https://github.com/easybuilders/easybuild-easyblocks/pull/3236)) + - ensure localrc is created in the correct subdir for NVHPC v22.9+ ([#3240](https://github.com/easybuilders/easybuild-easyblocks/pull/3240)) + - remove wrong configure option for LibInt 2.6.x ([#3249](https://github.com/easybuilders/easybuild-easyblocks/pull/3249)) + - do not rename GCC's `include-fixed` directory by default + add script to regenerate it ([#3254](https://github.com/easybuilders/easybuild-easyblocks/pull/3254)) +- other changes: + - update copyright lines to 2024 ([#3268](https://github.com/easybuilders/easybuild-easyblocks/pull/3268)) + +**easyconfigs** + +- added example easyconfig files for 101 new software packages: + - AMICA ([#19842](https://github.com/easybuilders/easybuild-easyconfigs/pull/19842)), AreTomo2 ([#19681](https://github.com/easybuilders/easybuild-easyconfigs/pull/19681)), btllib ([#19779](https://github.com/easybuilders/easybuild-easyconfigs/pull/19779)), bwa-mem2 ([#20217](https://github.com/easybuilders/easybuild-easyconfigs/pull/20217)), CENSO ([#19826](https://github.com/easybuilders/easybuild-easyconfigs/pull/19826)), Circlator ([#19847](https://github.com/easybuilders/easybuild-easyconfigs/pull/19847)), Clarabel.rs ([#20149](https://github.com/easybuilders/easybuild-easyconfigs/pull/20149)), + code-cli ([#19645](https://github.com/easybuilders/easybuild-easyconfigs/pull/19645)), Concorde ([#19768](https://github.com/easybuilders/easybuild-easyconfigs/pull/19768)), contextily ([#19807](https://github.com/easybuilders/easybuild-easyconfigs/pull/19807)), CUTLASS ([#19304](https://github.com/easybuilders/easybuild-easyconfigs/pull/19304)), DeepLoc ([#19514](https://github.com/easybuilders/easybuild-easyconfigs/pull/19514)), Delft3D ([#19869](https://github.com/easybuilders/easybuild-easyconfigs/pull/19869)), DeltaLake ([#19758](https://github.com/easybuilders/easybuild-easyconfigs/pull/19758)), + denseweight ([#20139](https://github.com/easybuilders/easybuild-easyconfigs/pull/20139)), desktop-file-utils ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), devbio-napari ([#19586](https://github.com/easybuilders/easybuild-easyconfigs/pull/19586)), DjVuLibre ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), Elmer ([#19448](https://github.com/easybuilders/easybuild-easyconfigs/pull/19448)), + EnergyPlus ([#19565](https://github.com/easybuilders/easybuild-easyconfigs/pull/19565)), EpiSCORE ([#18618](https://github.com/easybuilders/easybuild-easyconfigs/pull/18618)), evince ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), ExpressBetaDiversity ([#19938](https://github.com/easybuilders/easybuild-easyconfigs/pull/19938)), ExtremeLy ([#19870](https://github.com/easybuilders/easybuild-easyconfigs/pull/19870)), f90nml ([#19171](https://github.com/easybuilders/easybuild-easyconfigs/pull/19171)), + FFAVES ([#19822](https://github.com/easybuilders/easybuild-easyconfigs/pull/19822)), fugue ([#19694](https://github.com/easybuilders/easybuild-easyconfigs/pull/19694)), gcsfs ([#20042](https://github.com/easybuilders/easybuild-easyconfigs/pull/20042)), GenomeComb ([#19749](https://github.com/easybuilders/easybuild-easyconfigs/pull/19749)), GI-DocGen ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), GKlib-METIS ([#20096](https://github.com/easybuilders/easybuild-easyconfigs/pull/20096)), GRASP-suite ([#19665](https://github.com/easybuilders/easybuild-easyconfigs/pull/19665)), + gspell ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), GUIDANCE ([#20063](https://github.com/easybuilders/easybuild-easyconfigs/pull/20063)), hdWGCNA ([#20124](https://github.com/easybuilders/easybuild-easyconfigs/pull/20124)), HF-Datasets ([#20166](https://github.com/easybuilders/easybuild-easyconfigs/pull/20166)), IDG ([#18924](https://github.com/easybuilders/easybuild-easyconfigs/pull/18924)), igvShiny ([#19714](https://github.com/easybuilders/easybuild-easyconfigs/pull/19714)), inflection ([#20036](https://github.com/easybuilders/easybuild-easyconfigs/pull/20036)), + InterOp ([#19303](https://github.com/easybuilders/easybuild-easyconfigs/pull/19303)), IonQuant ([#19812](https://github.com/easybuilders/easybuild-easyconfigs/pull/19812)), Lab-Streaming-Layer ([#19945](https://github.com/easybuilders/easybuild-easyconfigs/pull/19945)), Levenshtein ([#19771](https://github.com/easybuilders/easybuild-easyconfigs/pull/19771)), libfyaml ([#19856](https://github.com/easybuilders/easybuild-easyconfigs/pull/19856)), libgxps ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), + libhandy ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), libspectre ([#19701](https://github.com/easybuilders/easybuild-easyconfigs/pull/19701)), lit ([#20252](https://github.com/easybuilders/easybuild-easyconfigs/pull/20252)), lmoments3 ([#19870](https://github.com/easybuilders/easybuild-easyconfigs/pull/19870)), Markdown ([#20239](https://github.com/easybuilders/easybuild-easyconfigs/pull/20239)), MetaDecoder ([#20123](https://github.com/easybuilders/easybuild-easyconfigs/pull/20123)), mfqe ([#19781](https://github.com/easybuilders/easybuild-easyconfigs/pull/19781)), + Miniforge3 ([#20227](https://github.com/easybuilders/easybuild-easyconfigs/pull/20227)), MLflow ([#19893](https://github.com/easybuilders/easybuild-easyconfigs/pull/19893)), MODFLOW ([#20142](https://github.com/easybuilders/easybuild-easyconfigs/pull/20142)), morphosamplers ([#20000](https://github.com/easybuilders/easybuild-easyconfigs/pull/20000)), MotionCor3 ([#19681](https://github.com/easybuilders/easybuild-easyconfigs/pull/19681)), MSFragger ([#19811](https://github.com/easybuilders/easybuild-easyconfigs/pull/19811)), + multiprocess ([#19986](https://github.com/easybuilders/easybuild-easyconfigs/pull/19986)), nf-core ([#19107](https://github.com/easybuilders/easybuild-easyconfigs/pull/19107)), noise ([#20048](https://github.com/easybuilders/easybuild-easyconfigs/pull/20048)), OpenMEEG ([#19853](https://github.com/easybuilders/easybuild-easyconfigs/pull/19853)), OpenSlide-Java ([#19962](https://github.com/easybuilders/easybuild-easyconfigs/pull/19962)), PAGAN2 ([#19618](https://github.com/easybuilders/easybuild-easyconfigs/pull/19618)), PASA ([#19570](https://github.com/easybuilders/easybuild-easyconfigs/pull/19570)), + pblat ([#19570](https://github.com/easybuilders/easybuild-easyconfigs/pull/19570)), PBZIP2 ([#19677](https://github.com/easybuilders/easybuild-easyconfigs/pull/19677)), PDM ([#20012](https://github.com/easybuilders/easybuild-easyconfigs/pull/20012)), Philosopher ([#19383](https://github.com/easybuilders/easybuild-easyconfigs/pull/19383)), phyluce ([#19779](https://github.com/easybuilders/easybuild-easyconfigs/pull/19779)), poppunk ([#17402](https://github.com/easybuilders/easybuild-easyconfigs/pull/17402)), PSASS ([#20160](https://github.com/easybuilders/easybuild-easyconfigs/pull/20160)), psycopg ([#19107](https://github.com/easybuilders/easybuild-easyconfigs/pull/19107)), + PyInstaller ([#19519](https://github.com/easybuilders/easybuild-easyconfigs/pull/19519)), PyQt-builder ([#16703](https://github.com/easybuilders/easybuild-easyconfigs/pull/16703)), pytest-workflow ([#19107](https://github.com/easybuilders/easybuild-easyconfigs/pull/19107)), python-casacore ([#20089](https://github.com/easybuilders/easybuild-easyconfigs/pull/20089)), pytorch-3dunet ([#19290](https://github.com/easybuilders/easybuild-easyconfigs/pull/19290)), pyXDF ([#19916](https://github.com/easybuilders/easybuild-easyconfigs/pull/19916)), + q2-krona ([#19633](https://github.com/easybuilders/easybuild-easyconfigs/pull/19633)), QuPath ([#19962](https://github.com/easybuilders/easybuild-easyconfigs/pull/19962)), radian ([#19484](https://github.com/easybuilders/easybuild-easyconfigs/pull/19484)), remake ([#19581](https://github.com/easybuilders/easybuild-easyconfigs/pull/19581)), rethinking ([#19755](https://github.com/easybuilders/easybuild-easyconfigs/pull/19755)), RHEIA ([#19496](https://github.com/easybuilders/easybuild-easyconfigs/pull/19496)), s3fs ([#19576](https://github.com/easybuilders/easybuild-easyconfigs/pull/19576)), + safestringlib ([#20217](https://github.com/easybuilders/easybuild-easyconfigs/pull/20217)), scikit-extremes ([#19870](https://github.com/easybuilders/easybuild-easyconfigs/pull/19870)), SemiBin ([#19767](https://github.com/easybuilders/easybuild-easyconfigs/pull/19767)), semla ([#19747](https://github.com/easybuilders/easybuild-easyconfigs/pull/19747)), Sentence-Transformers ([#19509](https://github.com/easybuilders/easybuild-easyconfigs/pull/19509)), sinto ([#13846](https://github.com/easybuilders/easybuild-easyconfigs/pull/13846)), + sktime ([#19692](https://github.com/easybuilders/easybuild-easyconfigs/pull/19692)), SQLAlchemy ([#20242](https://github.com/easybuilders/easybuild-easyconfigs/pull/20242)), tiny-cuda-nn ([#19304](https://github.com/easybuilders/easybuild-easyconfigs/pull/19304)), tox ([#16178](https://github.com/easybuilders/easybuild-easyconfigs/pull/16178)), Vamb ([#17457](https://github.com/easybuilders/easybuild-easyconfigs/pull/17457)), xpdf ([#20024](https://github.com/easybuilders/easybuild-easyconfigs/pull/20024)), yt ([#20263](https://github.com/easybuilders/easybuild-easyconfigs/pull/20263)), Zeo++ ([#19555](https://github.com/easybuilders/easybuild-easyconfigs/pull/19555)), + zUMIs ([#19949](https://github.com/easybuilders/easybuild-easyconfigs/pull/19949)) +- added additional easyconfigs for various supported software packages, including: + - Abseil 20240116.1, ABySS 2.3.7, AMS 2023.104, Anaconda3 2024.02, anndata 0.10.5.post1, anvio 8, ArchR 1.0.2, + archspec 0.2.2, Armadillo 12.8.0, arpack-ng 3.9.1, arrow-R 14.0.0.2, ASAP3 3.13.3, assimp 5.3.1, autopep8 2.0.4, + basemap 1.3.9, BerkeleyGW 3.1.0 + 4.0, BiG-SCAPE 1.1.5, Biopython 1.83, Blosc 1.21.5, Blosc2 2.13.2, Boost.MPI 1.82.0, + Boost.Python 1.83.0, Braindecode 0.8.1, Brotli-python 1.1.0, build 1.0.3, buildenv-default foss-2023b + intel-2023b, + bx-python 0.10.0, CapnProto 1.0.1.1, c-ares 1.27.0, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, cclib 1.8, + CellBender 0.3.1, CellTypist 1.6.2, CFITSIO 4.3.1, Cgl 0.60.8, Clang-Python-bindings 16.0.6, Clp 1.17.9, CmdStanR 0.7.1, + COBRApy 0.29.0, code-server 4.22.1, CoinUtils 2.11.10, CoordgenLibs 3.0.2, CREST 2.12, cryoCARE 0.3.0, CSBLAST 2.2.4, + CUDA 12.3.2 + 12.4.0, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, CVXPY 1.4.2, Cython 3.0.8, + dask 2023.12.1, datalad 0.19.5, DB_File 1.859, deepdiff 6.7.1, DeepLabCut 2.3.6, DendroPy 4.6.1, Deprecated 1.2.14, + DFT-D4 3.6.0, DIAMOND 2.1.9, Dice 20240101, dlb 3.4, DLPack 0.8, dorado 0.5.1, EggLib 3.3.0, einops 0.7.0, ELPA 2023.11.001, + enchant-2 2.6.5, ESMF 8.4.2, eSpeak-NG 1.51, ETE 3.1.3, expecttest 0.2.1, fastjet 3.4.2, fastjet-contrib 1.053, FDS 6.8.0, + fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, FLINT 3.1.1, Flye 2.9.3, fmt 10.2.0, freebayes 1.3.7, + GATK 4.5.0.0, gawk 5.3.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, GHC 9.4.6, Ghostscript 10.02.1, GIMIC 2.2.1, + git-lfs 3.5.1, GitPython 3.1.42, GLFW 3.4, Go 1.22.1, GPAW 24.1.0, GPAW-setups 24.1.0, gperftools 2.14, Gradle 8.6, + graph-tool 2.55, Greenlet 3.0.3, GROMACS 2024.1, gRPC 1.62.1, GTK3 3.24.39, Gurobi 11.0.0, HDF5 1.14.3, HeFFTe 2.4.0, + HepMC3 3.2.6, hunspell 1.7.2, igraph 0.10.10, infercnvpy 0.4.3, iperf 3.16, IQ-TREE 2.2.2.7, ISA-L 2.31.0, Java/19 (19.0.2), + Java/21 (21.0.2), json-c 0.17, Julia 1.10.0, KaHIP 3.16, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2, + libcint 5.5.0, libgit2 1.7.2, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libtirpc 1.3.4, + libxml2-python 2.11.4, likwid 5.3.0, LLVM 14.0.6, MACS3 3.0.1, maeparser 1.3.1, Mamba 23.11.0-0, MATIO 1.5.26, + matplotlib 3.8.2, maturin 1.5.0, MCR R2023a, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, Meson 1.3.1, MiXCR 4.6.0, + MNE-Python-1.6., MOABB 1.0.0, molmod 1.4.8, MONAI 1.3.0, mpi4py 3.1.5, mrcfile 1.5.0, NCCL 2.20.5, NCO 5.1.9, NECI 20230620, + netcdf4-python-1.6.5, networkx 3.2.1, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3, + nlohmann_json 3.11.3, NLTK 3.8.1, ntCard 1.2.2, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0, + onedrive 2.4.25, ONNX 1.15.0, ONNX-Runtime 1.16.3, ont-fast5-api 4.1.2, OPARI2 2.0.8, OpenFOAM v2306 + v2312, OpenSSL/3, + Optuna 3.5.0, Osi 0.108.9, PAPI 7.1.0, Parallel-Hashmap 1.3.12, ParaView 5.12.0, PDT 3.25.2, PETSc 3.20.3, PGPLOT 5.2.2, + phonemizer 3.2.1, phono3py 2.7.0, Pillow 10.2.0, Pint 0.23, plotly.py 5.18.0, poetry 1.7.1, presto-1.0.0 20230501, + PROJ 9.3.1, prompt-toolkit 3.0.36, protobuf 25.3, protobuf-python 4.25.3, psmc 0.6.5_20221121, pstoedit 3.78, + psycopg2 2.9.9, PuLP 2.8.0, PyCheMPS2 1.8.12, pycodestyle 2.11.1, pydantic 1.10.13 + 2.5.3 2.6.4, pydicom 2.4.4, pydot 2.0.0, + pyfaidx 0.8.1.1, PyFrag 2023-dev.20240220, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1, + PyQt5 5.15.10, Pysam 0.22.0, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest-rerunfailures 14.0, python-igraph 0.11.4, + python-irodsclient 2.0.0, python-isal 1.6.1, python-libsbml 5.20.2, python-xxhash 3.4.1, PyTorch-Ignite 0.4.13, + PyTorch-Lightning 2.2.1, PyZMQ 25.1.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1, + QuantumESPRESSO 7.3, R 4.3.3, rasterio 1.3.9, R-bundle-Bioconductor 3.18, rclone 1.66.0, RE2 2024-03-01, Redis 7.2.4, + redis-py 5.0.1, rioxarray 0.15.0, Rivet 3.1.9, rMATS-turbo 4.2.0, RNA-Bloom 2.0.1, rocm-smi 5.6.0, rpy2 3.5.15, + ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0 + 1.76.0, Salmon 1.10.1, Sambamba 1.0.1, Saxon-HE 12.4, SBCL 2.4.1, + ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scib 1.1.4, scikit-bio 0.5.9, scikit-learn 1.4.0, scikit-lego 0.7.4, + scikit-misc 0.3.1, SCons 4.6.0, Score-P 8.4, scVelo 0.3.1, Seaborn 0.13.2, SentencePiece 0.1.99, Seqmagick 0.8.6, + Seurat 5.0.1, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, SLEPc 3.20.1, snakemake 8.4.2, SNAPE-pooled 20150707, + SOAPdenovo-Trans 1.0.5, Spark 3.5.1, spdlog 1.12.0, spoa 4.1.0, SRA-Toolkit 3.0.10, Stack 2.13.1, STAR 2.7.11b, + statsmodels 0.14.1, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorflow-probability 0.20.0, texinfo 7.1, timm 0.9.7, + torchvision 0.16.0, tqdm 4.66.2, TRIQS 3.2.0, TRIQS-cthyb 3.2.1, TRIQS-dft_tools 3.2.0, TRIQS-tprf 3.2.1, + typing-extensions 4.9.0, UCX 1.16.0, UDUNITS 2.2.28, umap-learn 0.5.5, UMI-tools 1.1.4, Vala 0.56.14, VEP 111, + Vim 9.1.0004, vsc-mympirun 5.4.0, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.2, WIEN2k 23.2, wrf-python 1.3.4.1, + Xerces-C++ 3.2.5, XlsxWriter 3.1.9, XML-LibXML v2.0209, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9 +- minor enhancements, including: + - add build info message to easyconfig for NLTK 3.7 ([#18550](https://github.com/easybuilders/easybuild-easyconfigs/pull/18550)) + - enable KLU and CUDA solvers in SUNDIALS v6.6.0 ([#19490](https://github.com/easybuilders/easybuild-easyconfigs/pull/19490)) + - add extensions to R-bundle-CRAN v2023.12: tidybayes ([#19712](https://github.com/easybuilders/easybuild-easyconfigs/pull/19712)), spdep ([#19729](https://github.com/easybuilders/easybuild-easyconfigs/pull/19729)), fixest ([#20055](https://github.com/easybuilders/easybuild-easyconfigs/pull/20055)) + - add plyranges extension to R-bundle-Bioconductor (for zUMIs) ([#19949](https://github.com/easybuilders/easybuild-easyconfigs/pull/19949)) + - add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 ([#20007](https://github.com/easybuilders/easybuild-easyconfigs/pull/20007)) + - use system architecture template in DB_File ([#20014](https://github.com/easybuilders/easybuild-easyconfigs/pull/20014)), GD ([#20015](https://github.com/easybuilders/easybuild-easyconfigs/pull/20015)), and GDGraph ([#20016](https://github.com/easybuilders/easybuild-easyconfigs/pull/20016)) + - add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency ([#20069](https://github.com/easybuilders/easybuild-easyconfigs/pull/20069)) + - add MODIStsp extension (+ required dependencies) to R 4.2.2 ([#20113](https://github.com/easybuilders/easybuild-easyconfigs/pull/20113)) + - enable LittleCMS2 and WebP support in recent Pillow ([#20195](https://github.com/easybuilders/easybuild-easyconfigs/pull/20195)) + - improve test for validity of easyconfig files ([#20205](https://github.com/easybuilders/easybuild-easyconfigs/pull/20205)) + - add easyconfig test that checks if backdoored XZ versions are introduced ([#20267](https://github.com/easybuilders/easybuild-easyconfigs/pull/20267)) +- various bug fixes, including: + - add patch for Bison 3.7.1 to fix build error on old OS versions ([#12291](https://github.com/easybuilders/easybuild-easyconfigs/pull/12291)) + - add missing pkg-config build dependency for recent p11-kit easyconfigs ([#16318](https://github.com/easybuilders/easybuild-easyconfigs/pull/16318)) + - fix dependencies and configure flags of GnuTLS 3.7.x ([#19070](https://github.com/easybuilders/easybuild-easyconfigs/pull/19070)) + - remove numa configure option from hwloc 2.5+ ([#19085](https://github.com/easybuilders/easybuild-easyconfigs/pull/19085)) + - add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK ([#19280](https://github.com/easybuilders/easybuild-easyconfigs/pull/19280)) + - add patch to fix flaky scipy build in SciPy-bundle v2023.11 ([#19481](https://github.com/easybuilders/easybuild-easyconfigs/pull/19481)) + - add missing SciPy-bundle dependency to TensorRT easyconfig ([#19486](https://github.com/easybuilders/easybuild-easyconfigs/pull/19486)) + - fix lapack test failures in OpenBLAS 0.3.23/24 ([#19495](https://github.com/easybuilders/easybuild-easyconfigs/pull/19495)) + - add patch for Arrow v8.0.0 - v11.0.0 to add missing `__arrow_ext_class__` method to `BaseExtensionType` class ([#19532](https://github.com/easybuilders/easybuild-easyconfigs/pull/19532)) + - change homepage for argtable ([#19551](https://github.com/easybuilders/easybuild-easyconfigs/pull/19551)) + - add patches for PyTorch v2.1.2 with `foss/2022a` ([#19571](https://github.com/easybuilders/easybuild-easyconfigs/pull/19571)), `foss/2022b` ([#19572](https://github.com/easybuilders/easybuild-easyconfigs/pull/19572)), and `foss/2023a` ([#19573](https://github.com/easybuilders/easybuild-easyconfigs/pull/19573)) to fix test failures on non-x86 platforms + - use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 ([#19584](https://github.com/easybuilders/easybuild-easyconfigs/pull/19584)) + - remove `osdependencies` from ccache easyconfigs using GCCcore toolchain ([#19600](https://github.com/easybuilders/easybuild-easyconfigs/pull/19600)) + - use https source URL for alsa-lib ([#19628](https://github.com/easybuilders/easybuild-easyconfigs/pull/19628)) + - add missing dm-tree dependency for dm-reverb 0.2.0 ([#19653](https://github.com/easybuilders/easybuild-easyconfigs/pull/19653)) + - add libyaml import check to PyYAML and fix builds since split to minimal Python ([#19662](https://github.com/easybuilders/easybuild-easyconfigs/pull/19662)) + - demote meson-python to a build dependency in recent matplotlib easyconfigs ([#19670](https://github.com/easybuilders/easybuild-easyconfigs/pull/19670)) + - add patch to fix upb CopyFrom error in protobuf-python 4.24.0 ([#19671](https://github.com/easybuilders/easybuild-easyconfigs/pull/19671)) + - demote poetry to build dep in expecttest ([#19675](https://github.com/easybuilders/easybuild-easyconfigs/pull/19675)) + - add zlib dependency to YODA and Rivet ([#19679](https://github.com/easybuilders/easybuild-easyconfigs/pull/19679)) + - fix missing spaces in Graphviz configure options ([#19687](https://github.com/easybuilders/easybuild-easyconfigs/pull/19687)) + - strip iconv from pkgconfig file for libarchive v3.6.2 ([#19698](https://github.com/easybuilders/easybuild-easyconfigs/pull/19698)) + - use separate bcrypt easyconfig (using `CargoPythonPackage`) as dependency for JupyterHub v4.0.2 ([#19703](https://github.com/easybuilders/easybuild-easyconfigs/pull/19703)) + - use maturin easyconfig using `CargoPythonPackage` as a dependency for fastparquet v2023.4.0 ([#19704](https://github.com/easybuilders/easybuild-easyconfigs/pull/19704)) + - add patches for Perl-bundle-CPAN v5.36.1 to fix installation of `Sys::Info::Driver::Linux*` extensions on Debian Bookworm ([#19727](https://github.com/easybuilders/easybuild-easyconfigs/pull/19727)) + - explicitly specify Fortran compiler for recent CDO versions to fix issues on non-x86_64 architectures ([#19735](https://github.com/easybuilders/easybuild-easyconfigs/pull/19735)) + - add patch for `jupyter_core` extension in `jupyter-server` to set jupyter path by `$EB_ENV_JUPYTER_ROOT` ([#19737](https://github.com/easybuilders/easybuild-easyconfigs/pull/19737)) + - add Python build dependency to 1.9.x Doxygen ([#19743](https://github.com/easybuilders/easybuild-easyconfigs/pull/19743)) + - fix Arrow v14.0.1 to install pyarrow as an extension ([#19758](https://github.com/easybuilders/easybuild-easyconfigs/pull/19758)) + - fix homepage + source URL for Gblocks 0.91b ([#19797](https://github.com/easybuilders/easybuild-easyconfigs/pull/19797)) + - make sure that Brunsli libraries are installed into `lib` ([#19805](https://github.com/easybuilders/easybuild-easyconfigs/pull/19805)) + - fix dependency with `libidn.so.11` in tbl2asn v20220427 and v20230713 easyconfigs ([#19821](https://github.com/easybuilders/easybuild-easyconfigs/pull/19821)) + - add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 ([#19829](https://github.com/easybuilders/easybuild-easyconfigs/pull/19829)) + - remove numa configure option from hwloc 2+ ([#19833](https://github.com/easybuilders/easybuild-easyconfigs/pull/19833)) + - avoid spurious test failure when enabling RPATH for Perl ([#19835](https://github.com/easybuilders/easybuild-easyconfigs/pull/19835)) + - add missing Python deps and packages in PSI4 1.7 ([#19836](https://github.com/easybuilders/easybuild-easyconfigs/pull/19836)) + - add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 ([#20140](https://github.com/easybuilders/easybuild-easyconfigs/pull/20140)), 4.0.3 ([#19944](https://github.com/easybuilders/easybuild-easyconfigs/pull/19944)), and 4.0.5 ([#19837](https://github.com/easybuilders/easybuild-easyconfigs/pull/19837)) + - demote meson-python to build dependency for matplotlib v3.7.2 w/ `iimkl/2023a` ([#19892](https://github.com/easybuilders/easybuild-easyconfigs/pull/19892)) + - demote hatchling to build dependency in easyconfig for einops 0.7.0 ([#19915](https://github.com/easybuilders/easybuild-easyconfigs/pull/19915)) + - add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs ([#19940](https://github.com/easybuilders/easybuild-easyconfigs/pull/19940)) + - stop using non-existent `--disable-libdeflate` option for LibTIFF 4.1.0 ([#19951](https://github.com/easybuilders/easybuild-easyconfigs/pull/19951)) + - add patch to remove git version check and fix test command for molmod 1.4.8 ([#19952](https://github.com/easybuilders/easybuild-easyconfigs/pull/19952)) + - replace SYSTEM-level GCC dependency in git-annex with binutils ([#19956](https://github.com/easybuilders/easybuild-easyconfigs/pull/19956)) + - stop using non-existing `--with-doc` configure option for groff 1.23 ([#19969](https://github.com/easybuilders/easybuild-easyconfigs/pull/19969)) + - fix test failures of Perl-bundle-CPAN-5.38 in non-English locales ([#19971](https://github.com/easybuilders/easybuild-easyconfigs/pull/19971)) + - add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support ([#19974](https://github.com/easybuilders/easybuild-easyconfigs/pull/19974), [#20218](https://github.com/easybuilders/easybuild-easyconfigs/pull/20218)) + - drop checksum from easyconfig for VSCode 1.85.0 since tarball are not stable ([#19995](https://github.com/easybuilders/easybuild-easyconfigs/pull/19995)) + - respect `sysroot` in recent Pillow-SIMD easyconfigs, when in use ([#19996](https://github.com/easybuilders/easybuild-easyconfigs/pull/19996)) + - remove `--disable-docs` configure option from FriBidi 1.0.5+ ([#19998](https://github.com/easybuilders/easybuild-easyconfigs/pull/19998)) + - fix geotiff configure option in GDAL ([#19999](https://github.com/easybuilders/easybuild-easyconfigs/pull/19999)) + - unpack SCG database to `db` subdirectory for DAS_Tool ([#20008](https://github.com/easybuilders/easybuild-easyconfigs/pull/20008)) + - remove Jasper dependency and configure option from GDAL 3.5+ ([#20009](https://github.com/easybuilders/easybuild-easyconfigs/pull/20009)) + - update homepage and source URLs for SPAdes ([#20018](https://github.com/easybuilders/easybuild-easyconfigs/pull/20018)) + - fix GDAL 3.5.0 install on high-core-count machines ([#20027](https://github.com/easybuilders/easybuild-easyconfigs/pull/20027)) + - remove disable-visibility configure flag from GTK3 ([#20028](https://github.com/easybuilders/easybuild-easyconfigs/pull/20028)) + - remove mpi configure option from libfdf 0.2.2 ([#20034](https://github.com/easybuilders/easybuild-easyconfigs/pull/20034)) + - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs ([#20035](https://github.com/easybuilders/easybuild-easyconfigs/pull/20035)) + - fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig ([#20039](https://github.com/easybuilders/easybuild-easyconfigs/pull/20039)) + - remove hdf5 configure option from MDSplus 7.96.12 ([#20041](https://github.com/easybuilders/easybuild-easyconfigs/pull/20041)) + - fix python configure option of MEME ([#20043](https://github.com/easybuilders/easybuild-easyconfigs/pull/20043)) + - fix configure options of FFLAS-FFPACK ([#20052](https://github.com/easybuilders/easybuild-easyconfigs/pull/20052)) + - find the correct Python in xtensor ([#20056](https://github.com/easybuilders/easybuild-easyconfigs/pull/20056)) + - fix geotiff configure option in GDAL 2.2.3 ([#20057](https://github.com/easybuilders/easybuild-easyconfigs/pull/20057)) + - fix configure option and remove gperftools dependency for MIRA 5.0 ([#20061](https://github.com/easybuilders/easybuild-easyconfigs/pull/20061)) + - fix confgure options in GRASS ([#20062](https://github.com/easybuilders/easybuild-easyconfigs/pull/20062)) + - fix configure of LinBox 1.7.0 ([#20064](https://github.com/easybuilders/easybuild-easyconfigs/pull/20064)) + - remove unknown configure option from GnuTLS 3.7.2 ([#20065](https://github.com/easybuilders/easybuild-easyconfigs/pull/20065)) + - use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse ([#20075](https://github.com/easybuilders/easybuild-easyconfigs/pull/20075)) + - find correct Python for MDI ([#20083](https://github.com/easybuilders/easybuild-easyconfigs/pull/20083)) + - add `pixman` and `FriBidi` dependencies to recent ImageMagick easyconfigs ([#20086](https://github.com/easybuilders/easybuild-easyconfigs/pull/20086)) + - add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 ([#20090](https://github.com/easybuilders/easybuild-easyconfigs/pull/20090)) and v5.38.0 ([#20118](https://github.com/easybuilders/easybuild-easyconfigs/pull/20118)) + - add patches for minimus2 in AMOS-3.1.0 ([#20114](https://github.com/easybuilders/easybuild-easyconfigs/pull/20114)) + - fix download url for cuSPARSELt 0.3.0.3 ([#20129](https://github.com/easybuilders/easybuild-easyconfigs/pull/20129)) + - add patches to fix test issues for PyTorch 2.1.2 with `foss/2023a` + CUDA 12.1.1 ([#20156](https://github.com/easybuilders/easybuild-easyconfigs/pull/20156)) + - remove easyconfig for UCX-CUDA 1.15.0 using incompatible combo of CUDA 12.3.0 + GCC 13.2.0 ([#20158](https://github.com/easybuilders/easybuild-easyconfigs/pull/20158)) + - remove flake8 suppressions for invalid escape sequences ([#20161](https://github.com/easybuilders/easybuild-easyconfigs/pull/20161)) + - fix post-install command for SuperLU_DIST in case library prefix is `lib` instead of `lib64` ([#20162](https://github.com/easybuilders/easybuild-easyconfigs/pull/20162)) + - switch to gitlab source URL for libxc + add alternative checksum ([#20163](https://github.com/easybuilders/easybuild-easyconfigs/pull/20163)) + - enable `download_dep_fail` in Pythonpackage easyconfigs where it was wrongly disabled ([#20174](https://github.com/easybuilders/easybuild-easyconfigs/pull/20174)) + - add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+ ([#20176](https://github.com/easybuilders/easybuild-easyconfigs/pull/20176), [#20177](https://github.com/easybuilders/easybuild-easyconfigs/pull/20177), [#20178](https://github.com/easybuilders/easybuild-easyconfigs/pull/20178), [#20179](https://github.com/easybuilders/easybuild-easyconfigs/pull/20179), [#20180](https://github.com/easybuilders/easybuild-easyconfigs/pull/20180), [#20181](https://github.com/easybuilders/easybuild-easyconfigs/pull/20181), [#20182](https://github.com/easybuilders/easybuild-easyconfigs/pull/20182)) + - disable tests for `Time::HiRes` extension in Perl-bundle-CPAN v5.36.1 ([#20187](https://github.com/easybuilders/easybuild-easyconfigs/pull/20187)) + - fix several typos in GlobalArrays 5.8 configure step ([#20188](https://github.com/easybuilders/easybuild-easyconfigs/pull/20188)) + - fix broken homepage from older SCOTCH easyconfigs ([#20192](https://github.com/easybuilders/easybuild-easyconfigs/pull/20192)) + - remove dead URL for ISL from `source_urls` in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 ([#20193](https://github.com/easybuilders/easybuild-easyconfigs/pull/20193)) + - fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using `GCCcore/8.2.0`) ([#20194](https://github.com/easybuilders/easybuild-easyconfigs/pull/20194)) + - add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency ([#20214](https://github.com/easybuilders/easybuild-easyconfigs/pull/20214)) + - fix cuSPARSELt easyconfigs for aarch64 ([#20216](https://github.com/easybuilders/easybuild-easyconfigs/pull/20216)) + - fix python shebang in napari easyconfigs ([#20219](https://github.com/easybuilders/easybuild-easyconfigs/pull/20219)) + - add patch to fix scipy test failure for SciPy-bundle 2023.02 with `gfbf/2022b` ([#20235](https://github.com/easybuilders/easybuild-easyconfigs/pull/20235)) + - fix `incompatible types` errors when building the R extension `dbarts` on Arm ([#20238](https://github.com/easybuilders/easybuild-easyconfigs/pull/20238)) + - add patch to fix for libarchive to fix error reporting in tar ([#20254](https://github.com/easybuilders/easybuild-easyconfigs/pull/20254)) + - add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin ([#20260](https://github.com/easybuilders/easybuild-easyconfigs/pull/20260)) + - fix download for python-parasail 1.3.4 by adding missing source URL ([#20263](https://github.com/easybuilders/easybuild-easyconfigs/pull/20263)) +- other changes: + - update DualSPHysics easyconfig to use custom easyblock ([#19400](https://github.com/easybuilders/easybuild-easyconfigs/pull/19400)) + - fix name for DETONATE in existing easyconfig (was `detonate`) ([#19569](https://github.com/easybuilders/easybuild-easyconfigs/pull/19569)) + - rename `VSCode` to `code-cli` (to match with existing `code-server`) ([#19585](https://github.com/easybuilders/easybuild-easyconfigs/pull/19585), [#19645](https://github.com/easybuilders/easybuild-easyconfigs/pull/19645)) + - remove urllib3 extension from wandb easyconfig, not neeed since Python-bundle-PyPI dependency already provides it ([#19725](https://github.com/easybuilders/easybuild-easyconfigs/pull/19725)) + - stop using custom easyblock for Doxygen ([#19742](https://github.com/easybuilders/easybuild-easyconfigs/pull/19742)) + - move `setuptools_scm` extension from hatchling to Python easyconfig ([#19777](https://github.com/easybuilders/easybuild-easyconfigs/pull/19777), [#20200](https://github.com/easybuilders/easybuild-easyconfigs/pull/20200)) + - move xtb v6.6.1 to gfbf/2023a ([#19826](https://github.com/easybuilders/easybuild-easyconfigs/pull/19826)) + - unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) ([#20050](https://github.com/easybuilders/easybuild-easyconfigs/pull/20050)) + - use GPAW-setups v24.1.0 in existing GPAW easyconfigs ([#20117](https://github.com/easybuilders/easybuild-easyconfigs/pull/20117)) + - fix duplicate dict entries and enable fatal error checking for easyconfigs via `flake8` ([#20173](https://github.com/easybuilders/easybuild-easyconfigs/pull/20173)) + - move Greenlet 2.0.2 to GCCcore toolchain ([#20241](https://github.com/easybuilders/easybuild-easyconfigs/pull/20241)) + - update Java/8 wrapper to Java 8.402 ([#20261](https://github.com/easybuilders/easybuild-easyconfigs/pull/20261)) + - update copyright lines to 2024 ([#20276](https://github.com/easybuilders/easybuild-easyconfigs/pull/20276)) + + ## EasyBuild v4.9.0 (29 Dec 2023) {: #release_notes_eb490 } feature release diff --git a/docs/unit-tests.md b/docs/unit-tests.md index c6d94d192..a9766bce1 100644 --- a/docs/unit-tests.md +++ b/docs/unit-tests.md @@ -126,18 +126,19 @@ instead. Thus, to set a particular configuration option `--foo`, you should defi #### Modules tool to use for running tests {: #unit_tests_modules_tool } One particular configuration option worth mentioning explicitly is the modules tool that is to be used by the EasyBuild -framework, which is by default the traditional Tcl/C environment modules, referred to as `EnvironmentModulesC` in -EasyBuild configuration terms (see `eb --help` and `eb --avail-modules-tools`). +framework, which is by default Lmod, referred to as `Lmod` in EasyBuild configuration terms (see `eb --help` and +`eb --avail-modules-tools`). To run the EasyBuild framework unit tests with a particular modules tool, simply define the `$TEST_EASYBUILD_MODULES_TOOL` environment variable with the corresponding value. For example:: ``` shell -export TEST_EASYBUILD_MODULES_TOOL=Lmod +export TEST_EASYBUILD_MODULES_TOOL=EnvironmentModules ``` Just like for EasyBuild itself, the EasyBuild framework unit test suite expects that the modules tool binary/script -(`modulecmd`, `modulecmd.tcl` or `lmod`) is available via `$PATH`, see [Required modules tool][required_modules_tool]. +(`modulecmd`, `modulecmd.tcl` or `lmod`) is available via `$PATH` or referenced via a module tool-specific environment +variable, see [Required modules tool][required_modules_tool]. #### Installing a GitHub token for the unit tests {: #unit_tests_github_token } @@ -173,10 +174,12 @@ other than `suite`, to focus on testing a particular aspect. See for an overview of the available Python modules corresponding to subgroups of tests (note: `__init__.py` and `utilities.py` are *not* such modules). -For example, to run the full EasyBuild framework unit test suite using Lmod as a modules tool:: +For example, to run the full EasyBuild framework unit test suite using Environment Modules as a modules tool and Tcl as +module file syntax:: ``` shell -export TEST_EASYBUILD_MODULES_TOOL=Lmod +export TEST_EASYBUILD_MODULES_TOOL=EnvironmentModules +export TEST_EASYBUILD_MODULE_SYNTAX=Tcl python -m test.framework.suite ``` diff --git a/docs/version-specific/easyblocks.md b/docs/version-specific/easyblocks.md index c89912d03..67ddb9c66 100644 --- a/docs/version-specific/easyblocks.md +++ b/docs/version-specific/easyblocks.md @@ -60,6 +60,7 @@ - ConfigureMake - CMakeMake - CMakeMakeCp + - EB_DualSPHysics - CMakeNinja - CMakePythonPackage - EB_DOLFIN @@ -191,6 +192,7 @@ - EB_XCrySDen - MakeCp - CMakeMakeCp + - EB_DualSPHysics - CmdCp - EB_fastStructure - EB_BamTools diff --git a/docs/version-specific/easyconfig-license-constants.md b/docs/version-specific/easyconfig-license-constants.md index ac378dba8..8c7a18ef7 100644 --- a/docs/version-specific/easyconfig-license-constants.md +++ b/docs/version-specific/easyconfig-license-constants.md @@ -7,7 +7,7 @@ License name |License description ``GPLv2`` |The GNU General Public License is a free, copyleft license for software and other kinds of works. |``2`` ``GPLv3`` |The GNU General Public License is a free, copyleft license for software and other kinds of works. |``3`` ``Libpng`` |Permission is granted to use, copy, modify, and distribute the source code, or portions hereof, for any purpose, without fee, subject to 3 restrictions; http://libpng.org/pub/png/src/libpng-LICENSE.txt for full license |``None`` -``Unknown`` |None |``None`` -``VeryRestrictive``|None |``None`` +``Unknown`` | |``None`` +``VeryRestrictive``| |``None`` *(see also* ``eb --avail-easyconfig-licenses`` *)* diff --git a/docs/version-specific/easyconfig-parameters.md b/docs/version-specific/easyconfig-parameters.md index 5f0f4bbf3..d2a56d135 100644 --- a/docs/version-specific/easyconfig-parameters.md +++ b/docs/version-specific/easyconfig-parameters.md @@ -118,6 +118,7 @@ **Parameter name** |**Description** |**Default value** ----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------- +`allow_append_abs_path` |Allow specifying absolute paths to append in modextrapaths_append |`False` `allow_prepend_abs_path` |Allow specifying absolute paths to prepend in modextrapaths |`False` `citing` |Free-form text that describes how the software should be cited in publications |`None` `docpaths` |List of paths for documentation relative to installation directory |`None` @@ -126,6 +127,7 @@ `modaliases` |Aliases to be defined in module file |`{}` `modaltsoftname` |Module name to use (rather than using software name |`None` `modextrapaths` |Extra paths to be prepended in module file |`{}` +`modextrapaths_append` |Extra paths to be appended in module file |`{}` `modextravars` |Extra environment variables to be added to module file |`{}` `modloadmsg` |Message that should be printed when generated module is loaded |`{}` `modluafooter` |Footer to include in generated module file (Lua syntax) |`""` diff --git a/docs/version-specific/eb-help.md b/docs/version-specific/eb-help.md index e501b4251..65a4ac992 100644 --- a/docs/version-specific/eb-help.md +++ b/docs/version-specific/eb-help.md @@ -139,10 +139,12 @@ Option flag |Option description ``--close-pr-msg=CLOSE-PR-MSG`` |Custom close message for pull request closed with --close-pr; (type ) ``--close-pr-reasons=CLOSE-PR-REASONS`` |Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) ``--dump-test-report=DUMP-TEST-REPORT`` |Dump test report to specified path (default: test_report.md) +``--from-commit=commit_SHA`` |Obtain easyconfigs from specified commit (type str) ``--from-pr=PR#`` |Obtain easyconfigs from specified PR (type comma-separated list) ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` |Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` |GitHub organization (type ) ``--github-user=GITHUB-USER`` |GitHub username (type ) +``--include-easyblocks-from-commit=commit_SHA`` |Include easyblocks from specified commit (type str) ``--include-easyblocks-from-pr=PR#`` |Include easyblocks from specified PR (type comma-separated list) ``--install-github-token`` |Install GitHub token (requires --github-user) (default: False) ``--list-prs=STATE,ORDER,DIRECTION`` |List pull requests (type ; default: open,created,desc) @@ -225,7 +227,7 @@ Option flag |Option ``--allow-loaded-modules=ALLOW-LOADED-MODULES`` |List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) ``--allow-modules-tool-mismatch`` |Allow mismatch of modules tool and definition of 'module' function (default: False) ``--allow-use-as-root-and-accept-consequences`` |Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) -``--backup-modules`` |Back up an existing module file, if any. Only works when using --module-only +``--backup-modules`` |Back up an existing module file, if any. Auto-enabled when using --module-only or --skip ``--backup-patched-files`` |Create a backup (*.orig) file when applying a patch (default: False) ``--banned-linked-shared-libs=BANNED-LINKED-SHARED-LIBS`` |Comma-separated list of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library (type comma-separated list) ``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` |Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) diff --git a/docs/version-specific/generic-easyblocks.md b/docs/version-specific/generic-easyblocks.md index d7f3841a7..f8ac959de 100644 --- a/docs/version-specific/generic-easyblocks.md +++ b/docs/version-specific/generic-easyblocks.md @@ -349,6 +349,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed`` |Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` @@ -433,6 +434,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed`` |Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -476,6 +478,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed``|Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -657,6 +660,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed`` |Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` @@ -757,6 +761,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed``|Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -1111,6 +1116,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed`` |Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -1146,6 +1152,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed``|Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -1285,47 +1292,48 @@ if an actual version is specified, it is checked against the derived version of ### Extra easyconfig parameters specific to ``SystemCompiler`` 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`` -``build_cmd`` |Build command to use |``"make"`` -``build_cmd_targets`` |Target name (string) or list of target names to build |``""`` -``build_type`` |Value to provide to --build 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`` -``clooguseisl`` |Use ISL with CLooG or not |``False`` -``components`` |List of components to install: tuples w/ name, version and easyblock to use |``()`` -``configure_cmd`` |Configure command to use |``"./configure"`` -``configure_cmd_prefix`` |Prefix to be glued before ./configure |``""`` -``configure_without_installdir``|Avoid passing an install directory to the configure command (such as via --prefix) |``False`` -``default_component_specs`` |Default specs to use for every component |``{}`` -``default_easyblock`` |Default easyblock to use for components |``None`` -``generate_standalone_module`` |Add known path/library extensions and environment variables for the compiler to the final module |``False`` -``generic`` |Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) |``None`` -``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"`` -``languages`` |List of languages to build GCC for (--enable-languages) |``[]`` -``license_activation`` |License activation type |``"license_server"`` -``m32`` |Enable 32-bit toolchain |``False`` -``multilib`` |Build multilib gcc (both i386 and x86_64) |``False`` -``pplwatchdog`` |Enable PPL watchdog |``False`` -``prefer_lib_subdir`` |Configure GCC to prefer 'lib' subdirs over 'lib64' when linking |``False`` -``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` -``profiled`` |Bootstrap GCC with profile-guided optimizations |``False`` -``requires_runtime_license`` |Boolean indicating whether or not a runtime license is required |``True`` -``sanity_check_all_components`` |Enable sanity checks for all components |``False`` -``sanity_check_components`` |List of components for which to run sanity checks |``[]`` -``serial_number`` |Serial number for the product |``None`` -``tar_config_opts`` |Override tar settings as determined by configure. |``False`` -``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` -``use_gold_linker`` |Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) |``None`` -``usetmppath`` |Use temporary path for installation |``False`` -``withamdgcn`` |Build GCC with AMD GCN offload support |``False`` -``withcloog`` |Build GCC with CLooG support |``False`` -``withisl`` |Build GCC with ISL support |``False`` -``withlibiberty`` |Enable installing of libiberty |``False`` -``withlto`` |Enable LTO support |``True`` -``withnvptx`` |Build GCC with NVPTX offload support |``False`` -``withppl`` |Build GCC with PPL support |``False`` +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`` +``build_cmd`` |Build command to use |``"make"`` +``build_cmd_targets`` |Target name (string) or list of target names to build |``""`` +``build_type`` |Value to provide to --build 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`` +``clooguseisl`` |Use ISL with CLooG or not |``False`` +``components`` |List of components to install: tuples w/ name, version and easyblock to use |``()`` +``configure_cmd`` |Configure command to use |``"./configure"`` +``configure_cmd_prefix`` |Prefix to be glued before ./configure |``""`` +``configure_without_installdir``|Avoid passing an install directory to the configure command (such as via --prefix) |``False`` +``default_component_specs`` |Default specs to use for every component |``{}`` +``default_easyblock`` |Default easyblock to use for components |``None`` +``generate_standalone_module`` |Add known path/library extensions and environment variables for the compiler to the final module |``False`` +``generic`` |Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) |``None`` +``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"`` +``languages`` |List of languages to build GCC for (--enable-languages) |``[]`` +``license_activation`` |License activation type |``"license_server"`` +``m32`` |Enable 32-bit toolchain |``False`` +``multilib`` |Build multilib gcc (both i386 and x86_64) |``False`` +``pplwatchdog`` |Enable PPL watchdog |``False`` +``prefer_lib_subdir`` |Configure GCC to prefer 'lib' subdirs over 'lib64' when linking |``False`` +``prefix_opt`` |Prefix command line option for configure script ('--prefix=' if None) |``None`` +``profiled`` |Bootstrap GCC with profile-guided optimizations |``False`` +``rename_include_fixed`` |Rename the 'include-fixed' directory to avoid that it is used by GCC. This avoids issues when upgrading the OS but might limit the functionality of GCC, especially if the OS GLIBC is older than GCC. A script to (re-)generate the include-fixed folder is created in the 'easybuild' subfolder inside the installation directory.|``False`` +``requires_runtime_license`` |Boolean indicating whether or not a runtime license is required |``True`` +``sanity_check_all_components`` |Enable sanity checks for all components |``False`` +``sanity_check_components`` |List of components for which to run sanity checks |``[]`` +``serial_number`` |Serial number for the product |``None`` +``tar_config_opts`` |Override tar settings as determined by configure. |``False`` +``test_cmd`` |Test command to use ('runtest' value is appended, default: 'make') |``None`` +``use_gold_linker`` |Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) |``None`` +``usetmppath`` |Use temporary path for installation |``False`` +``withamdgcn`` |Build GCC with AMD GCN offload support |``False`` +``withcloog`` |Build GCC with CLooG support |``False`` +``withisl`` |Build GCC with ISL support |``False`` +``withlibiberty`` |Enable installing of libiberty |``False`` +``withlto`` |Enable LTO support |``True`` +``withnvptx`` |Build GCC with NVPTX offload support |``False`` +``withppl`` |Build GCC with PPL support |``False`` ## ``SystemMPI`` @@ -1438,6 +1446,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed``|Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` @@ -1471,6 +1480,7 @@ easyconfig parameter |description ``options`` |Dictionary with extension options. |``{}`` ``pip_ignore_installed``|Let pip ignore installed Python packages (i.e. don't remove them) |``True`` ``pip_no_index`` |Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True |``None`` +``pip_verbose`` |Pass --verbose to 'pip install' (if pip is used). Enabled by default if the EB option --debug is used. |``None`` ``req_py_majver`` |Required major Python version (only relevant when using system Python) |``None`` ``req_py_minver`` |Required minor Python version (only relevant when using system Python) |``None`` ``runtest`` |Run unit tests. |``True`` diff --git a/docs/version-specific/supported-software.md b/docs/version-specific/supported-software.md index 3915dd8b4..d77f6b67b 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 3369 different software packages (incl. toolchains, bundles): +EasyBuild supports 3470 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) - [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) - [AICSImageIO](#aicsimageio) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [ALL](#all) - [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) - [anadama2](#anadama2) - [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) - [ANTIC](#antic) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOFlagger](#aoflagger) - [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) - [Artemis](#artemis) - [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](#abaqus) - [ABINIT](#abinit) - [ABRA2](#abra2) - [ABRicate](#abricate) - [Abseil](#abseil) - [abTEM](#abtem) - [ABySS](#abyss) - [ack](#ack) - [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) - [AICSImageIO](#aicsimageio) - [AIMAll](#aimall) - [aiohttp](#aiohttp) - [ALADIN](#aladin) - [ALAMODE](#alamode) - [Albacore](#albacore) - [Albumentations](#albumentations) - [alevin-fry](#alevin-fry) - [ALFA](#alfa) - [Alfred](#alfred) - [ALL](#all) - [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) - [AMICA](#amica) - [AMOS](#amos) - [AMPHORA2](#amphora2) - [AMPL-MP](#ampl-mp) - [amplimap](#amplimap) - [AMPtk](#amptk) - [AMRFinderPlus](#amrfinderplus) - [AmrPlusPlus](#amrplusplus) - [AMS](#ams) - [Anaconda2](#anaconda2) - [Anaconda3](#anaconda3) - [anadama2](#anadama2) - [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) - [ANTIC](#antic) - [antiSMASH](#antismash) - [ANTLR](#antlr) - [ANTs](#ants) - [anvio](#anvio) - [any2fasta](#any2fasta) - [AOCC](#aocc) - [AOFlagger](#aoflagger) - [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) - [AreTomo2](#aretomo2) - [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) - [Artemis](#artemis) - [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 @@ -138,6 +138,7 @@ version |toolchain ``20210324.2``|``GCCcore/11.2.0`` ``20230125.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``20230125.3``|``GCCcore/12.3.0`` +``20240116.1``|``GCCcore/13.2.0`` ### abTEM @@ -163,6 +164,7 @@ version |toolchain ``2.0.3``|``foss/2017b``, ``intel/2017b`` ``2.1.5``|``foss/2019b`` ``2.2.5``|``foss/2020b`` +``2.3.7``|``foss/2023a`` ### ack @@ -717,6 +719,16 @@ version |toolchain ``3.5.671``|``system`` ``4.1.424``|``system`` +### AMICA + +Code for AMICA: Adaptive Mixture ICA with shared components + +*homepage*: + +version |toolchain +-------------|--------------- +``2024.1.19``|``intel/2023a`` + ### AMOS The AMOS consortium is committed to the development of open-source whole genome assembly software @@ -724,8 +736,8 @@ The AMOS consortium is committed to the development of open-source whole genome *homepage*: version |toolchain ----------|------------------------------ -``3.1.0``|``foss/2018b``, ``foss/2021b`` +---------|---------------------------------------------- +``3.1.0``|``foss/2018b``, ``foss/2021b``, ``foss/2023a`` ### AMPHORA2 @@ -798,6 +810,7 @@ version |versionsuffix|toolchain ``2020.102``|``-intelmpi``|``iimpi/2020b`` ``2022.102``|``-intelmpi``|``iimpi/2021b`` ``2023.101``|``-intelmpi``|``iimpi/2022a`` +``2023.104``|``-intelmpi``|``iimpi/2022b`` ### Anaconda2 @@ -846,6 +859,7 @@ version |toolchain ``2023.03-1``|``system`` ``2023.07-2``|``system`` ``2023.09-0``|``system`` +``2024.02-1``|``system`` ### anadama2 @@ -900,7 +914,7 @@ version |toolchain ``0.925``|``foss/2018b`` ``0.933``|``GCC/8.3.0``, ``iccifort/2019.5.281`` ``0.935``|``GCC/10.2.0`` -``0.940``|``GCC/11.2.0`` +``0.940``|``GCC/11.2.0``, ``GCC/12.3.0`` ### ANIcalculator @@ -918,10 +932,11 @@ anndata is a Python package for handling annotated data matrices in memory and o *homepage*: -version |toolchain ----------|-------------- -``0.8.0``|``foss/2022a`` -``0.9.2``|``foss/2021a`` +version |toolchain +----------------|-------------- +``0.8.0`` |``foss/2022a`` +``0.9.2`` |``foss/2021a`` +``0.10.5.post1``|``foss/2023a`` ### Annif @@ -1015,6 +1030,7 @@ version |versionsuffix |toolchain ``1.10.12``|``-Java-11`` |``system`` ``1.10.12``|``-Java-17`` |``system`` ``1.10.14``|``-Java-11`` |``system`` +``1.10.14``|``-Java-21`` |``system`` ### ANTIC @@ -1077,6 +1093,7 @@ An analysis and visualization platform for 'omics data. version|versionsuffix |toolchain -------|-----------------|--------------- ``6.1``|``-Python-3.7.4``|``intel/2019b`` +``8`` | |``foss/2022b`` ### any2fasta @@ -1110,8 +1127,8 @@ The AOFlagger is a tool that can find and remove radio-frequency interference (R *homepage*: version |toolchain ----------|-------------- -``3.4.0``|``foss/2022a`` +---------|------------------------------ +``3.4.0``|``foss/2022a``, ``foss/2023b`` ### AOMP @@ -1240,8 +1257,8 @@ Provide an interface to ZIP archive files. *homepage*: version |toolchain ---------|------------------------------------------------------------------------------ -``1.68``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +--------|-------------------------------------------------------------------------------------------------- +``1.68``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### ArchR @@ -1252,6 +1269,7 @@ ArchR is a full-featured R package for processing and analyzing single-cell ATAC version |versionsuffix|toolchain ---------|-------------|-------------- ``1.0.1``|``-R-4.1.2`` |``foss/2021b`` +``1.0.2``|``-R-4.3.2`` |``foss/2023a`` ### archspec @@ -1268,6 +1286,17 @@ version |versionsuffix |toolchain ``0.1.4``| |``GCCcore/11.3.0`` ``0.2.0``| |``GCCcore/12.2.0`` ``0.2.1``| |``GCCcore/12.3.0`` +``0.2.2``| |``GCCcore/13.2.0`` + +### AreTomo2 + +AreTomo2, a multi-GPU accelerated software package that fully automates motion- corrected marker-free tomographic alignment and reconstruction, now includes robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single package. AreTomo2 is part of our endeavor to build a fully-automated high- throughput processing pipeline that enables real-time reconstruction of tomograms in parallel with tomographic data collection. It strives to be fast and accurate, as well as provides for easy integration into subtomogram processing workflows by generating IMod compatible files containing alignment and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also be used for on-the-fly reconstruction of tomograms and CTF estimation in parallel with tilt series collection, enabling real-time assessment of sample quality and adjustment of collection parameters + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|------------------ +``1.0.0``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` ### ARGoS @@ -1284,11 +1313,11 @@ version |versionsuffix |toolchain Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. -*homepage*: +*homepage*: version |toolchain ---------|---------------------------------------------------------------------------------------------------------------------------------------------- -``2.13``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------ +``2.13``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ### aria2 @@ -1332,6 +1361,7 @@ version |versionsuffix |toolchain ``10.7.5`` | |``foss/2021a`` ``11.4.3`` | |``foss/2022a``, ``foss/2022b`` ``12.6.2`` | |``foss/2023a`` +``12.8.0`` | |``foss/2023b`` ### arosics @@ -1367,7 +1397,8 @@ 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`` +``3.9.0``|``foss/2023a``, ``foss/2023b`` +``3.9.1``|``foss/2023b`` ### ArrayFire @@ -1401,7 +1432,7 @@ Apache Arrow (incl. PyArrow Python bindings), a cross-language development platf *homepage*: version |versionsuffix |toolchain -----------|------------------|--------------------------------------------------- +----------|------------------|---------------------------------------------------------------- ``0.7.1`` |``-Python-3.6.3`` |``intel/2017b`` ``0.12.0``|``-Python-2.7.15``|``foss/2018b``, ``intel/2018b`` ``0.12.0``|``-Python-3.6.6`` |``intel/2018b`` @@ -1410,7 +1441,7 @@ version |versionsuffix |toolchain ``0.17.1``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``6.0.0`` | |``foss/2021a``, ``foss/2021b`` ``6.0.1`` | |``foss/2021a`` -``8.0.0`` | |``foss/2021a``, ``foss/2022.05``, ``foss/2022a`` +``8.0.0`` | |``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022a`` ``11.0.0``| |``gfbf/2022b`` ``14.0.1``| |``gfbf/2023a`` @@ -1428,6 +1459,7 @@ version |versionsuffix|toolchain ``6.0.0.2`` |``-R-4.2.0`` |``foss/2021b`` ``8.0.0`` |``-R-4.2.1`` |``foss/2022a`` ``11.0.0.3``|``-R-4.2.2`` |``foss/2022b`` +``14.0.0.2``|``-R-4.3.2`` |``foss/2023a`` ### ART @@ -1525,6 +1557,7 @@ 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`` ``3.13.2`` | |``foss/2023a`` +``3.13.3`` | |``foss/2023a``, ``intel/2023a`` ### ASCAT @@ -1544,7 +1577,7 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: version |versionsuffix |toolchain ---------------|------------------|----------------------------------------------------------------------------------------------------------------- +--------------|------------------|---------------------------------------------------------------------------------------------------------------------------------- ``3.9.1.4567``|``-Python-2.7.11``|``intel/2016a`` ``3.10.0`` |``-Python-2.7.11``|``intel/2016.02-GCC-4.9`` ``3.11.0`` |``-Python-2.7.12``|``intel/2016b`` @@ -1570,7 +1603,7 @@ version |versionsuffix |toolchain ``3.21.1`` | |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.21.1`` |``-Python-3.8.2`` |``foss/2020a`` ``3.22.0`` | |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` -``3.22.1`` | |``foss/2021b``, ``foss/2022a``, ``gfbf/2022b``, ``gfbf/2023a``, ``gomkl/2021a``, ``intel/2021b``, ``intel/2022a`` +``3.22.1`` | |``foss/2021b``, ``foss/2022a``, ``gfbf/2022b``, ``gfbf/2023a``, ``gomkl/2021a``, ``iimkl/2023a``, ``intel/2021b``, ``intel/2022a`` ### ASF-SearchAPI @@ -1625,6 +1658,7 @@ version |toolchain ---------|------------------ ``5.0.1``|``GCCcore/8.3.0`` ``5.2.5``|``GCCcore/12.3.0`` +``5.3.1``|``GCCcore/13.2.0`` ### Assimulo @@ -1776,11 +1810,11 @@ Tools to make using job arrays a lot more convenient. *homepage*: version |versionsuffix |toolchain ----------|------------------|-------------------------------------- +---------|------------------|---------------------------------------------------------- ``1.4.2``|``-Python-2.7.12``|``intel/2016b`` ``1.4.6``|``-Python-2.7.16``|``GCCcore/8.3.0`` ``1.4.8``|``-Python-2.7.18``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.5.1``| |``GCCcore/11.2.0`` +``1.5.1``| |``GCCcore/11.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### atropos @@ -2009,6 +2043,7 @@ A tool that automatically formats Python code to conform to the PEP 8 style guid version |versionsuffix |toolchain ---------|-----------------|--------------- ``1.4.4``|``-Python-3.6.4``|``intel/2018a`` +``2.0.4``| |``foss/2022a`` ### Autotools @@ -2087,7 +2122,7 @@ 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) - [bases2fastq](#bases2fastq) - [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) - [BgeeCall](#bgeecall) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [BiasAdjustCXX](#biasadjustcxx) - [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) - [biobakery-workflows](#biobakery-workflows) - [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) - [BMTK](#bmtk) - [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) - [BOPTEST](#boptest) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [BRiAl](#brial) - [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) - [bases2fastq](#bases2fastq) - [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) - [BgeeCall](#bgeecall) - [BgeeDB](#bgeedb) - [bgen](#bgen) - [bgen-reader](#bgen-reader) - [BiasAdjustCXX](#biasadjustcxx) - [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) - [biobakery-workflows](#biobakery-workflows) - [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) - [BMTK](#bmtk) - [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) - [BOPTEST](#boptest) - [boto3](#boto3) - [Bottleneck](#bottleneck) - [Bowtie](#bowtie) - [Bowtie2](#bowtie2) - [Bpipe](#bpipe) - [bpp](#bpp) - [bpytop](#bpytop) - [Bracken](#bracken) - [Braindecode](#braindecode) - [BRAKER](#braker) - [BreakDancer](#breakdancer) - [breseq](#breseq) - [BRiAl](#brial) - [Brotli](#brotli) - [Brotli-python](#brotli-python) - [Brunsli](#brunsli) - [bsddb3](#bsddb3) - [BSMAPz](#bsmapz) - [Bsoft](#bsoft) - [BSseeker2](#bsseeker2) - [btllib](#btllib) - [BuDDy](#buddy) - [BUFRLIB](#bufrlib) - [build](#build) - [buildenv](#buildenv) - [buildingspy](#buildingspy) - [Bullet](#bullet) - [BUSCO](#busco) - [BUStools](#bustools) - [BWA](#bwa) - [bwa-mem2](#bwa-mem2) - [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 @@ -2275,6 +2310,7 @@ version |versionsuffix |toolchain ``1.2.0``|``-Python-3.6.6`` |``intel/2018b`` ``1.2.2``|``-Python-3.8.2`` |``foss/2020a`` ``1.3.6``| |``foss/2022a`` +``1.3.9``| |``foss/2023a`` ### bases2fastq @@ -2744,6 +2780,8 @@ version |versionsuffix |toolchain ``2.0.0`` | |``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.1.0`` |``-Python-3.7.4``|``foss/2019b``, ``intel/2019b`` ``3.0.1`` | |``foss/2020b``, ``foss/2021a`` +``3.1.0`` | |``foss/2022a``, ``intel/2022a`` +``4.0`` | |``foss/2022a`` ### BFAST @@ -2846,6 +2884,7 @@ BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynt version |versionsuffix |toolchain ---------|-----------------|--------------- ``1.0.1``|``-Python-3.7.4``|``intel/2019b`` +``1.1.5``| |``foss/2022a`` ### BigDFT @@ -2899,11 +2938,11 @@ Read files using HTSlib including BAM/CRAM, Tabix and BCF database files *homepage*: version |versionsuffix |toolchain ---------|----------------|---------------------------------------------- +--------|----------------|-------------------------------------------------------------- ``2.11``|``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` ``2.11``|``-Perl-5.26.1``|``intel/2018a`` ``2.11``|``-Perl-5.28.0``|``foss/2018b`` -``3.01``| |``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``3.01``| |``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ``3.01``|``-Perl-5.28.1``|``GCC/8.2.0-2.31.1`` ### Bio-EUtilities @@ -3007,10 +3046,10 @@ 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`` @@ -3022,7 +3061,7 @@ 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``, ``GCCcore/12.2.0`` +``1.7.8`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### BioPP @@ -3063,6 +3102,7 @@ version |versionsuffix |toolchain ``1.78``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``1.79``| |``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` ``1.81``| |``foss/2022b`` +``1.83``| |``foss/2023a`` ### BioServices @@ -3272,9 +3312,9 @@ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------- +---------|--------------------------------------------------------------------------------------------------------------------- ``0.10`` |``GCCcore/6.4.0``, ``foss/2016a`` -``1.0.2``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` +``1.0.2``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0``, ``GCCcore/9.3.0`` ### BlobTools @@ -3293,8 +3333,8 @@ Block implements the density matrix renormalization group (DMRG) algorithm for q *homepage*: version |toolchain -------------------|-------------- -``1.5.3-20200525``|``foss/2022a`` +------------------|------------------------------ +``1.5.3-20200525``|``foss/2022a``, ``foss/2022b`` ### Blosc @@ -3313,6 +3353,7 @@ version |toolchain ``1.21.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.21.1``|``GCCcore/11.2.0`` ``1.21.3``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.21.5``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Blosc2 @@ -3320,13 +3361,14 @@ Blosc, an extremely fast, multi-threaded, meta-compressor library *homepage*: -version |toolchain ----------|------------------ -``2.0.3``|``GCCcore/10.2.0`` -``2.0.4``|``GCCcore/10.3.0`` -``2.4.3``|``GCCcore/11.3.0`` -``2.6.1``|``GCCcore/11.3.0`` -``2.8.0``|``GCCcore/12.2.0`` +version |toolchain +----------|-------------------------------------- +``2.0.3`` |``GCCcore/10.2.0`` +``2.0.4`` |``GCCcore/10.3.0`` +``2.4.3`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.6.1`` |``GCCcore/11.3.0`` +``2.8.0`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.13.2``|``GCCcore/13.2.0`` ### BLT @@ -3524,10 +3566,12 @@ Boost provides free peer-reviewed portable C++ source libraries. *homepage*: version |toolchain -----------|--------------- +----------|-------------------------------- ``1.76.0``|``gompi/2021a`` ``1.77.0``|``gompi/2021b`` -``1.79.0``|``gompi/2022a`` +``1.79.0``|``gompi/2022a``, ``gompi/2022b`` +``1.81.0``|``gompi/2022b`` +``1.82.0``|``gompi/2023a`` ### Boost.Python @@ -3550,6 +3594,7 @@ version |versionsuffix |toolchain ``1.76.0``| |``GCC/10.3.0`` ``1.77.0``| |``GCC/11.2.0`` ``1.79.0``| |``GCC/11.3.0`` +``1.83.0``| |``GCC/13.2.0`` ### Boost.Python-NumPy @@ -3643,7 +3688,7 @@ 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``, ``GCC/12.3.0`` +``2.5.1`` |``GCC/10.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` ### Bpipe @@ -3696,10 +3741,11 @@ Braindecode is an open-source Python toolbox for decoding raw electrophysiologic *homepage*: -version|versionsuffix |toolchain --------|-------------------------------|-------------- -``0.7``|``-PyTorch-1.10.0`` |``foss/2021a`` -``0.7``|``-PyTorch-1.10.0-CUDA-11.3.1``|``foss/2021a`` +version |versionsuffix |toolchain +---------|-------------------------------|-------------- +``0.7`` |``-PyTorch-1.10.0`` |``foss/2021a`` +``0.7`` |``-PyTorch-1.10.0-CUDA-11.3.1``|``foss/2021a`` +``0.8.1``|``-PyTorch-2.1.2`` |``foss/2023a`` ### BRAKER @@ -3766,6 +3812,7 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data version |toolchain ---------|------------------------------------------------------------------------------ ``1.0.9``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.1.0``|``GCCcore/13.2.0`` ### Brunsli @@ -3820,6 +3867,16 @@ version |versionsuffix |toolchain ---------|------------------|-------------------------------------- ``2.1.8``|``-Python-2.7.16``|``GCC/8.3.0``, ``iccifort/2019.5.281`` +### btllib + +Bioinformatics Technology Lab common code library + +*homepage*: + +version |toolchain +---------|-------------- +``1.7.0``|``GCC/12.3.0`` + ### BuDDy A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more. @@ -3849,6 +3906,7 @@ A simple, correct Python build frontend. version |toolchain ----------|------------------------------ ``0.10.0``|``foss/2022a``, ``foss/2022b`` +``1.0.3`` |``foss/2023a``, ``foss/2023b`` ### buildenv @@ -3857,8 +3915,8 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: version |versionsuffix |toolchain ------------|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``default``| |``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b``, ``nvompi/2022.07`` +-----------|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``default``| |``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``foss/2023b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a``, ``intel/2023b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b``, ``nvompi/2022.07`` ``default``|``-CUDA-11.3.1``|``foss/2021a`` ``default``|``-CUDA-11.4.1``|``foss/2021b`` ``default``|``-CUDA-11.7.0``|``foss/2022a`` @@ -3922,13 +3980,24 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: -version |toolchain ------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``0.7.12`` |``foss/2016b`` -``0.7.13`` |``foss/2016a``, ``intel/2016a`` -``0.7.15`` |``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a``|``foss/2016b``, ``intel/2017a`` -``0.7.17`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``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/2018a``, ``intel/2018b`` +version |toolchain +-------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``0.7.12`` |``foss/2016b`` +``0.7.13`` |``foss/2016a``, ``intel/2016a`` +``0.7.15`` |``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` |``foss/2016b``, ``intel/2017a`` +``0.7.17`` |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``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/2018a``, ``intel/2018b`` +``0.7.17-20220923``|``GCCcore/12.3.0`` + +### bwa-mem2 + +The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. + +*homepage*: + +version |toolchain +---------|---------------------------- +``2.2.1``|``intel-compilers/2023.1.0`` ### bwa-meth @@ -3991,6 +4060,7 @@ version |versionsuffix |toolchain ``0.8.11``| |``foss/2021a`` ``0.8.13``| |``foss/2021b`` ``0.9.0`` | |``foss/2022a`` +``0.10.0``| |``foss/2023a`` ### BXH_XCEDE_TOOLS @@ -4038,7 +4108,7 @@ 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) - [castor](#castor) - [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) - [CellBender](#cellbender) - [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) - [CIRIquant](#ciriquant) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clair3](#clair3) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [CLEAR](#clear) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [cliquer](#cliquer) - [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) - [ConcurrentVersionsSystem](#concurrentversionssystem) - [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) - [cpio](#cpio) - [CPLEX](#cplex) - [CPMD](#cpmd) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppyy](#cppyy) - [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) - [CUDD](#cudd) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CVglasso](#cvglasso) - [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) - [castor](#castor) - [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) - [CellBender](#cellbender) - [CellChat](#cellchat) - [CellMix](#cellmix) - [CellOracle](#celloracle) - [Cellpose](#cellpose) - [CellRanger](#cellranger) - [CellRanger-ARC](#cellranger-arc) - [CellRanger-ATAC](#cellranger-atac) - [CellRank](#cellrank) - [CellTypist](#celltypist) - [CENSO](#censo) - [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) - [Circlator](#circlator) - [Circos](#circos) - [Circuitscape](#circuitscape) - [CIRI](#ciri) - [CIRI-long](#ciri-long) - [CIRIquant](#ciriquant) - [cisTEM](#cistem) - [CITE-seq-Count](#cite-seq-count) - [Clair3](#clair3) - [Clang](#clang) - [Clang-AOMP](#clang-aomp) - [Clang-Python-bindings](#clang-python-bindings) - [CLAPACK](#clapack) - [Clarabel.rs](#clarabel.rs) - [CLEAR](#clear) - [CLEASE](#clease) - [CLHEP](#clhep) - [CliMetLab](#climetlab) - [CLIP](#clip) - [cliquer](#cliquer) - [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-cli](#code-cli) - [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) - [Concorde](#concorde) - [ConcurrentVersionsSystem](#concurrentversionssystem) - [configparser](#configparser) - [configurable-http-proxy](#configurable-http-proxy) - [CONN](#conn) - [connected-components-3d](#connected-components-3d) - [ConnectomeWorkbench](#connectomeworkbench) - [contextily](#contextily) - [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) - [cpio](#cpio) - [CPLEX](#cplex) - [CPMD](#cpmd) - [CPPE](#cppe) - [CppHeaderParser](#cppheaderparser) - [CppUnit](#cppunit) - [cppy](#cppy) - [cppyy](#cppyy) - [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) - [CUDD](#cudd) - [cuDNN](#cudnn) - [Cufflinks](#cufflinks) - [CUnit](#cunit) - [CuPy](#cupy) - [cURL](#curl) - [cuSPARSELt](#cusparselt) - [custodian](#custodian) - [cutadapt](#cutadapt) - [cuTENSOR](#cutensor) - [cuteSV](#cutesv) - [CUTLASS](#cutlass) - [CVglasso](#cvglasso) - [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 @@ -4052,6 +4122,7 @@ 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`` +``1.27.0``|``GCCcore/13.2.0`` ### C3D @@ -4153,8 +4224,8 @@ A Free Software Three-Dimensional Structural Finite Element Program *homepage*: version |toolchain ---------|------------------------------ -``2.20``|``foss/2021a``, ``foss/2022b`` +--------|---------------------------------------------- +``2.20``|``foss/2021a``, ``foss/2022b``, ``foss/2023a`` ### Calendrical @@ -4251,15 +4322,16 @@ Cap’n Proto is an insanely fast data interchange format and capability-based R *homepage*: -version |toolchain -----------|---------------------------------------------------------- -``0.6.1`` |``GCCcore/6.4.0`` -``0.7.0`` |``GCCcore/7.3.0`` -``0.8.0`` |``GCCcore/9.3.0`` -``0.9.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``0.10.2``|``GCCcore/11.3.0`` -``0.10.3``|``GCCcore/12.2.0`` -``1.0.1`` |``GCCcore/12.3.0`` +version |toolchain +-----------|---------------------------------------------------------- +``0.6.1`` |``GCCcore/6.4.0`` +``0.7.0`` |``GCCcore/7.3.0`` +``0.8.0`` |``GCCcore/9.3.0`` +``0.9.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.10.2`` |``GCCcore/11.3.0`` +``0.10.3`` |``GCCcore/12.2.0`` +``1.0.1`` |``GCCcore/12.3.0`` +``1.0.1.1``|``GCCcore/13.2.0`` ### captum @@ -4316,6 +4388,7 @@ version |versionsuffix |toolchain ``0.19.0.post1``| |``foss/2020b``, ``intel/2020b`` ``0.20.0`` | |``foss/2021a`` ``0.20.3`` | |``foss/2021b``, ``foss/2022a`` +``0.22.0`` | |``foss/2023a`` ### CASA @@ -4334,9 +4407,9 @@ A suite of C++ libraries for radio astronomy data processing. The ephemerides da *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``3.4.0``|``foss/2021b`` -``3.5.0``|``foss/2022a`` +``3.5.0``|``foss/2022a``, ``foss/2023b`` ### Casanovo @@ -4514,10 +4587,11 @@ 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``, ``foss/2022b`` +version |toolchain +-----------|---------------------------------------------- +``2.10.3`` |``foss/2018b`` +``2.10.5`` |``foss/2020b``, ``foss/2021a``, ``foss/2022b`` +``2.10.11``|``foss/2023a`` ### CBLAS @@ -4536,7 +4610,7 @@ 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`` @@ -4547,6 +4621,7 @@ version |versionsuffix|toolchain ``4.6.3`` | |``GCCcore/11.3.0``, ``system`` ``4.7.5`` | |``system`` ``4.8.3`` | |``system`` +``4.9`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### CCfits @@ -4565,11 +4640,11 @@ Clozure CL (often called CCL for short) is a free Common Lisp implementation wi *homepage*: version |toolchain -----------|------------------ +----------|---------------------------------------------------------- ``1.11.5``|``system`` ``1.12`` |``GCCcore/9.3.0`` ``1.12.1``|``GCCcore/10.3.0`` -``1.12.2``|``GCCcore/11.3.0`` +``1.12.2``|``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### cclib @@ -4582,6 +4657,7 @@ version |versionsuffix |toolchain ``1.5`` |``-Python-3.5.2``|``foss/2016b`` ``1.6.3``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` ``1.7.2``| |``foss/2021b`` +``1.8`` | |``foss/2023a`` ### cctbx-base @@ -4698,7 +4774,7 @@ version |toolchain ``2.0.5`` |``gompi/2021b`` ``2.0.6`` |``gompi/2022a`` ``2.1.1`` |``gompi/2021a`` -``2.2.2`` |``gompi/2023a`` +``2.2.2`` |``gompi/2023a``, ``gompi/2023b`` ### cdo-bindings @@ -4740,9 +4816,12 @@ CellBender is a software package for eliminating technical artifacts from high-t *homepage*: -version |toolchain ----------|-------------- -``0.2.2``|``foss/2022a`` +version |versionsuffix |toolchain +---------|----------------|-------------- +``0.2.1``|``-CUDA-11.3.1``|``foss/2021a`` +``0.2.2``| |``foss/2022a`` +``0.3.1``| |``foss/2022a`` +``0.3.1``|``-CUDA-11.7.0``|``foss/2022a`` ### CellChat @@ -4851,6 +4930,17 @@ A tool for semi-automatic cell type annotation version |toolchain ---------|-------------- ``1.0.0``|``foss/2021b`` +``1.6.2``|``foss/2023a`` + +### CENSO + +Commandline Energetic SOrting (CENSO) is a sorting algorithm for efficient evaluation of Structure Ensembles (SE). The input ensemble (or single structure) originating from a CREST[SQM/FF] run can be ranked by free energy at DFT level and/or geometries can be optimized using DFT. + +*homepage*: + +version |toolchain +---------|----------------------------------- +``1.2.0``|``GCCcore/12.3.0``, ``intel/2022a`` ### centerline @@ -4917,9 +5007,9 @@ version |toolchain ### 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 ---------|---------------------------------------------------------- @@ -4932,6 +5022,7 @@ version |toolchain ``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`` +``4.3.1``|``GCCcore/13.2.0`` ### cftime @@ -4996,6 +5087,7 @@ version |toolchain ``0.60.2``|``foss/2018b`` ``0.60.3``|``foss/2020b``, ``foss/2021a`` ``0.60.7``|``foss/2022b`` +``0.60.8``|``foss/2023a`` ### CGmapTools @@ -5050,9 +5142,9 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------------------- +----------|--------------------------------------------------------------------------------------------------------------------- ``0.12.0``|``GCCcore/6.4.0`` -``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``0.15.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0``, ``GCCcore/9.3.0`` ### CheckM @@ -5130,7 +5222,7 @@ version |toolchain ``1.8.8`` |``intel/2018b`` ``1.8.9`` |``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b`` ``1.8.11`` |``foss/2021b`` -``1.8.12`` |``foss/2022a`` +``1.8.12`` |``foss/2022a``, ``foss/2022b`` ### CHERAB @@ -5259,6 +5351,16 @@ version |versionsuffix |toolchain ``2.3.3``|``-Python-2.7.14``|``intel/2018a`` ``2.3.8``|``-Python-2.7.18``|``foss/2020b``, ``foss/2021b`` +### Circlator + +A tool to circularize genome assemblies.s + +*homepage*: + +version |toolchain +---------|-------------- +``1.5.5``|``foss/2023a`` + ### Circos Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. @@ -5385,6 +5487,7 @@ version |versionsuffix |toolchain ``15.0.5``| |``GCCcore/11.3.0`` ``16.0.4``| |``GCCcore/12.2.0`` ``16.0.6``| |``GCCcore/12.3.0`` +``16.0.6``|``-CUDA-12.1.1`` |``GCCcore/12.3.0`` ### Clang-AOMP @@ -5407,6 +5510,7 @@ version |versionsuffix |toolchain ``8.0.0`` |``-Python-2.7.15``|``GCCcore/8.2.0`` ``10.0.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``13.0.1``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``16.0.6``| |``GCCcore/12.3.0`` ### CLAPACK @@ -5418,6 +5522,16 @@ version |toolchain ---------|--------------------------------------------------------------------------- ``3.2.1``|``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a`` +### Clarabel.rs + +Interior-point solver for convex conic optimisation problems in Rust. + +*homepage*: + +version |toolchain +---------|-------------- +``0.7.1``|``gfbf/2023a`` + ### CLEAR Direct comparison of circular and linear RNA expression @@ -5542,6 +5656,7 @@ version |toolchain ``1.17.6``|``foss/2020b``, ``foss/2021a`` ``1.17.7``|``foss/2021b`` ``1.17.8``|``foss/2022b`` +``1.17.9``|``foss/2023a`` ### Clustal-Omega @@ -5550,9 +5665,9 @@ Clustal Omega is a multiple sequence alignment program for proteins. It produce *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------- +---------|--------------------------------------------------------------------------------------------------------------------------------------------- ``1.2.0``|``foss/2016b`` -``1.2.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``foss/2018b``, ``intel-compilers/2021.2.0``, ``intel/2018a``, ``intel/2018b`` +``1.2.4``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b``, ``intel-compilers/2021.2.0``, ``intel/2018a``, ``intel/2018b`` ### ClustalW2 @@ -5561,8 +5676,8 @@ ClustalW2 is a general purpose multiple sequence alignment program for DNA or pr *homepage*: version|toolchain --------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``2.1``|``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` +-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``2.1``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/12.3.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` ### Cluster-Buster @@ -5656,6 +5771,7 @@ version |versionsuffix|toolchain ---------|-------------|-------------- ``0.5.0``|``-R-4.1.2`` |``foss/2021b`` ``0.5.2``|``-R-4.2.1`` |``foss/2022a`` +``0.7.1``|``-R-4.3.2`` |``foss/2023a`` ### cmocean @@ -5731,6 +5847,7 @@ COBRApy is a package for constraint-based modeling of metabolic networks. version |toolchain ----------|-------------- ``0.26.0``|``foss/2021a`` +``0.29.0``|``foss/2023b`` ### CoCoALib @@ -5754,6 +5871,16 @@ version|toolchain -------|-------------- ``1.2``|``foss/2021b`` +### code-cli + +Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|---------- +``1.85.1``|``-x64`` |``system`` + ### code-server Run VS Code on any machine anywhere and access it in the browser. @@ -5765,6 +5892,8 @@ version |toolchain ``3.7.3`` |``system`` ``4.9.1`` |``system`` ``4.16.1``|``system`` +``4.21.1``|``system`` +``4.22.1``|``system`` ### CODEX2 @@ -5812,12 +5941,13 @@ CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functi *homepage*: -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`` +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`` +``2.11.10``|``GCC/12.3.0`` ### ColabFold @@ -5868,8 +5998,8 @@ Low-Level Interface to zlib or zlib-ng compression library *homepage*: version |toolchain ----------|------------------ -``2.202``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``2.202``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ### COMSOL @@ -5917,6 +6047,16 @@ version |versionsuffix |toolchain ``1.1.0``|``-Python-2.7.15``|``foss/2019a`` ``1.1.0``|``-Python-2.7.18``|``foss/2020b`` +### Concorde + +Concorde is a computer code for the symmetric traveling salesman problem (TSP) and some related network optimization problems + +*homepage*: + +version |toolchain +------------|-------------- +``20031219``|``GCC/12.3.0`` + ### ConcurrentVersionsSystem CVS is a version control system, an important component of Source Configuration Management (SCM). @@ -5989,6 +6129,16 @@ version |versionsuffix |toolchain ``1.4.2``|``-rh_linux64``|``system`` ``1.5.0``| |``GCCcore/10.3.0`` +### contextily + +contextily is a small Python 3 package to retrieve tile maps from the internet. It can add those tiles as basemap to matplotlib figures or write tile maps to disk into geospatial raster files. Bounding boxes can be passed in both WGS84 (EPSG:4326) and Spheric Mercator (EPSG:3857). + +*homepage*: + +version |toolchain +---------|-------------- +``1.5.0``|``foss/2023a`` + ### Control-FREEC Copy number and genotype annotation from whole genome and whole exome sequencing data. @@ -6020,6 +6170,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.3.2``|``gompi/2019a``, ``iimpi/2019a`` ``3.0.1``|``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` +``3.0.2``|``gompi/2023a`` ### Coot @@ -6100,7 +6251,7 @@ 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`` +``7.2.3``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``7.2.7``| |``GCCcore/11.3.0`` ### cowsay @@ -6194,8 +6345,8 @@ CPPE is an open-source, light-weight C++ and Python library for Polarizable Embe *homepage*: version |toolchain ----------|-------------- -``0.3.1``|``GCC/11.3.0`` +---------|------------------------------ +``0.3.1``|``GCC/11.3.0``, ``GCC/12.2.0`` ### CppHeaderParser @@ -6214,9 +6365,9 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: version |toolchain -----------|------------------------------------------------------------------------------------------------ +----------|-------------------------------------------------------------------------------------------------------------------- ``1.12.1``|``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` -``1.15.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.15.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### cppy @@ -6225,9 +6376,9 @@ 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``, ``GCCcore/12.3.0`` +``1.2.1``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### cppyy @@ -6338,9 +6489,10 @@ CREST is an utility/driver program for the xtb program. Originally it was design *homepage*: version |toolchain -----------|--------------- +----------|------------------------------- ``2.11`` |``intel/2021a`` ``2.11.2``|``intel/2021a`` +``2.12`` |``gfbf/2023a``, ``intel/2022a`` ### CRF++ @@ -6444,6 +6596,7 @@ This package is a memory efficient implementation of cryoCARE. This setup train version |versionsuffix |toolchain ---------|----------------|-------------- ``0.2.1``|``-CUDA-11.3.1``|``foss/2021a`` +``0.3.0``|``-CUDA-11.7.0``|``foss/2022a`` ### cryoDRGN @@ -6508,6 +6661,7 @@ version |versionsuffix |toolchain ---------|-----------------|---------------------------------- ``0.4.1``|``-Python-3.7.2``|``foss/2019a``, ``fosscuda/2019a`` ``0.7.4``| |``foss/2022a`` +``0.7.4``|``-CUDA-11.7.0`` |``foss/2022a`` ### CSBLAST @@ -6516,8 +6670,9 @@ Context-specific extension of BLAST that significantly improves sensitivity and *homepage*: version |toolchain ----------|----------------- +---------|------------------ ``2.2.3``|``GCCcore/8.3.0`` +``2.2.4``|``GCCcore/11.3.0`` ### cscope @@ -6607,7 +6762,7 @@ version |toolchain ``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`` -``4.8.2``|``GCCcore/12.2.0`` +``4.8.2``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` ### CubeWriter @@ -6621,7 +6776,7 @@ version |toolchain ``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`` -``4.8.2``|``GCCcore/12.2.0`` +``4.8.2``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` ### CuCLARK @@ -6675,6 +6830,8 @@ version |toolchain ``12.2.0`` |``system`` ``12.2.2`` |``system`` ``12.3.0`` |``system`` +``12.3.2`` |``system`` +``12.4.0`` |``system`` ### CUDA-Samples @@ -6772,6 +6929,7 @@ version |versionsuffix |toolchain ``8.8.0.121``|``-CUDA-12.0.0`` |``system`` ``8.9.2.26`` |``-CUDA-12.1.1`` |``system`` ``8.9.2.26`` |``-CUDA-12.2.0`` |``system`` +``8.9.7.29`` |``-CUDA-12.3.0`` |``system`` ### Cufflinks @@ -6806,6 +6964,7 @@ version |versionsuffix |toolchain ``8.5.0`` | |``fosscuda/2020b`` ``11.4.0``|``-CUDA-11.4.1`` |``foss/2021b`` ``12.1.0``|``-CUDA-12.0.0`` |``foss/2022b`` +``13.0.0``|``-CUDA-12.1.1`` |``foss/2023a`` ### cURL @@ -6851,6 +7010,7 @@ NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix version |versionsuffix |toolchain -----------|----------------|---------- ``0.3.0.3``|``-CUDA-11.4.1``|``system`` +``0.6.0.6``|``-CUDA-12.1.1``|``system`` ### custodian @@ -6906,6 +7066,8 @@ version |versionsuffix |toolchain ``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`` +``2.0.1.2``|``-CUDA-12.1.1``|``system`` +``2.0.1.2``|``-CUDA-12.2.2``|``system`` ### cuteSV @@ -6917,6 +7079,16 @@ version |toolchain ---------|-------------- ``2.0.3``|``foss/2022a`` +### CUTLASS + +CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these "moving parts" into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``2.11.0``|``-CUDA-11.7.0``|``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. @@ -6954,6 +7126,7 @@ version |versionsuffix |toolchain ``1.0.24``| |``foss/2019a`` ``1.0.28``|``-Python-3.7.4``|``foss/2019b`` ``1.3.0`` | |``foss/2022a`` +``1.4.2`` | |``foss/2023a`` ### CWIPI @@ -7005,7 +7178,7 @@ Cython is an optimising static compiler for both the Python programming language *homepage*: version |versionsuffix |toolchain ------------|------------------|------------------------------- +-----------|------------------|-------------------------------------- ``0.23.4`` |``-Python-2.7.10``|``gimkl/2.11.5`` ``0.24.1`` |``-Python-2.7.11``|``foss/2016a`` ``0.25.2`` |``-Python-2.7.12``|``foss/2016b`` @@ -7015,6 +7188,8 @@ version |versionsuffix |toolchain ``0.29.10``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` ``0.29.22``| |``GCCcore/10.2.0`` ``0.29.33``| |``GCCcore/11.3.0`` +``3.0.7`` | |``GCCcore/12.3.0`` +``3.0.8`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``3.0a5`` | |``GCCcore/10.2.0`` ### cython-blis @@ -7072,7 +7247,7 @@ 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) - [datalad](#datalad) - [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) - [Demystify](#demystify) - [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) - [dftd4](#dftd4) - [DGL](#dgl) - [DIA-NN](#dia-nn) - [DIAL](#dial) - [dialog](#dialog) - [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) - [DP3](#dp3) - [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) - [dynesty](#dynesty) +[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) - [datalad](#datalad) - [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) - [DeepLoc](#deeploc) - [deepmedic](#deepmedic) - [DeepMod2](#deepmod2) - [DeepSurv](#deepsurv) - [deepTools](#deeptools) - [DEICODE](#deicode) - [Delft3D](#delft3d) - [Delly](#delly) - [DeltaLake](#deltalake) - [DeMixT](#demixt) - [Demystify](#demystify) - [DendroPy](#dendropy) - [denseweight](#denseweight) - [DensPart](#denspart) - [Deprecated](#deprecated) - [desktop-file-utils](#desktop-file-utils) - [destiny](#destiny) - [Detectron2](#detectron2) - [DETONATE](#detonate) - [devbio-napari](#devbio-napari) - [Devito](#devito) - [DFA](#dfa) - [DFT-D3](#dft-d3) - [DFT-D4](#dft-d4) - [DFTB+](#dftb+) - [dftd3-lib](#dftd3-lib) - [dftd4](#dftd4) - [DGL](#dgl) - [DIA-NN](#dia-nn) - [DIAL](#dial) - [dialog](#dialog) - [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) - [DjVuLibre](#djvulibre) - [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) - [DP3](#dp3) - [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) - [dynesty](#dynesty) ### dadi @@ -7211,6 +7386,7 @@ version |versionsuffix |toolchain ``2022.10.0``| |``foss/2022a`` ``2023.7.1`` | |``foss/2022b`` ``2023.9.2`` | |``foss/2023a`` +``2023.12.1``| |``foss/2023a`` ### dask-labextension @@ -7231,6 +7407,7 @@ DataLad is a free and open source distributed data management system that keeps version |toolchain ----------|------------------ ``0.18.4``|``GCCcore/12.2.0`` +``0.19.5``|``GCCcore/12.3.0`` ### datamash @@ -7285,6 +7462,7 @@ version |versionsuffix |toolchain ``1.856``| |``GCCcore/10.3.0`` ``1.857``| |``GCCcore/11.2.0`` ``1.858``| |``GCCcore/11.3.0`` +``1.859``| |``GCCcore/12.3.0`` ### DBCSR @@ -7303,14 +7481,14 @@ Perl binding for MySQL *homepage*: version |versionsuffix |toolchain ----------|----------------|---------------------------------------------- +---------|----------------|-------------------------------------------------------------- ``4.032``|``-Perl-5.22.2``|``intel/2016a`` ``4.033``|``-Perl-5.24.0``|``intel/2016b`` ``4.042``|``-Perl-5.24.1``|``intel/2017a`` ``4.046``|``-Perl-5.26.0``|``foss/2017b``, ``intel/2017b`` ``4.046``|``-Perl-5.26.1``|``intel/2018a`` ``4.048``|``-Perl-5.28.0``|``foss/2018b`` -``4.050``| |``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``4.050``| |``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` ``4.050``|``-Perl-5.28.1``|``foss/2019a`` ### DBG2OLC @@ -7467,13 +7645,14 @@ DeepDiff: Deep Difference of dictionaries, iterables and almost any other object *homepage*: version |versionsuffix |toolchain ----------|------------------|------------------------------- +---------|------------------|-------------------------------------- ``3.3.0``|``-Python-2.7.15``|``intel/2018b`` ``3.3.0``|``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` ``4.0.6``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``5.0.2``|``-Python-3.7.4`` |``GCCcore/8.3.0`` ``5.7.0``| |``GCCcore/11.2.0`` ``5.8.1``| |``GCCcore/11.3.0`` +``6.7.1``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### DeepLabCut @@ -7485,6 +7664,17 @@ version |versionsuffix |toolchain -----------|----------------|-------------- ``2.2.0.6``| |``foss/2021a`` ``2.2.0.6``|``-CUDA-11.3.1``|``foss/2021a`` +``2.3.6`` |``-CUDA-11.7.0``|``foss/2022a`` + +### DeepLoc + +DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins + +*homepage*: + +version|toolchain +-------|-------------- +``2.0``|``foss/2022b`` ### deepmedic @@ -7543,6 +7733,16 @@ version |toolchain ---------|-------------- ``0.2.4``|``foss/2022a`` +### Delft3D + +Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including sediments. Delft3D-FLOW is part of Delft3D 4. + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|-------------- +``4.04.01``|``-FLOW`` |``foss/2022a`` + ### Delly Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. @@ -7556,6 +7756,16 @@ version |versionsuffix |toolchain ``1.1.5``| |``GCC/11.3.0`` ``1.1.6``| |``GCC/12.2.0`` +### DeltaLake + +Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease. + +*homepage*: + +version |toolchain +----------|-------------- +``0.15.1``|``gfbf/2023a`` + ### DeMixT Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms. @@ -7588,6 +7798,17 @@ version |versionsuffix |toolchain ``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``, ``GCCcore/12.2.0`` ``4.5.2``|``-Python-2.7.18``|``GCCcore/10.2.0`` +``4.6.1``| |``GCCcore/12.3.0`` + +### denseweight + +This package implements the method for imbalanced regression DenseWeight. The corresponding paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow training machine learning models for regression tasks that emphasize performance for data points with rare target values in comparison to data points with more common target values. + +*homepage*: + +version |toolchain +---------|------------------------------ +``0.1.2``|``foss/2022a``, ``foss/2023a`` ### DensPart @@ -7608,6 +7829,17 @@ If you need to mark a function or a method as deprecated, you can use the @depre version |toolchain ----------|------------------------------ ``1.2.13``|``foss/2021a``, ``foss/2022a`` +``1.2.14``|``foss/2023a`` + +### desktop-file-utils + +desktop-file-utils contains a few command line utilities for working with desktop entries: * desktop-file-validate: validates a desktop file and prints warnings/errors about desktop entry specification violations. * desktop-file-install: installs a desktop file to the applications directory, optionally munging it a bit in transit. * update-desktop-database: updates the database containing a cache of MIME types handled by desktop files. It requires GLib to compile, because the implementation requires Unicode utilities and such. + +*homepage*: + +version |toolchain +--------|------------------ +``0.27``|``GCCcore/12.3.0`` ### destiny @@ -7630,15 +7862,26 @@ version|versionsuffix |toolchain ``0.6``| |``foss/2021a`` ``0.6``|``-CUDA-11.3.1``|``foss/2021a`` -### detonate +### DETONATE DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences. *homepage*: version |toolchain ---------|--------------- -``1.11``|``intel/2017b`` +--------|------------------------------- +``1.11``|``GCC/12.3.0``, ``intel/2017b`` + +### devbio-napari + +A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology. + +*homepage*: + +version |versionsuffix |toolchain +----------|----------------|-------------- +``0.10.1``| |``foss/2022a`` +``0.10.1``|``-CUDA-11.7.0``|``foss/2022a`` ### Devito @@ -7680,6 +7923,7 @@ Generally Applicable Atomic-Charge Dependent London Dispersion Correction. version |versionsuffix |toolchain ---------|-----------------|--------------- ``3.2.0``|``-Python-3.7.4``|``intel/2019b`` +``3.6.0``| |``intel/2022a`` ### DFTB+ @@ -7785,6 +8029,7 @@ version |toolchain ``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``, ``GCC/12.2.0``, ``GCC/12.3.0`` +``2.1.9`` |``GCC/13.2.0`` ### Dice @@ -7795,6 +8040,7 @@ Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI version |toolchain ------------|-------------- ``20221025``|``foss/2022a`` +``20240101``|``foss/2022b`` ### DiCE-ML @@ -7908,6 +8154,16 @@ version|toolchain -------|--------------- ``1.0``|``gompi/2021a`` +### DjVuLibre + +DjVuLibre is an open source (GPL'ed) implementation of DjVu, including viewers, browser plugins, decoders, simple encoders, and utilities. + +*homepage*: + +version |toolchain +----------|------------------ +``3.5.28``|``GCCcore/12.3.0`` + ### DL_POLY_4 DL_POLY is a general purpose classical molecular dynamics (MD) simulation software @@ -7941,6 +8197,7 @@ version |toolchain ---------|-------------------------------- ``3.2`` |``gompi/2022a``, ``iimpi/2022a`` ``3.3.1``|``gompi/2022a``, ``iimpi/2022a`` +``3.4`` |``gompi/2023b``, ``iimpi/2023b`` ### dlib @@ -7962,6 +8219,7 @@ DLPack is a stable in-memory data structure for an ndarray system to interact wi version|toolchain -------|-------------- ``0.3``|``GCC/10.3.0`` +``0.8``|``GCC/11.3.0`` ### dm-haiku @@ -7996,7 +8254,7 @@ version |toolchain ``0.1.1``|``GCCcore/8.3.0`` ``0.1.5``|``GCCcore/10.2.0`` ``0.1.6``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``0.1.8``|``GCCcore/11.3.0`` +``0.1.8``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### DMCfun @@ -8015,8 +8273,8 @@ DMLC-Core is the backbone library to support all DMLC projects, offers the brick *homepage*: version|toolchain --------|-------------- -``0.5``|``GCC/10.3.0`` +-------|------------------------------ +``0.5``|``GCC/10.3.0``, ``GCC/11.3.0`` ### DMTCP @@ -8065,6 +8323,7 @@ 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`` +``0.5.1``|``-CUDA-11.7.0``|``foss/2022a`` ### Doris @@ -8124,7 +8383,7 @@ version |toolchain ``3.1.5``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ``3.2.0``|``GCCcore/11.3.0`` ``3.2.1``|``GCCcore/12.2.0`` -``3.3.0``|``GCCcore/12.3.0`` +``3.3.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### DoubletFinder @@ -8168,8 +8427,8 @@ DP3: streaming processing pipeline for radio interferometric data. *homepage*: version|toolchain --------|-------------- -``6.0``|``foss/2022a`` +-------|------------------------------ +``6.0``|``foss/2022a``, ``foss/2023b`` ### DRAGMAP @@ -8394,7 +8653,7 @@ version |toolchain ## E -[E-ANTIC](#e-antic) - [e3nn](#e3nn) - [ea-utils](#ea-utils) - [earthengine-api](#earthengine-api) - [easel](#easel) - [EasyBuild](#easybuild) - [EasyQC](#easyqc) - [ebGSEA](#ebgsea) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ECL](#ecl) - [eclib](#eclib) - [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) - [epct](#epct) - [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) - [EUKulele](#eukulele) - [Evcxr-REPL](#evcxr-repl) - [EveryBeam](#everybeam) - [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) - [ebGSEA](#ebgsea) - [ecBuild](#ecbuild) - [ecCodes](#eccodes) - [eccodes-python](#eccodes-python) - [ecFlow](#ecflow) - [ECL](#ecl) - [eclib](#eclib) - [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) - [Elmer](#elmer) - [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) - [EnergyPlus](#energyplus) - [EnsEMBLCoreAPI](#ensemblcoreapi) - [entrypoints](#entrypoints) - [epct](#epct) - [EPD](#epd) - [EPIC](#epic) - [epiScanpy](#episcanpy) - [EpiSCORE](#episcore) - [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) - [EUKulele](#eukulele) - [Evcxr-REPL](#evcxr-repl) - [EveryBeam](#everybeam) - [EvidentialGene](#evidentialgene) - [evince](#evince) - [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) - [ExpressBetaDiversity](#expressbetadiversity) - [Extrae](#extrae) - [ExtremeLy](#extremely) - [EZC3D](#ezc3d) ### E-ANTIC @@ -8557,6 +8816,7 @@ version |toolchain ``4.8.0`` |``system`` ``4.8.1`` |``system`` ``4.8.2`` |``system`` +``4.9.0`` |``system`` ### EasyQC @@ -8596,7 +8856,7 @@ ecCodes is a package developed by ECMWF which provides an application programmin *homepage*: version |versionsuffix |toolchain -----------|------------------|-------------------------------- +----------|------------------|------------------------------------------------- ``2.7.3`` | |``intel/2018a`` ``2.7.3`` |``-Python-2.7.14``|``intel/2017b`` ``2.8.2`` | |``intel/2018a`` @@ -8609,7 +8869,7 @@ 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`` +``2.31.0``| |``gompi/2022b``, ``gompi/2023a``, ``gompi/2023b`` ### eccodes-python @@ -8671,9 +8931,9 @@ Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected da *homepage*: version |toolchain ------------------|------------------ +-----------------|-------------------------------------- ``19.7.20230531``|``GCCcore/10.3.0`` -``20.5.20231006``|``GCCcore/12.3.0`` +``20.5.20231006``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### edlib @@ -8682,21 +8942,22 @@ 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``, ``GCC/12.2.0`` +``1.3.9`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` ### EggLib EggLib is a C++/Python library and program package for evolutionary genetics and genomics. -*homepage*: +*homepage*: version |toolchain ----------|--------------- ``2.1.10``|``intel/2016a`` +``3.3.0`` |``GCC/13.2.0`` ### eggnog-mapper @@ -8790,6 +9051,7 @@ version |toolchain ---------|-------------------------------------- ``0.3.2``|``GCCcore/10.2.0`` ``0.4.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``0.7.0``|``GCCcore/12.3.0`` ### elastix @@ -8852,6 +9114,16 @@ version |toolchain ``7.2.42``|``foss/2021a`` ``8.5.2`` |``foss/2022a`` +### Elmer + +Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). + +*homepage*: + +version|toolchain +-------|-------------- +``9.0``|``foss/2022b`` + ### ELPA Eigenvalue SoLvers for Petaflop-Applications. @@ -8876,6 +9148,7 @@ version |versionsuffix |toolchain ``2022.05.001`` |``-CUDA-11.7.0``|``foss/2022a`` ``2022.05.001`` |``-CUDA-12.0.0``|``foss/2022b`` ``2023.05.001`` | |``foss/2023a``, ``intel/2023a`` +``2023.11.001`` | |``foss/2023b``, ``intel/2023b`` ### ELPH @@ -9029,6 +9302,17 @@ Enchant aims to provide a simple but comprehensive abstraction for dealing with version |toolchain ---------|-------------------------------------- ``2.3.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.6.5``|``GCCcore/12.3.0`` + +### EnergyPlus + +EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings. + +*homepage*: + +version |toolchain +----------|-------------- +``23.2.0``|``foss/2022a`` ### EnsEMBLCoreAPI @@ -9090,9 +9374,19 @@ EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and si *homepage*: version |toolchain ----------|-------------- +---------|------------------------------ ``0.3.1``|``foss/2021a`` -``0.4.0``|``foss/2022a`` +``0.4.0``|``foss/2022a``, ``foss/2023a`` + +### EpiSCORE + +Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles + +*homepage*: + +version |versionsuffix|toolchain +------------------|-------------|-------------- +``0.9.5-20220621``|``-R-4.2.1`` |``foss/2022a`` ### eQuilibrator @@ -9131,8 +9425,8 @@ ESM-2 outperforms all tested single-sequence protein language models across a r *homepage*: version |versionsuffix |toolchain ----------|----------------|-------------- -``2.0.0``| |``foss/2021a`` +---------|----------------|------------------------------ +``2.0.0``| |``foss/2021a``, ``foss/2022b`` ``2.0.0``|``-CUDA-11.3.1``|``foss/2021a`` ### ESMF @@ -9153,6 +9447,7 @@ version |versionsuffix |toolchain ``8.1.1`` | |``foss/2021a``, ``intel/2021a`` ``8.2.0`` | |``foss/2021b``, ``intel/2021b`` ``8.3.0`` | |``foss/2022a``, ``intel/2022a`` +``8.4.2`` | |``foss/2022a`` ### ESMPy @@ -9185,6 +9480,7 @@ The eSpeak NG is a compact open source software text-to-speech synthesizer for L version |toolchain --------|--------------- ``1.50``|``gompi/2020a`` +``1.51``|``gfbf/2023a`` ### ESPResSo @@ -9193,8 +9489,8 @@ 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``| |``foss/2021a``, ``foss/2022a``, ``foss/2023a`` ``4.2.1``|``-CUDA-11.3.1``|``foss/2021a`` ``4.2.1``|``-CUDA-11.8.0``|``foss/2022a`` @@ -9221,6 +9517,7 @@ version |versionsuffix |toolchain ``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`` +``3.1.3`` | |``foss/2022b``, ``foss/2023a`` ### ETSF_IO @@ -9271,8 +9568,8 @@ Library that provides the antenna response pattern for several instruments, such *homepage*: version |toolchain ----------|-------------- -``0.5.2``|``foss/2022a`` +---------|------------------------------ +``0.5.2``|``foss/2022a``, ``foss/2023b`` ### EvidentialGene @@ -9285,6 +9582,16 @@ version |versionsuffix |toolchain ``2018.01.01``|``-Perl-5.24.1``|``intel/2017a`` ``2022.01.14``| |``gompi/2021b`` +### evince + +Evince is a document viewer for multiple document formats. The goal of evince is to replace the multiple document viewers that exist on the GNOME Desktop with a single simple application. + +*homepage*: + +version |toolchain +--------|-------------- +``45.0``|``GCC/12.3.0`` + ### evmix evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation @@ -9398,6 +9705,7 @@ version |toolchain ---------|-------------------------------------------------------------------------------------------------- ``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`` +``0.2.1``|``GCCcore/13.2.0`` ### eXpress @@ -9409,6 +9717,16 @@ version |toolchain ---------|--------------- ``1.5.1``|``intel/2017b`` +### ExpressBetaDiversity + +Taxon- and phylogenetic-based beta diversity measures. + +*homepage*: + +version |toolchain +----------|-------------- +``1.0.10``|``GCC/12.3.0`` + ### Extrae Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application. @@ -9423,6 +9741,16 @@ version |toolchain ``3.8.3``|``gompi/2021a`` ``4.0.4``|``gompi/2022a`` +### ExtremeLy + +A python package for Extreme Value Analysis. + +*homepage*: + +version |toolchain +---------|-------------- +``2.3.0``|``foss/2022a`` + ### EZC3D EZC3D is an easy to use reader, modifier and writer for C3D format files. It is written en C++ with proper binders for Python and MATLAB/Octave scripting langages. @@ -9436,7 +9764,7 @@ version |toolchain ## F -[f90cache](#f90cache) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [FACE](#face) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fasta-reader](#fasta-reader) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastml](#fastml) - [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) - [forbear](#forbear) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [fplll](#fplll) - [FPM](#fpm) - [fpocket](#fpocket) - [fpylll](#fpylll) - [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) - [ftfy](#ftfy) - [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) - [f90nml](#f90nml) - [f90wrap](#f90wrap) - [Faber](#faber) - [FabIO](#fabio) - [FACE](#face) - [faceswap](#faceswap) - [FALCON](#falcon) - [FANN](#fann) - [fast5](#fast5) - [FASTA](#fasta) - [fasta-reader](#fasta-reader) - [fastahack](#fastahack) - [fastai](#fastai) - [FastaIndex](#fastaindex) - [FastANI](#fastani) - [Fastaq](#fastaq) - [FastFold](#fastfold) - [fastjet](#fastjet) - [fastjet-contrib](#fastjet-contrib) - [FastME](#fastme) - [fastml](#fastml) - [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) - [FFAVES](#ffaves) - [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) - [forbear](#forbear) - [FORD](#ford) - [foss](#foss) - [fosscuda](#fosscuda) - [FoX](#fox) - [FOX-Toolkit](#fox-toolkit) - [fplll](#fplll) - [FPM](#fpm) - [fpocket](#fpocket) - [fpylll](#fpylll) - [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) - [ftfy](#ftfy) - [FTGL](#ftgl) - [fugue](#fugue) - [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 @@ -9449,6 +9777,16 @@ version |toolchain --------|---------- ``0.96``|``system`` +### f90nml + +A Python module and command line tool for parsing Fortran namelist files + +*homepage*: + +version |toolchain +---------|-------------------------------------- +``1.4.4``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` + ### f90wrap f90wrap is a tool to automatically generate Python extension modules which interface to Fortran code that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user. @@ -9561,8 +9899,8 @@ 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/11.3.0``, ``GCCcore/9.3.0`` +---------|--------------------------------------------------------------------------------------------------------------------- +``1.0.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### fastai @@ -9607,8 +9945,8 @@ Python3 scripts to manipulate FASTA and FASTQ files. *homepage*: version |toolchain -----------|-------------- -``3.17.0``|``GCC/10.3.0`` +----------|------------------------------ +``3.17.0``|``GCC/10.3.0``, ``GCC/12.3.0`` ### FastFold @@ -9629,6 +9967,7 @@ A software package for jet finding in pp and e+e- collisions version |toolchain ---------|--------------- ``3.4.0``|``gompi/2022a`` +``3.4.2``|``gompi/2023a`` ### fastjet-contrib @@ -9639,6 +9978,7 @@ version |toolchain version |toolchain ---------|--------------- ``1.049``|``gompi/2022a`` +``1.053``|``gompi/2023a`` ### FastME @@ -9674,7 +10014,7 @@ version |toolchain ``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`` +``0.23.4``|``GCC/12.2.0``, ``GCC/12.3.0`` ### fastparquet @@ -9816,9 +10156,9 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme *homepage*: version |toolchain -----------|--------------------------------------------------------------------------------------------------------------------------------------- +----------|----------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1.10``|``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.11``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### FastViromeExplorer @@ -9918,6 +10258,7 @@ version |versionsuffix|toolchain ``6.7.6``| |``intel/2020b`` ``6.7.7``| |``intel/2021b`` ``6.7.9``| |``intel/2022a`` +``6.8.0``| |``intel/2022b`` ### fdstools @@ -9969,8 +10310,8 @@ Standalone C library for assembling Illumina short reads in small regions. *homepage*: version |toolchain -------------|----------------------------------------------------------------------------- -``20190320``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +------------|------------------------------------------------------------------------------------------------- +``20190320``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### Ferret @@ -9991,8 +10332,8 @@ University of Edinburgh's Festival Speech Synthesis Systems is a free software m *homepage*: <['http://festvox.org/festival/']> version |toolchain ----------|----------------- -``2.5.0``|``GCCcore/9.3.0`` +---------|------------------------------------- +``2.5.0``|``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### fetchMG @@ -10004,6 +10345,16 @@ version|toolchain -------|------------------------------------ ``1.0``|``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +### FFAVES + +Functional Feature Amplification Via Entropy Sorting (FFAVES). Use FFAVES to amplify the signal of groups of co-regulating genes in an unsupervised, multivariate manner. By amplifying the signal of genes with correlated expression, while filtering out genes that are randomly expressed, we can identify a subset of genes more predictive of different cell types. The output of FFAVES can then be used in our second algorithm, entropy sort feature weighting (ESFW), to create a ranked list of genes that are most likely to pertain to distinct sub-populations of cells in an scRNA-seq dataset. + +*homepage*: + +version |toolchain +-------------|-------------- +``2022.11.1``|``foss/2022a`` + ### FFC The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. @@ -10098,8 +10449,8 @@ A library that intercepts FFTW calls and adds features on top of it. In particu *homepage*: version |toolchain -------------|--------------- -``20170628``|``gompi/2020b`` +------------|-------------------------------- +``20170628``|``gompi/2020b``, ``gompi/2022a`` ### FFTW @@ -10216,7 +10567,7 @@ The file command is 'a file type guesser', that is, a command-line tool that te *homepage*: version |toolchain ---------|------------------------------------ +--------|-------------------------------------- ``5.17``|``GCC/4.8.2`` ``5.25``|``intel/2016a`` ``5.28``|``foss/2016b`` @@ -10227,7 +10578,7 @@ version |toolchain ``5.39``|``GCCcore/10.2.0`` ``5.40``|``GCCcore/10.3.0`` ``5.41``|``GCCcore/11.2.0`` -``5.43``|``GCCcore/11.3.0`` +``5.43``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### filevercmp @@ -10236,9 +10587,9 @@ 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``, ``GCCcore/11.3.0`` +``20191210``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### Filtlong @@ -10300,6 +10651,7 @@ A package for population structure inference from RAD-seq data version |toolchain ------------|--------------- ``20180709``|``intel/2018a`` +``20210514``|``GCC/12.3.0`` ### fineSTRUCTURE @@ -10322,6 +10674,7 @@ version |toolchain ``3.30``|``GCCcore/10.3.0`` ``3.32``|``GCCcore/11.3.0`` ``3.34``|``GCCcore/12.2.0`` +``3.36``|``GCCcore/12.3.0`` ### Fiona @@ -10337,6 +10690,7 @@ version |versionsuffix |toolchain ``1.8.20`` | |``foss/2020b``, ``foss/2021a``, ``intel/2020b`` ``1.8.21`` | |``foss/2021b``, ``foss/2022a`` ``1.9.2`` | |``foss/2022b`` +``1.9.5`` | |``foss/2023a`` ### Firefox @@ -10473,6 +10827,7 @@ version |versionsuffix |toolchain ``2.2.2``| |``GCCcore/11.3.0`` ``2.2.3``| |``GCCcore/12.2.0`` ``2.3.3``| |``GCCcore/12.3.0`` +``3.0.0``| |``GCCcore/13.2.0`` ### flatbuffers @@ -10486,7 +10841,7 @@ version |toolchain ``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`` +``23.5.26``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### flatbuffers-python @@ -10584,6 +10939,7 @@ version |toolchain ``2.7.1``|``GCC/10.3.0`` ``2.8.4``|``foss/2021b`` ``2.9.0``|``gfbf/2022a``, ``gfbf/2022b`` +``3.1.1``|``gfbf/2023b`` ### flit @@ -10666,6 +11022,7 @@ version |versionsuffix |toolchain ``2.9`` | |``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``2.9.1``| |``GCC/11.2.0`` ``2.9.2``| |``GCC/11.3.0`` +``2.9.3``| |``GCC/10.3.0``, ``GCC/12.3.0`` ### FMILibrary @@ -10736,6 +11093,7 @@ version |toolchain ``9.1.0`` |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``10.0.0``|``GCCcore/12.3.0`` ``10.1.0``|``GCCcore/12.3.0`` +``10.2.0``|``GCCcore/13.2.0`` ### FoBiS @@ -10953,8 +11311,8 @@ FragGeneScan is an application for finding (fragmented) genes in short reads. *homepage*: version |toolchain ---------|--------------------------------------------------------------------------------------------- -``1.31``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +--------|----------------------------------------------------------------------------------------------------------------- +``1.31``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``foss/2018b`` ### FragPipe @@ -10998,6 +11356,7 @@ version |versionsuffix |toolchain ``1.3.5``|``-Python-3.8.2``|``GCC/9.3.0`` ``1.3.6``|``-R-4.1.0`` |``foss/2021a`` ``1.3.6``|``-R-4.1.2`` |``foss/2021b`` +``1.3.7``|``-R-4.3.2`` |``gfbf/2023a`` ### FreeFEM @@ -11042,8 +11401,8 @@ 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/12.2.0``, ``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/12.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### FreeSASA @@ -11230,7 +11589,7 @@ 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`` +``20151117``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### FSON @@ -11263,6 +11622,16 @@ version |toolchain ``2.1.3-rc5``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` ``2.4.0`` |``GCCcore/11.3.0`` +### fugue + +Fugue is a unified interface for distributed computing that lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. Fugue is most commonly used for: Parallelizing or scaling existing Python and Pandas code by bringing it to Spark, Dask, or Ray with minimal rewrites. Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. FugueSQL is an enhanced SQL interface that can invoke Python code. + +*homepage*: + +version |toolchain +---------|-------------- +``0.8.7``|``foss/2022a`` + ### Fujitsu Toolchain using Fujitsu compilers and libraries. @@ -11404,7 +11773,7 @@ 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) - [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) - [Gdspy](#gdspy) - [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) - [GFF3-toolkit](#gff3-toolkit) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [giac](#giac) - [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-annex](#git-annex) - [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) - [GMP-ECM](#gmp-ecm) - [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) - [GSD](#gsd) - [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) - [gcsfs](#gcsfs) - [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) - [Gdspy](#gdspy) - [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) - [GenomeComb](#genomecomb) - [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) - [GFF3-toolkit](#gff3-toolkit) - [GffCompare](#gffcompare) - [gffread](#gffread) - [gffutils](#gffutils) - [gflags](#gflags) - [GFOLD](#gfold) - [gh](#gh) - [GHC](#ghc) - [Ghostscript](#ghostscript) - [GI-DocGen](#gi-docgen) - [giac](#giac) - [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-annex](#git-annex) - [git-extras](#git-extras) - [git-lfs](#git-lfs) - [GitPython](#gitpython) - [Givaro](#givaro) - [Giza](#giza) - [GKeyll](#gkeyll) - [GKlib-METIS](#gklib-metis) - [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) - [GMP-ECM](#gmp-ecm) - [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) - [GRASP-suite](#grasp-suite) - [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) - [GSD](#gsd) - [GSEA](#gsea) - [gsettings-desktop-schemas](#gsettings-desktop-schemas) - [GSL](#gsl) - [gSOAP](#gsoap) - [gspell](#gspell) - [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) - [GUIDANCE](#guidance) - [Guile](#guile) - [GULP](#gulp) - [Gurobi](#gurobi) - [GUSHR](#gushr) - [gzip](#gzip) ### G-PhoCS @@ -11636,6 +12005,7 @@ version |versionsuffix |toolchain ``4.2.6.1`` |``-Java-11`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.3.0.0`` |``-Java-11`` |``GCCcore/11.3.0`` ``4.4.0.0`` |``-Java-17`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.5.0.0`` |``-Java-17`` |``GCCcore/12.3.0`` ### Gaussian @@ -11658,6 +12028,7 @@ version |toolchain ---------|---------------------------------------------- ``5.1.0``|``GCC/10.2.0`` ``5.1.1``|``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``5.3.0``|``GCC/12.2.0``, ``GCC/13.2.0`` ### gbasis @@ -11673,7 +12044,7 @@ version |toolchain Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis -*homepage*: +*homepage*: version |toolchain ---------|---------- @@ -11889,6 +12260,16 @@ version |toolchain ---------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``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`` +### gcsfs + +Pythonic file-system interface for Google Cloud Storage. + +*homepage*: + +version |toolchain +-------------------|-------------- +``2023.12.2.post1``|``foss/2023a`` + ### GCTA GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). @@ -11898,7 +12279,7 @@ 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`` +``1.94.1`` |``gfbf/2022a``, ``gfbf/2023a`` ### Gctf @@ -12289,6 +12670,16 @@ version|versionsuffix |toolchain -------|----------------|-------------- ``2.1``|``-Perl-5.24.0``|``foss/2016b`` +### GenomeComb + +Genomecomb is a package designed to analyze, combine, annotate and query genome as well as transcriptome sequencing data. + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|---------- +``0.106.0``|``-x86_64`` |``system`` + ### GenomeMapper GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. This version is used to align against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use this one. @@ -12390,11 +12781,12 @@ version |versionsuffix |toolchain Tool to convert geopandas vector data into rasterized xarray data. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.0.14``|``-Python-3.8.2``|``foss/2020a`` +``0.4.3`` | |``foss/2023a`` ### geopandas @@ -12411,17 +12803,19 @@ version |versionsuffix |toolchain ``0.10.2``| |``foss/2021a`` ``0.11.0``| |``foss/2021b`` ``0.12.2``| |``foss/2022a``, ``foss/2022b`` +``0.14.2``| |``foss/2023a`` ### geopy -geopy is a Python client for several popular geocoding web services. geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, and landmarks across the globe using third-party geocoders and other data sources. +geopy is a Python client for several popular geocoding web services. geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, and landmarks across the globe using third-party geocoders and other data sources. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-----------------|------------------ ``1.11.0``|``-Python-3.6.1``|``intel/2017a`` ``2.1.0`` | |``GCCcore/10.2.0`` +``2.4.1`` | |``GCCcore/12.3.0`` ### georges @@ -12475,13 +12869,13 @@ version |versionsuffix|toolchain ### Gerris -Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow +Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow *homepage*: version |toolchain -------------|-------------- -``20131206``|``foss/2017b`` +------------|------------------------------- +``20131206``|``foss/2017b``, ``gompi/2023a`` ### GETORB @@ -12605,10 +12999,10 @@ The gflags package contains a C++ library that implements commandline flags proc *homepage*: version |toolchain ----------|--------------------------------------------------------------------------------------------------------------------------------------- +---------|----------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1.2``|``foss/2016a`` ``2.2.1``|``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``2.2.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.2.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### GFOLD @@ -12642,6 +13036,7 @@ version |versionsuffix|toolchain ``6.12.3``| |``system`` ``8.6.5`` |``-x86_64`` |``system`` ``9.2.2`` |``-x86_64`` |``system`` +``9.4.6`` |``-x86_64`` |``system`` ### Ghostscript @@ -12666,6 +13061,17 @@ version |versionsuffix |toolchain ``9.56.1`` | |``GCCcore/11.3.0`` ``10.0.0`` | |``GCCcore/12.2.0`` ``10.01.2``| |``GCCcore/12.3.0`` +``10.02.1``| |``GCCcore/13.2.0`` + +### GI-DocGen + +GI-DocGen is a document generator for GObject-based libraries. GObject is the base type system of the GNOME project. GI-Docgen reuses the introspection data generated by GObject-based libraries to generate the API reference of these libraries, as well as other ancillary documentation. + +*homepage*: + +version |toolchain +----------|------------------ +``2023.3``|``GCCcore/12.3.0`` ### giac @@ -12717,6 +13123,7 @@ The GIMIC program calculates magnetically induced currents in molecules. You ne version |versionsuffix |toolchain --------------|------------------|--------------- +``2.2.1`` | |``foss/2022a`` ``2018.04.20``|``-Python-2.7.14``|``intel/2018a`` ### gimkl @@ -12854,8 +13261,8 @@ git-annex allows managing large files with git, without storing the file content *homepage*: version |toolchain ----------------|------------------ -``10.20230802``|``GCCcore/12.2.0`` +---------------|-------------------------------------- +``10.20230802``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### git-extras @@ -12880,6 +13287,8 @@ version |toolchain ``2.11.0``|``system`` ``3.2.0`` |``system`` ``3.4.0`` |``system`` +``3.4.1`` |``system`` +``3.5.1`` |``system`` ### GitPython @@ -12900,6 +13309,7 @@ version |versionsuffix |toolchain ``3.1.27``| |``GCCcore/11.3.0`` ``3.1.31``| |``GCCcore/12.2.0`` ``3.1.40``| |``GCCcore/12.3.0`` +``3.1.42``| |``GCCcore/13.2.0`` ### Givaro @@ -12932,6 +13342,16 @@ version |versionsuffix |toolchain ------------|-----------------|-------------- ``20220803``|``-Python-3.8.2``|``foss/2020a`` +### GKlib-METIS + +A library of various helper routines and frameworks used by many of the lab's software + +*homepage*: + +version |toolchain +---------|------------------ +``5.1.1``|``GCCcore/11.3.0`` + ### gkmSVM Gapped-Kmer Support Vector Machine. @@ -12994,6 +13414,7 @@ version |toolchain ``3.3.3``|``GCCcore/10.2.0`` ``3.3.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.3.8``|``GCCcore/11.3.0`` +``3.4`` |``GCCcore/12.2.0`` ### GLI @@ -13181,12 +13602,12 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: version |toolchain ---------|----------------------------------------------------------------------------------------------------------------- +--------|---------------------------------------------------------------------------------------------------------------------- ``4.58``|``foss/2016a``, ``intel/2016a`` ``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``, ``GCCcore/12.3.0`` +``5.0`` |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### glproto @@ -13294,7 +13715,7 @@ version |versionsuffix |toolchain ``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/2021.4.0``, ``intel-compilers/2022.1.0`` -``2.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0`` +``2.1.5`` | |``GCC/12.2.0``, ``GCC/12.3.0``, ``GCC/13.2.0`` ### gmsh @@ -13426,6 +13847,8 @@ version |toolchain ``1.20.4``|``system`` ``1.21.1``|``system`` ``1.21.2``|``system`` +``1.21.6``|``system`` +``1.22.1``|``system`` ### goalign @@ -13674,10 +14097,11 @@ version |versionsuffix |toolchain ``21.6.0`` |``-ASE-3.22.0`` |``foss/2020b``, ``intel/2020b`` ``22.8.0`` | |``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` ``23.9.1`` | |``foss/2022a``, ``foss/2023a``, ``intel/2022a`` +``24.1.0`` | |``foss/2022a``, ``foss/2023a``, ``intel/2022a``, ``intel/2023a`` ### GPAW-setups -PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. +PAW setups for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, which can be manually selected. Otherwise no changes are made, so no results will change. *homepage*: @@ -13687,6 +14111,7 @@ version |toolchain ``0.9.9672`` |``system`` ``0.9.11271``|``system`` ``0.9.20000``|``system`` +``24.1.0`` |``system`` ### gperf @@ -13715,6 +14140,7 @@ version |toolchain ``2.10`` |``GCCcore/11.3.0`` ``2.12`` |``GCCcore/12.3.0`` ``2.13`` |``GCCcore/13.2.0`` +``2.14`` |``GCCcore/12.2.0`` ### gpustat @@ -13779,11 +14205,12 @@ Complete Gradle install. From mobile apps to microservices, from small startups *homepage*: -version |toolchain ----------|---------- -``4.5.1``|``system`` -``6.1.1``|``system`` -``6.9.1``|``system`` +version |versionsuffix|toolchain +---------|-------------|---------- +``4.5.1``| |``system`` +``6.1.1``| |``system`` +``6.9.1``| |``system`` +``8.6`` |``-Java-17`` |``system`` ### gradunwarp @@ -13807,6 +14234,7 @@ version |versionsuffix |toolchain --------|-----------------|-------------- ``2.26``|``-Python-3.6.3``|``foss/2017b`` ``2.27``|``-Python-3.6.6``|``foss/2018b`` +``2.55``| |``foss/2022a`` ### GraphDB @@ -13929,6 +14357,16 @@ version |toolchain --------|-------------- ``2018``|``foss/2019b`` +### GRASP-suite + +GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction. + +*homepage*: + +version |versionsuffix|toolchain +--------------|-------------|---------- +``2023-05-09``|``-Java-17`` |``system`` + ### GRASS The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization @@ -13948,12 +14386,14 @@ 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``, ``foss/2022b`` +``2.0.2`` | |``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.0.2`` | |``GCCcore/12.3.0`` +``3.0.3`` | |``GCCcore/13.2.0`` ### Grep @@ -14099,6 +14539,8 @@ version |versionsuffix |toolchain ``2023.1``|``-CUDA-11.7.0`` |``foss/2022a`` ``2023.3``| |``foss/2022a``, ``foss/2023a`` ``2023.3``|``-CUDA-11.7.0`` |``foss/2022a`` +``2023.3``|``-CUDA-12.1.1-PLUMED-2.9.0``|``foss/2023a`` +``2024.1``| |``foss/2023b`` ### GromacsWrapper @@ -14131,6 +14573,7 @@ version |toolchain ----------|------------------ ``1.44.0``|``GCCcore/11.2.0`` ``1.57.0``|``GCCcore/12.3.0`` +``1.62.1``|``GCCcore/13.2.0`` ### GSD @@ -14169,7 +14612,7 @@ 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`` @@ -14177,7 +14620,7 @@ 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``, ``GCC/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``, ``GCC/13.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0``, ``intel-compilers/2022.1.0`` ### gSOAP @@ -14190,6 +14633,16 @@ version |toolchain ``2.8.48`` |``GCCcore/6.3.0`` ``2.8.100``|``GCCcore/8.3.0`` +### gspell + +gspell provides a flexible API to add spell-checking to a GTK application. + +*homepage*: + +version |toolchain +----------|------------------ +``1.12.2``|``GCCcore/12.3.0`` + ### gsport GSPORT command-line tool for accessing GenomeScan Customer Portal @@ -14286,7 +14739,7 @@ version |versionsuffix |toolchain ``1.7.0``| |``foss/2020b``, ``foss/2021a``, ``intel/2020b`` ``2.0.0``| |``foss/2021a``, ``intel/2021b`` ``2.1.1``| |``foss/2021b`` -``2.3.2``| |``foss/2022a`` +``2.3.2``| |``foss/2022a``, ``foss/2023a`` ### GTK+ @@ -14330,6 +14783,7 @@ version |toolchain ``3.24.33``|``GCCcore/11.3.0`` ``3.24.35``|``GCCcore/12.2.0`` ``3.24.37``|``GCCcore/12.3.0`` +``3.24.39``|``GCCcore/13.2.0`` ### GTK4 @@ -14395,6 +14849,16 @@ version |versionsuffix|toolchain --------------|-------------|--------------- ``2019.07.05``|``-mpi`` |``iimpi/2019a`` +### GUIDANCE + +GUIDANCE is a software package for aligning biological sequences (DNA or amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating confidence scores for each column, sequence and residue in the alignment. + +*homepage*: + +version |toolchain +--------|-------------- +``2.02``|``GCC/12.3.0`` + ### Guile Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. @@ -14449,6 +14913,7 @@ version |versionsuffix |toolchain ``9.5.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``9.5.2`` | |``GCCcore/11.3.0`` ``10.0.1``| |``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``11.0.0``| |``GCCcore/12.3.0`` ### GUSHR @@ -14477,7 +14942,7 @@ version |toolchain ## H -[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) - [HepMC](#hepmc) - [HepMC3](#hepmc3) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [hic-straw](#hic-straw) - [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) - [HPCC](#hpcc) - [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](#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) - [hdWGCNA](#hdwgcna) - [HEALPix](#healpix) - [Health-GPS](#health-gps) - [heaptrack](#heaptrack) - [hector](#hector) - [HeFFTe](#heffte) - [Hello](#hello) - [help2man](#help2man) - [HepMC](#hepmc) - [HepMC3](#hepmc3) - [HF-Datasets](#hf-datasets) - [HH-suite](#hh-suite) - [HiC-Pro](#hic-pro) - [hic-straw](#hic-straw) - [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) - [HPCC](#hpcc) - [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 @@ -14754,7 +15219,7 @@ version |versionsuffix |toolchain ``4.2.14`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.2.15`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` ``4.2.16`` | |``GCCcore/12.3.0`` -``4.2.16-2``| |``GCCcore/12.3.0`` +``4.2.16-2``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### HDF-EOS @@ -14821,6 +15286,7 @@ version |versionsuffix|toolchain ``1.13.1`` | |``gompi/2022a``, ``iimpi/2022a`` ``1.13.1`` |``-serial`` |``GCC/11.3.0`` ``1.14.0`` | |``gompi/2022b``, ``gompi/2023a``, ``iimpi/2022b``, ``iimpi/2023a`` +``1.14.3`` | |``gompi/2023b``, ``iimpi/2023b`` ### hdf5storage @@ -14843,6 +15309,16 @@ version |versionsuffix |toolchain ``2.14``|``-Java-1.8.0_152-centos6``|``system`` ``2.14``|``-Java-1.8.0_152-centos7``|``system`` +### hdWGCNA + +hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies modules of highly co-expressed genes and provides context for these modules via statistical testing and biological knowledge sources. hdWGCNA uses datasets formatted as Seurat objects. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|-------------- +``0.3.00``|``-R-4.3.2`` |``foss/2023a`` + ### HEALPix Hierarchical Equal Area isoLatitude Pixelation of a sphere. @@ -14890,9 +15366,10 @@ Highly Efficient FFT for Exascale (HeFFTe) library *homepage*: -version|toolchain --------|-------------- -``1.0``|``foss/2020a`` +version |toolchain +---------|-------------- +``1.0`` |``foss/2020a`` +``2.4.0``|``foss/2023b`` ### Hello @@ -14944,6 +15421,17 @@ HepMC is a standard for storing Monte Carlo event data. version |toolchain ---------|-------------- ``3.2.5``|``GCC/11.3.0`` +``3.2.6``|``GCC/12.3.0`` + +### HF-Datasets + +The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools. + +*homepage*: + +version |toolchain +----------|-------------- +``2.18.0``|``gfbf/2023a`` ### HH-suite @@ -15094,9 +15582,9 @@ Hiredis is a minimalistic C client library for the Redis database. It is minima *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.0.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``1.2.0``|``GCCcore/12.3.0`` +``1.2.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### HISAT2 @@ -15184,10 +15672,10 @@ hmmlearn is a set of algorithms for unsupervised learning and inference of Hidde *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------- +---------|------------------|------------------------------ ``0.2.0``|``-Python-2.7.14``|``intel/2017b`` ``0.2.0``|``-Python-3.6.4`` |``intel/2018a`` -``0.3.0``| |``foss/2022b`` +``0.3.0``| |``foss/2022b``, ``gfbf/2023a`` ### HOME @@ -15423,7 +15911,7 @@ version|toolchain ### hunspell -Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. +Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. *homepage*: @@ -15432,6 +15920,7 @@ version |toolchain ``1.6.1``|``intel/2017a`` ``1.7.0``|``GCCcore/8.2.0`` ``1.7.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.7.2``|``GCCcore/12.3.0`` ### hwloc @@ -15486,9 +15975,9 @@ Hydra is an open-source Python framework that simplifies the development of rese *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``1.1.1``|``GCCcore/10.3.0`` -``1.3.2``|``GCCcore/11.3.0`` +``1.3.2``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### Hyperopt @@ -15593,7 +16082,7 @@ version |toolchain ## 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) - [iced](#iced) - [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) - [IML](#iml) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [imutils](#imutils) - [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) - [iperf](#iperf) - [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](#i-cistarget) - [i-PI](#i-pi) - [I-TASSER](#i-tasser) - [i7z](#i7z) - [ICA-AROMA](#ica-aroma) - [icc](#icc) - [iccifort](#iccifort) - [iccifortcuda](#iccifortcuda) - [iced](#iced) - [ichorCNA](#ichorcna) - [icmake](#icmake) - [iCount](#icount) - [ICU](#icu) - [IDBA-UD](#idba-ud) - [idemux](#idemux) - [IDG](#idg) - [ieeg-cli](#ieeg-cli) - [ifort](#ifort) - [IgBLAST](#igblast) - [IGMPlot](#igmplot) - [igraph](#igraph) - [IGV](#igv) - [igv-reports](#igv-reports) - [igvShiny](#igvshiny) - [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) - [IML](#iml) - [Imlib2](#imlib2) - [immunedeconv](#immunedeconv) - [IMOD](#imod) - [impi](#impi) - [IMPUTE2](#impute2) - [imutils](#imutils) - [InChI](#inchi) - [indicators](#indicators) - [Inelastica](#inelastica) - [inferCNV](#infercnv) - [infercnvpy](#infercnvpy) - [Inferelator](#inferelator) - [Infernal](#infernal) - [inflection](#inflection) - [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) - [InterOp](#interop) - [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) - [IonQuant](#ionquant) - [IOR](#ior) - [IOzone](#iozone) - [iperf](#iperf) - [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 @@ -15817,6 +16306,16 @@ version |toolchain ---------|------------------ ``0.1.6``|``GCCcore/10.2.0`` +### IDG + +Image Domain Gridding (IDG) is a fast method for convolutional resampling (gridding/degridding) of radio astronomical data (visibilities). Direction dependent effects (DDEs) or A-tems can be applied in the gridding process. The algorithm is described in "Image Domain Gridding: a fast method for convolutional resampling of visibilities", Van der Tol (2018). The implementation is described in "Radio-astronomical imaging on graphics processors", Veenboer (2020). Please cite these papers in publications using IDG. + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.0``|``foss/2023b`` + ### ieeg-cli IEEG.ORG is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. @@ -15891,17 +16390,18 @@ igraph is a collection of network analysis tools with the emphasis on efficiency *homepage*: -version |toolchain -----------|------------------------------------------------ -``0.7.1`` |``foss/2018b``, ``intel/2016b``, ``intel/2017b`` -``0.8.0`` |``foss/2019b`` -``0.8.2`` |``foss/2020a`` -``0.8.5`` |``foss/2020b`` -``0.9.1`` |``foss/2020b``, ``fosscuda/2020b`` -``0.9.4`` |``foss/2021a`` -``0.9.5`` |``foss/2021b`` -``0.10.3``|``foss/2022a`` -``0.10.6``|``foss/2022b`` +version |toolchain +-----------|------------------------------------------------ +``0.7.1`` |``foss/2018b``, ``intel/2016b``, ``intel/2017b`` +``0.8.0`` |``foss/2019b`` +``0.8.2`` |``foss/2020a`` +``0.8.5`` |``foss/2020b`` +``0.9.1`` |``foss/2020b``, ``fosscuda/2020b`` +``0.9.4`` |``foss/2021a`` +``0.9.5`` |``foss/2021b`` +``0.10.3`` |``foss/2022a`` +``0.10.6`` |``foss/2022b`` +``0.10.10``|``foss/2023a`` ### IGV @@ -15929,6 +16429,16 @@ version |versionsuffix |toolchain ---------|-----------------|------------- ``0.9.8``|``-Python-3.7.4``|``GCC/8.3.0`` +### igvShiny + +An htmlwidget version of igv, for RStudio and Shiny apps + +*homepage*: + +version |versionsuffix|toolchain +------------|-------------|-------------- +``20240112``|``-R-4.2.1`` |``foss/2022a`` + ### IGVTools This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. @@ -15964,6 +16474,7 @@ version |toolchain ``2022a``|``system`` ``2022b``|``system`` ``2023a``|``system`` +``2023b``|``system`` ### iimpi @@ -16399,9 +16910,10 @@ A series of convenience functions to make basic image processing operations such *homepage*: -version |toolchain ----------|------------------ -``0.5.4``|``fosscuda/2020b`` +version |versionsuffix |toolchain +---------|----------------|------------------ +``0.5.4``| |``fosscuda/2020b`` +``0.5.4``|``-CUDA-11.7.0``|``foss/2022a`` ### InChI @@ -16459,6 +16971,7 @@ version |toolchain ---------|-------------- ``0.4.0``|``foss/2021b`` ``0.4.2``|``foss/2022a`` +``0.4.3``|``foss/2023a`` ### Inferelator @@ -16481,6 +16994,16 @@ version |toolchain ``1.1.2``|``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` ``1.1.4``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2022b`` +### inflection + +inflection is a package that finds the inflection point of a planar curve which is given as a data frame of discrete (xi,yi) points + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``1.3.5``|``-R-4.3.2`` |``foss/2023a`` + ### Infomap Multi-level network clustering based on the Map equation. @@ -16690,7 +17213,7 @@ version |toolchain ### IntelDAAL -Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of Intel® architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making. +Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of Intel® architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making. *homepage*: @@ -16709,6 +17232,16 @@ version |versionsuffix |toolchain ``2.7.15``|``-2019.2.066``|``system`` ``3.6.8`` |``-2019.2.066``|``system`` +### InterOp + +The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k and NovaSeqX. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded. + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.4``|``foss/2021a`` + ### InterProScan InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data]. @@ -16741,8 +17274,8 @@ 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/11.3.0``, ``GCCcore/9.3.0`` +-------|--------------------------------------------------------------------------------------------------------------------- +``0.1``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### intervaltree-python @@ -16751,9 +17284,9 @@ 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``, ``GCCcore/11.3.0`` +``3.1.0``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### intltool @@ -16850,6 +17383,16 @@ version |toolchain ``2021a`` |``system`` ``2021b`` |``system`` +### IonQuant + +IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe. + +*homepage*: + +version |versionsuffix|toolchain +-----------|-------------|---------- +``1.10.12``|``-Java-11`` |``system`` + ### IOR The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. @@ -16882,6 +17425,7 @@ version |toolchain ---------|------------------ ``2.1.9``|``GCCcore/10.2.0`` ``3.15`` |``system`` +``3.16`` |``system`` ### IPM @@ -16934,8 +17478,8 @@ Leveraging the Jupyter interactive widgets framework, ipympl enables the interac *homepage*: version |toolchain ----------|-------------- -``0.9.3``|``foss/2022a`` +---------|------------------------------ +``0.9.3``|``foss/2022a``, ``foss/2023a`` ### ipyparallel @@ -17009,6 +17553,7 @@ version |versionsuffix|toolchain ``2.2.1`` | |``gompi/2021b`` ``2.2.2.3``| |``gompi/2022a`` ``2.2.2.6``| |``gompi/2022a``, ``gompi/2022b`` +``2.2.2.7``| |``gompi/2023a`` ### Iris @@ -17067,6 +17612,7 @@ Intelligent Storage Acceleration Library version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------- ``2.30.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.31.0``|``GCCcore/13.2.0`` ### ISL @@ -17210,11 +17756,11 @@ 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`` +``2.0.7``| |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### ITSx @@ -17354,6 +17900,7 @@ version |versionsuffix |toolchain ``8`` | |``system`` ``8.345`` | |``system`` ``8.362`` | |``system`` +``8.402`` | |``system`` ``11`` | |``system`` ``11.0.2`` | |``system`` ``11.0.6`` |``-ppc64le`` |``system`` @@ -17372,6 +17919,10 @@ version |versionsuffix |toolchain ``17.0.2`` | |``system`` ``17.0.4`` | |``system`` ``17.0.6`` | |``system`` +``19`` | |``system`` +``19.0.2`` | |``system`` +``21`` | |``system`` +``21.0.2`` | |``system`` ### JavaFX @@ -17571,6 +18122,7 @@ version |toolchain --------|---------------------------------------------------------- ``0.15``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``0.16``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``0.17``|``GCCcore/13.2.0`` ### json-fortran @@ -17579,8 +18131,8 @@ JSON-Fortran: A Modern Fortran JSON API *homepage*: version |toolchain ----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``8.3.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2022.0.1``, ``intel-compilers/2022.2.1`` +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``8.3.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2022.0.1``, ``intel-compilers/2022.1.0``, ``intel-compilers/2022.2.1`` ### JSON-GLib @@ -17636,32 +18188,34 @@ Julia is a high-level, high-performance dynamic programming language for numeric *homepage*: -version |versionsuffix |toolchain ----------|-----------------|---------- -``1.1.1``|``-linux-x86_64``|``system`` -``1.2.0``|``-linux-x86_64``|``system`` -``1.3.1``|``-linux-x86_64``|``system`` -``1.4.0``|``-linux-x86_64``|``system`` -``1.4.1``|``-linux-x86_64``|``system`` -``1.4.2``|``-linux-x86_64``|``system`` -``1.5.1``|``-linux-x86_64``|``system`` -``1.5.3``|``-linux-x86_64``|``system`` -``1.6.1``|``-linux-x86_64``|``system`` -``1.6.2``|``-linux-x86_64``|``system`` -``1.6.4``|``-linux-x86_64``|``system`` -``1.6.5``|``-linux-x86_64``|``system`` -``1.6.6``|``-linux-x86_64``|``system`` -``1.6.7``|``-linux-x86_64``|``system`` -``1.7.0``|``-linux-x86_64``|``system`` -``1.7.1``|``-linux-x86_64``|``system`` -``1.7.2``|``-linux-x86_64``|``system`` -``1.7.3``|``-linux-x86_64``|``system`` -``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`` -``1.9.2``|``-linux-x86_64``|``system`` -``1.9.3``|``-linux-x86_64``|``system`` +version |versionsuffix |toolchain +----------|------------------|---------- +``1.1.1`` |``-linux-x86_64`` |``system`` +``1.2.0`` |``-linux-x86_64`` |``system`` +``1.3.1`` |``-linux-x86_64`` |``system`` +``1.4.0`` |``-linux-x86_64`` |``system`` +``1.4.1`` |``-linux-x86_64`` |``system`` +``1.4.2`` |``-linux-x86_64`` |``system`` +``1.5.1`` |``-linux-x86_64`` |``system`` +``1.5.3`` |``-linux-x86_64`` |``system`` +``1.6.0`` |``-linux-aarch64``|``system`` +``1.6.1`` |``-linux-x86_64`` |``system`` +``1.6.2`` |``-linux-x86_64`` |``system`` +``1.6.4`` |``-linux-x86_64`` |``system`` +``1.6.5`` |``-linux-x86_64`` |``system`` +``1.6.6`` |``-linux-x86_64`` |``system`` +``1.6.7`` |``-linux-x86_64`` |``system`` +``1.7.0`` |``-linux-x86_64`` |``system`` +``1.7.1`` |``-linux-x86_64`` |``system`` +``1.7.2`` |``-linux-x86_64`` |``system`` +``1.7.3`` |``-linux-x86_64`` |``system`` +``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`` +``1.9.2`` |``-linux-x86_64`` |``system`` +``1.9.3`` |``-linux-x86_64`` |``system`` +``1.10.0``|``-linux-x86_64`` |``system`` ### JUnit @@ -17868,6 +18422,7 @@ The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. version |toolchain --------|-------------------------------- ``3.14``|``gompi/2022a``, ``gompi/2022b`` +``3.16``|``gompi/2023a`` ### Kaiju @@ -17888,9 +18443,9 @@ Fast static image export for web-based visualization libraries with zero depende *homepage*: version |toolchain ----------|---------------------------------------------------------- +---------|------------------------------------------------------------------------------ ``0.1.0``|``GCCcore/10.2.0`` -``0.2.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.2.1``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/13.2.0`` ### Kalign @@ -18043,11 +18598,11 @@ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collec *homepage*: version |toolchain ----------|---------------------------------------------------------------- +---------|-------------------------------------------------------------------------------------------- ``2.1.2``|``foss/2019a``, ``intel/2019a`` ``2.1.3``|``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.2.1``|``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -``2.3.0``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0`` +``2.3.0``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/12.3.0``, ``intel-compilers/2023.1.0`` ### kineto @@ -18225,11 +18780,11 @@ Krona Tools is a set of scripts to create Krona charts from several Bioinformat *homepage*: version |toolchain ----------|-------------------------------------- +---------|------------------------------------------------------------------------------ ``2.7`` |``GCCcore/7.3.0`` ``2.7.1``|``GCCcore/8.2.0`` ``2.8`` |``GCC/10.3.0``, ``GCCcore/10.2.0`` -``2.8.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.8.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### kwant @@ -18275,7 +18830,7 @@ 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++) - [lcalc](#lcalc) - [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) - [libaed2](#libaed2) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libbaseencode](#libbaseencode) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcotp](#libcotp) - [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) - [LoopTools](#looptools) - [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) - [Lab-Streaming-Layer](#lab-streaming-layer) - [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++) - [lcalc](#lcalc) - [LCov](#lcov) - [LDC](#ldc) - [lDDT](#lddt) - [LeadIT](#leadit) - [leafcutter](#leafcutter) - [leidenalg](#leidenalg) - [LEMON](#lemon) - [Leptonica](#leptonica) - [LERC](#lerc) - [less](#less) - [LevelDB](#leveldb) - [Levenshtein](#levenshtein) - [lftp](#lftp) - [LHAPDF](#lhapdf) - [LIANA](#liana) - [libaec](#libaec) - [libaed2](#libaed2) - [libaio](#libaio) - [libarchive](#libarchive) - [libav](#libav) - [libavif](#libavif) - [libbaseencode](#libbaseencode) - [libBigWig](#libbigwig) - [libbitmask](#libbitmask) - [libcdms](#libcdms) - [libcerf](#libcerf) - [libcint](#libcint) - [libcircle](#libcircle) - [libcmaes](#libcmaes) - [libconfig](#libconfig) - [libcotp](#libcotp) - [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) - [libfyaml](#libfyaml) - [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) - [libgxps](#libgxps) - [libhandy](#libhandy) - [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) - [libspectre](#libspectre) - [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) - [lit](#lit) - [LittleCMS](#littlecms) - [LLDB](#lldb) - [LLVM](#llvm) - [LMDB](#lmdb) - [LMfit](#lmfit) - [Lmod](#lmod) - [lmoments3](#lmoments3) - [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) - [LoopTools](#looptools) - [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 @@ -18289,6 +18844,16 @@ version |versionsuffix |toolchain ``20141124``|``-Perl-5.24.0``|``intel/2016b`` ``20190530``| |``GCC/11.3.0`` +### Lab-Streaming-Layer + +The lab streaming layer (LSL) is a system for the unified collection of measurement time series in research experiments that handles both the networking, time-synchronization, (near-) real-time access as well as optionally the centralized collection, viewing and disk recording of the data. + +*homepage*: + +version |toolchain +----------|------------------ +``1.16.2``|``GCCcore/12.3.0`` + ### Lace Building SuperTranscripts: A linear representation of transcriptome data @@ -18336,15 +18901,17 @@ 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``, ``foss/2022a`` -``23Jun2022``|``-kokkos-CUDA-11.3.1`` |``foss/2021a`` -``23Jun2022``|``-kokkos-CUDA-11.4.1`` |``foss/2021b`` +version |versionsuffix |toolchain +--------------------|-----------------------------|---------------------------------------------- +``2Aug2023_update2``|``-kokkos`` |``foss/2023a`` +``2Aug2023_update2``|``-kokkos-CUDA-12.1.1`` |``foss/2023a`` +``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``, ``foss/2022a`` +``23Jun2022`` |``-kokkos-CUDA-11.3.1`` |``foss/2021a`` +``23Jun2022`` |``-kokkos-CUDA-11.4.1`` |``foss/2021b`` ### lancet @@ -18395,12 +18962,13 @@ version |toolchain LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. -*homepage*: +*homepage*: version |toolchain -----------|--------------------------------- ``1.02.00``|``GCCcore/8.2.0``, ``foss/2016a`` ``1.04.03``|``foss/2019b`` +``1.04.22``|``GCC/12.3.0`` ### lavaan @@ -18468,6 +19036,7 @@ version |versionsuffix|toolchain ``1.25.1``| |``GCCcore/10.2.0`` ``1.26.0``| |``GCCcore/10.3.0`` ``1.30.0``| |``GCCcore/11.3.0`` +``1.36.0``| |``GCCcore/12.3.0`` ### lDDT @@ -18513,6 +19082,7 @@ version |versionsuffix |toolchain ``0.8.8`` | |``foss/2021b`` ``0.9.1`` | |``foss/2022a`` ``0.10.1``| |``foss/2022b`` +``0.10.2``| |``foss/2023a`` ### LEMON @@ -18544,9 +19114,9 @@ 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``, ``GCCcore/12.3.0`` +``4.0.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### less @@ -18570,6 +19140,16 @@ version |toolchain ``1.20``|``GCCcore/7.3.0`` ``1.22``|``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +### Levenshtein + +Python extension for computing string edit distances and similarities. + +*homepage*: + +version |toolchain +----------|------------------ +``0.24.0``|``GCCcore/12.2.0`` + ### lftp LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. @@ -18610,8 +19190,8 @@ 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``, ``GCCcore/12.3.0`` +---------|------------------------------------------------------------------------------------------------------------------------------------------ +``1.0.6``|``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/13.2.0`` ### libaed2 @@ -18743,6 +19323,7 @@ version |toolchain ``4.4.0``|``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` ``5.1.6``|``foss/2022a`` ``5.4.0``|``gfbf/2023a`` +``5.5.0``|``gfbf/2022b`` ### libcircle @@ -19088,6 +19669,16 @@ version |toolchain ---------|------------------------------------------------- ``1.1.3``|``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +### libfyaml + +Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the full YAML testsuite. + +*homepage*: + +version|toolchain +-------|------------------ +``0.9``|``GCCcore/12.2.0`` + ### libgcrypt Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG @@ -19167,6 +19758,7 @@ version |toolchain ``1.4.3``|``GCCcore/11.3.0`` ``1.5.0``|``GCCcore/12.2.0`` ``1.7.1``|``GCCcore/12.3.0`` +``1.7.2``|``GCCcore/13.2.0`` ### libglade @@ -19260,6 +19852,26 @@ version|toolchain -------|------------------------------------------------------------------ ``0.7``|``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` +### libgxps + +libgxps is a GObject based library for handling and rendering XPS documents. + +*homepage*: + +version |toolchain +---------|------------------ +``0.3.2``|``GCCcore/12.3.0`` + +### libhandy + +Building blocks for modern adaptive GNOME apps + +*homepage*: + +version |toolchain +---------|------------------ +``1.8.2``|``GCCcore/12.3.0`` + ### libharu libHaru is a free, cross platform, open source library for generating PDF files. @@ -19347,7 +19959,7 @@ Libidn2 implements the revised algorithm for internationalized domain names call version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------------- ``2.3.0``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.3.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.3.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### Libint @@ -19421,8 +20033,8 @@ Implements the Leiden algorithm in C++ *homepage*: version |toolchain -----------|-------------- -``0.11.1``|``foss/2022b`` +----------|------------------------------ +``0.11.1``|``foss/2022b``, ``foss/2023a`` ### LibLZF @@ -19484,8 +20096,8 @@ libMemcached is an open source C/C++ client library and tools for the memcached *homepage*: version |toolchain -----------|------------------------------------ -``1.0.18``|``GCCcore/6.4.0``, ``GCCcore/9.3.0`` +----------|-------------------------------------------------------- +``1.0.18``|``GCCcore/13.2.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` ### libmicrohttpd @@ -19738,9 +20350,10 @@ Python module for audio and music processing *homepage*: -version |versionsuffix |toolchain ----------|-----------------|---------------------------------- -``0.7.2``|``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` +version |versionsuffix |toolchain +----------|-----------------|---------------------------------- +``0.7.2`` |``-Python-3.7.4``|``foss/2019b``, ``fosscuda/2019b`` +``0.10.1``| |``foss/2023a`` ### librsb @@ -19769,6 +20382,7 @@ version |toolchain ``2.51.2`` |``GCCcore/10.3.0`` ``2.52.8`` |``GCCcore/11.2.0`` ``2.55.1`` |``GCCcore/11.3.0`` +``2.58.0`` |``GCCcore/13.2.0`` ### librttopo @@ -19799,6 +20413,7 @@ libSBML (Systems Biology Markup Language library) is a free, open-source program version |toolchain ----------|------------------------------ ``5.19.0``|``GCC/10.2.0``, ``GCC/10.3.0`` +``5.19.7``|``GCC/11.3.0`` ### libsigc++ @@ -19826,6 +20441,7 @@ version |toolchain ``2.11``|``GCCcore/6.4.0`` ``2.12``|``GCCcore/9.3.0`` ``2.13``|``GCCcore/10.2.0`` +``2.14``|``GCCcore/12.2.0`` ### libSM @@ -19893,7 +20509,7 @@ C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API version |toolchain ---------|-------------------------------------------------------------------------------------- ``1.8.5``|``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2018a`` -``1.9.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``1.9.3``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/13.2.0`` ### libspatialite @@ -19908,6 +20524,16 @@ version |versionsuffix |toolchain ``4.3.0a``|``-Python-3.7.4``|``GCC/8.3.0`` ``5.0.1`` | |``GCC/11.2.0`` +### libspectre + +libspectre is a small library for rendering Postscript documents. It provides a convenient easy to use API for handling and rendering Postscript documents. + +*homepage*: + +version |toolchain +----------|------------------ +``0.2.12``|``GCCcore/12.3.0`` + ### libssh Multiplatform C library implementing the SSHv2 protocol on client and server side @@ -20022,6 +20648,7 @@ version |toolchain ``1.3.1``|``GCCcore/10.2.0`` ``1.3.2``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``1.3.3``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.3.4``|``GCCcore/13.2.0`` ### libtool @@ -20199,7 +20826,7 @@ version |toolchain Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. -*homepage*: +*homepage*: version |toolchain ---------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- @@ -20217,7 +20844,7 @@ version |toolchain ``5.1.6``|``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ``5.2.3``|``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ``6.1.0``|``GCC/12.2.0``, ``intel-compilers/2022.2.1`` -``6.2.2``|``GCC/12.3.0``, ``intel-compilers/2023.1.0`` +``6.2.2``|``GCC/12.3.0``, ``GCC/13.2.0``, ``intel-compilers/2023.1.0``, ``intel-compilers/2023.2.1`` ### libxcb @@ -20382,6 +21009,7 @@ version |versionsuffix |toolchain ``2.9.8`` |``-Python-2.7.15``|``foss/2018b`` ``2.9.8`` |``-Python-3.7.2`` |``GCCcore/8.2.0`` ``2.9.13``| |``GCCcore/11.3.0`` +``2.11.4``| |``GCCcore/12.3.0`` ### libXmu @@ -20585,6 +21213,7 @@ version |toolchain ``5.2.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` ``5.2.1``|``GCC/11.2.0`` ``5.2.2``|``GCC/11.3.0`` +``5.3.0``|``GCC/12.3.0`` ### limix @@ -20641,6 +21270,16 @@ version|versionsuffix |toolchain ``8.1``| |``gompi/2022a`` ``8.1``|``-CUDA-11.7.0``|``gompi/2022a`` +### lit + +lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures. + +*homepage*: + +version |toolchain +----------|------------------ +``18.1.2``|``GCCcore/12.3.0`` + ### LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. @@ -20674,31 +21313,32 @@ The LLVM Core libraries provide a modern source- and target-independent optimiz *homepage*: -version |toolchain -----------|------------------------------------------------------------------------ -``3.7.1`` |``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.8.0`` |``foss/2016a``, ``intel/2016a`` -``3.8.1`` |``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` -``3.9.0`` |``foss/2016b``, ``intel/2016b`` -``3.9.1`` |``foss/2017a`` -``4.0.0`` |``foss/2017a``, ``intel/2017a`` -``4.0.1`` |``intel/2017a``, ``intel/2017b`` -``5.0.0`` |``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.0.1`` |``GCCcore/6.4.0`` -``6.0.0`` |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``7.0.0`` |``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``7.0.1`` |``GCCcore/8.2.0`` -``8.0.1`` |``GCCcore/8.3.0`` -``9.0.0`` |``GCCcore/8.3.0`` -``9.0.1`` |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``10.0.0``|``GCCcore/8.3.0`` -``10.0.1``|``GCCcore/10.2.0`` -``11.0.0``|``GCCcore/10.2.0`` -``11.1.0``|``GCCcore/10.3.0`` -``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``, ``GCCcore/13.2.0`` +version |versionsuffix|toolchain +----------|-------------|------------------------------------------------------------------------ +``3.7.1`` | |``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``3.8.0`` | |``foss/2016a``, ``intel/2016a`` +``3.8.1`` | |``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` +``3.9.0`` | |``foss/2016b``, ``intel/2016b`` +``3.9.1`` | |``foss/2017a`` +``4.0.0`` | |``foss/2017a``, ``intel/2017a`` +``4.0.1`` | |``intel/2017a``, ``intel/2017b`` +``5.0.0`` | |``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.0.1`` | |``GCCcore/6.4.0`` +``6.0.0`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``7.0.0`` | |``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``7.0.1`` | |``GCCcore/8.2.0`` +``8.0.1`` | |``GCCcore/8.3.0`` +``9.0.0`` | |``GCCcore/8.3.0`` +``9.0.1`` | |``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``10.0.0``| |``GCCcore/8.3.0`` +``10.0.1``| |``GCCcore/10.2.0`` +``11.0.0``| |``GCCcore/10.2.0`` +``11.1.0``| |``GCCcore/10.3.0`` +``12.0.1``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``14.0.3``| |``GCCcore/11.3.0`` +``14.0.6``|``-llvmlite``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``15.0.5``| |``GCCcore/12.2.0`` +``16.0.6``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### LMDB @@ -20756,6 +21396,16 @@ version |toolchain ``6.4.2``|``system`` ``7.3`` |``system`` +### lmoments3 + +Estimate linear moments for statistical distribution functions. + +*homepage*: + +version |toolchain +---------|-------------- +``1.0.6``|``foss/2022a`` + ### LncLOOM LncLOOM is a graph-based framework that uses integer programming to identify combinations of short motifs that are deeply conserved in rapidly evolving sequences. @@ -20869,9 +21519,9 @@ Python implementation of the Loom file format, an efficient file format for larg *homepage*: version |toolchain ----------|--------------------------------------------------------------- +---------|------------------------------------------------------------------------------- ``3.0.6``|``intel/2020b`` -``3.0.7``|``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` +``3.0.7``|``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``intel/2021b`` ### loomR @@ -20883,6 +21533,7 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``0.2.0-20180425``|``-R-4.2.1`` |``foss/2022a`` ``0.2.0-20180425``|``-R-4.2.2`` |``foss/2022b`` +``0.2.0-20180425``|``-R-4.3.2`` |``foss/2023a`` ### LoopTools @@ -20972,7 +21623,7 @@ 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`` +``2.4.1``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### LSMS @@ -21021,7 +21672,7 @@ 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`` +``5.4.6`` |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### LuaJIT @@ -21162,7 +21813,7 @@ version |toolchain ## M -[M1QN3](#m1qn3) - [M3GNet](#m3gnet) - [M4](#m4) - [m4ri](#m4ri) - [m4rie](#m4rie) - [MACH](#mach) - [MACS2](#macs2) - [MACS3](#macs3) - [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) - [Mashtree](#mashtree) - [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) - [MDI](#mdi) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [mdust](#mdust) - [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) - [MitoHiFi](#mitohifi) - [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) - [mpath](#mpath) - [MPB](#mpb) - [MPC](#mpc) - [MPFI](#mpfi) - [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) - [multicharge](#multicharge) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MUSCLE3](#muscle3) - [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) - [m4ri](#m4ri) - [m4rie](#m4rie) - [MACH](#mach) - [MACS2](#macs2) - [MACS3](#macs3) - [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) - [Markdown](#markdown) - [MARS](#mars) - [Mash](#mash) - [Mashtree](#mashtree) - [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) - [MDI](#mdi) - [MDSplus](#mdsplus) - [MDSplus-Java](#mdsplus-java) - [MDSplus-Python](#mdsplus-python) - [mdtest](#mdtest) - [MDTraj](#mdtraj) - [mdust](#mdust) - [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) - [MetaDecoder](#metadecoder) - [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) - [mfqe](#mfqe) - [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) - [Miniforge3](#miniforge3) - [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) - [MitoHiFi](#mitohifi) - [MitoZ](#mitoz) - [MiXCR](#mixcr) - [MixMHC2pred](#mixmhc2pred) - [mkl-dnn](#mkl-dnn) - [mkl-service](#mkl-service) - [mkl_fft](#mkl_fft) - [MLC](#mlc) - [MLflow](#mlflow) - [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) - [MODFLOW](#modflow) - [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) - [morphosamplers](#morphosamplers) - [mosdepth](#mosdepth) - [Mothur](#mothur) - [motif](#motif) - [MotionCor2](#motioncor2) - [MotionCor3](#motioncor3) - [motionSegmentation](#motionsegmentation) - [MoviePy](#moviepy) - [mpath](#mpath) - [MPB](#mpb) - [MPC](#mpc) - [MPFI](#mpfi) - [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) - [MSFragger](#msfragger) - [msgpack-c](#msgpack-c) - [MSM](#msm) - [MSPC](#mspc) - [msprime](#msprime) - [mstore](#mstore) - [MTL4](#mtl4) - [MuJoCo](#mujoco) - [mujoco-py](#mujoco-py) - [multicharge](#multicharge) - [multichoose](#multichoose) - [MultilevelEstimators](#multilevelestimators) - [MultiNest](#multinest) - [multiprocess](#multiprocess) - [MultiQC](#multiqc) - [Multiwfn](#multiwfn) - [muMerge](#mumerge) - [MUMmer](#mummer) - [MUMPS](#mumps) - [muParser](#muparser) - [muparserx](#muparserx) - [MuPeXI](#mupexi) - [MUSCLE](#muscle) - [MUSCLE3](#muscle3) - [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 @@ -21251,7 +21902,9 @@ Model Based Analysis for ChIP-Seq data version |toolchain -----------|-------------- +``3.0.0`` |``foss/2022b`` ``3.0.0b2``|``foss/2022b`` +``3.0.1`` |``gfbf/2023a`` ### MACSE @@ -21273,6 +21926,7 @@ version |toolchain ---------|------------------------------------------------------------------ ``1.2.2``|``gompi/2019a``, ``iimpi/2019a`` ``1.3.0``|``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` +``1.3.1``|``gompi/2023a`` ### MAFFT @@ -21346,6 +22000,7 @@ version |versionsuffix |toolchain ``2.6.2``|``-CUDA-11.7.0``|``foss/2022a`` ``2.7.1``|``-CUDA-12.0.0``|``foss/2022b`` ``2.7.2``|``-CUDA-12.1.1``|``foss/2023a`` +``2.7.2``|``-CUDA-12.4.0``|``foss/2023b`` ### MAGMA-gene-analysis @@ -21478,10 +22133,11 @@ Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, *homepage*: -version |toolchain -------------|---------- -``4.14.0-0``|``system`` -``23.1.0-4``|``system`` +version |toolchain +-------------|---------- +``4.14.0-0`` |``system`` +``23.1.0-4`` |``system`` +``23.11.0-0``|``system`` ### mandrake @@ -21599,6 +22255,16 @@ version |toolchain ``3.1.11``|``GCCcore/10.2.0`` ``3.2.2`` |``GCCcore/10.3.0`` +### Markdown + +This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few known issues. Additional features are supported by the Available Extensions. + +*homepage*: + +version|toolchain +-------|-------------------------------------- +``3.6``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` + ### MARS improving Multiple circular sequence Alignment using Refined Sequences @@ -21686,14 +22352,16 @@ 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``, ``GCCcore/12.2.0`` +``1.5.22``|``GCCcore/11.2.0`` +``1.5.23``|``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0`` +``1.5.26``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### MATLAB @@ -21795,7 +22463,8 @@ 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`` +``3.7.2``| |``gfbf/2023a``, ``iimkl/2023a`` +``3.8.2``| |``gfbf/2023b`` ### matplotlib-inline @@ -21824,10 +22493,13 @@ This project is meant as a zero configuration replacement for setuptools-rust an *homepage*: -version |toolchain ----------|-------------------------------------- -``1.1.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` -``1.3.1``|``GCCcore/13.2.0`` +version |versionsuffix |toolchain +---------|----------------|-------------------------------------- +``1.1.0``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.3.1``| |``GCCcore/13.2.0`` +``1.3.2``|``-Rust-1.65.0``|``GCCcore/11.3.0`` +``1.4.0``|``-Rust-1.75.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.5.0``|``-Rust-1.76.0``|``GCCcore/13.2.0`` ### Maude @@ -21942,8 +22614,8 @@ MBROLA is a speech synthesizer based on the concatenation of diphones. It takes *homepage*: <['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices']> version|versionsuffix |toolchain --------|--------------------|----------------- -``3.3``|``-voices-20200330``|``GCCcore/9.3.0`` +-------|--------------------|------------------------------------- +``3.3``|``-voices-20200330``|``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### mbuffer @@ -22009,6 +22681,7 @@ version |versionsuffix|toolchain ``R2022a``| |``system`` ``R2022a``|``.1`` |``system`` ``R2022a``|``.5`` |``system`` +``R2023a``| |``system`` ### mctc-lib @@ -22017,8 +22690,8 @@ Common tool chain for working with molecular structure data in various applicati *homepage*: version |toolchain ----------|------------------------------------------------------------ -``0.3.1``|``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.2.1`` +---------|------------------------------------------------------------------------------------------ +``0.3.1``|``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.1.0``, ``intel-compilers/2022.2.1`` ### mcu @@ -22043,6 +22716,7 @@ version |versionsuffix |toolchain ``2.0.0`` | |``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ``2.2.0`` | |``foss/2022a`` ``2.4.2`` | |``foss/2021a``, ``foss/2022b`` +``2.7.0`` | |``foss/2023a`` ### MDBM @@ -22063,6 +22737,7 @@ The MolSSI Driver Interface (MDI) project provides a standardized API for fast, version |toolchain ----------|--------------- ``1.4.16``|``gompi/2022b`` +``1.4.26``|``gompi/2023a`` ### MDSplus @@ -22149,7 +22824,7 @@ medaka is a tool to create a consensus sequence from nanopore sequencing data. *homepage*: version |versionsuffix |toolchain -----------|-----------------|-------------- +----------|-----------------|------------------------------ ``0.4.3`` |``-Python-3.6.6``|``foss/2018b`` ``0.11.4``|``-Python-3.6.6``|``foss/2018b`` ``0.12.0``|``-Python-3.6.6``|``foss/2018b`` @@ -22161,7 +22836,8 @@ version |versionsuffix |toolchain ``1.5.0`` | |``foss/2021a`` ``1.6.0`` | |``foss/2021b`` ``1.8.1`` | |``foss/2022a`` -``1.9.1`` | |``foss/2022a`` +``1.9.1`` | |``foss/2022a``, ``foss/2022b`` +``1.11.3``| |``foss/2022a``, ``foss/2023a`` ### medImgProc @@ -22226,14 +22902,14 @@ An ultra-fast single-node solution for large and complex metagenomics assembly *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------------------------------------------------------------------------------------- +---------|------------------|------------------------------------------------------------------------------------------------------------------------------------- ``1.1.2``|``-Python-2.7.14``|``foss/2018a`` ``1.1.3``|``-Python-2.7.14``|``foss/2017b``, ``foss/2018a`` ``1.1.3``|``-Python-3.6.3`` |``foss/2017b`` ``1.1.4``|``-Python-2.7.15``|``foss/2018b`` ``1.1.4``|``-Python-3.6.6`` |``foss/2018b`` ``1.2.8``| |``GCCcore/8.2.0`` -``1.2.9``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``1.2.9``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` ``1.2.9``|``-Python-2.7.18``|``GCCcore/10.2.0`` ### Megalodon @@ -22469,6 +23145,7 @@ version |versionsuffix |toolchain ``0.64.0``| |``GCCcore/12.2.0`` ``1.1.1`` | |``GCCcore/12.3.0`` ``1.2.3`` | |``GCCcore/13.2.0`` +``1.3.1`` | |``GCCcore/12.3.0`` ### meson-python @@ -22477,10 +23154,10 @@ Python build backend (PEP 517) for Meson projects *homepage*: version |toolchain -----------|------------------ +----------|-------------------------------------- ``0.11.0``|``GCCcore/12.2.0`` ``0.13.2``|``GCCcore/12.3.0`` -``0.15.0``|``GCCcore/13.2.0`` +``0.15.0``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Mesquite @@ -22525,6 +23202,16 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``2.0.1-20190827``|``-R-3.6.0`` |``foss/2019a`` +### MetaDecoder + +An algorithm for clustering metagenomic sequences + +*homepage*: + +version |toolchain +----------|-------------- +``1.0.19``|``foss/2023b`` + ### metaerg MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. @@ -22677,6 +23364,17 @@ version |versionsuffix|toolchain ``5.0.2``| |``gimkl/2.11.5`` ``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`` +``5.1.0``|``-int64`` |``GCCcore/11.3.0`` + +### mfqe + +extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names. + +*homepage*: + +version |toolchain +---------|-------------- +``0.5.0``|``GCC/12.3.0`` ### mgen @@ -22900,6 +23598,16 @@ version |versionsuffix |toolchain ``0.5.3``|``-Python-2.7.12-Boost-1.63.0``|``intel/2016b`` ``0.5.4``|``-Python-2.7.14`` |``intel/2018a`` +### Miniforge3 + +Miniforge is a free minimal installer for conda and Mamba specific to conda-forge. + +*homepage*: + +version |toolchain +------------|---------- +``24.1.2-0``|``system`` + ### Minimac4 Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality. @@ -22928,7 +23636,7 @@ 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`` +``2.26`` |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Minipolish @@ -23069,9 +23777,9 @@ version|versionsuffix |toolchain ### MiXCR -MiXCR processes big immunome data from raw sequences to quantitated clonotypes +MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-------------------|---------- @@ -23079,6 +23787,7 @@ version |versionsuffix |toolchain ``3.0.3`` |``-Java-1.8`` |``system`` ``3.0.13``|``-Java-1.8`` |``system`` ``3.0.13``|``-Java-11`` |``system`` +``4.6.0`` |``-Java-17`` |``system`` ### MixMHC2pred @@ -23135,6 +23844,16 @@ version|toolchain -------|---------- ``3.0``|``system`` +### MLflow + +MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models. + +*homepage*: + +version |toolchain +----------|-------------- +``2.10.2``|``gfbf/2023a`` + ### MLxtend Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks. @@ -23210,11 +23929,12 @@ version |toolchain MNE-Python software is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics. -*homepage*: +*homepage*: version |toolchain ----------|-------------- ``0.24.1``|``foss/2021a`` +``1.6.1`` |``foss/2023a`` ### MOABB @@ -23225,6 +23945,7 @@ Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algori version |toolchain ---------|-------------- ``0.4.6``|``foss/2021a`` +``1.0.0``|``foss/2023a`` ### MOABS @@ -23256,6 +23977,16 @@ version |toolchain ---------|--------------- ``0.1.7``|``gompi/2021b`` +### MODFLOW + +MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions. + +*homepage*: + +version |toolchain +---------|-------------- +``6.4.4``|``foss/2023a`` + ### modred Compute modal decompositions and reduced-order models, easily, efficiently, and in parallel. @@ -23337,7 +24068,7 @@ MolMod is a Python library with many compoments that are useful to write molecul *homepage*: version |versionsuffix |toolchain ----------|------------------|---------------------------------------------- +---------|------------------|-------------------------------------------------------------- ``1.1`` |``-Python-2.7.11``|``intel/2016a`` ``1.1`` |``-Python-2.7.12``|``intel/2016b`` ``1.1`` |``-Python-2.7.13``|``intel/2017a`` @@ -23348,7 +24079,7 @@ version |versionsuffix |toolchain ``1.4.4``|``-Python-3.7.2`` |``intel/2019a`` ``1.4.5``|``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` ``1.4.5``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` -``1.4.8``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``1.4.8``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2023a`` ### Molpro @@ -23385,6 +24116,7 @@ version |versionsuffix |toolchain ``0.8.0``|``-CUDA-11.3.1``|``foss/2021a`` ``1.0.1``| |``foss/2022a`` ``1.0.1``|``-CUDA-11.7.0``|``foss/2022a`` +``1.3.0``| |``foss/2023a`` ### MONAI-Label @@ -23480,6 +24212,16 @@ version|toolchain -------|------------- ``4.9``|``GCC/8.3.0`` +### morphosamplers + +A library for sampling image data along morphological objects such as splines and surfaces. + +*homepage*: + +version |toolchain +----------|-------------- +``0.0.10``|``gfbf/2023a`` + ### mosdepth Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing @@ -23512,10 +24254,10 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: version |toolchain ----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.3.5``|``foss/2016a``, ``intel/2016a`` ``2.3.7``|``intel/2017a`` -``2.3.8``|``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``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +``2.3.8``|``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``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` ### MotionCor2 @@ -23532,6 +24274,16 @@ version |toolchain ``1.4.4``|``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.5.0``|``GCCcore/11.3.0`` +### MotionCor3 + +Anisotropic correction of beam induced motion for cryo-electron microscopy and cryo-electron tomography images. MotionCor3, an improved implementation of MotionCor2 with addition of CTF (Contrast Transfer Function) estimation, is a multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryo-electron microscopy and cryo-electron tomography images. The iterative, patch-based motion detection combined with spatial and temporal constraints and dose weighting provides robust and accurate correction. By refining the measurement of early motion, MotionCor3 further improves correction on tilted samples. The efficiency achieved by multi-GPU acceleration and parallelization enables correction to keep pace with automated data collection. The recent addition of a very robust GPU-accelerated CTF estimation makes MotionCor3 more versatile in cryoEM and cryoET processing pipeline. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|------------------ +``1.0.1``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` + ### motionSegmentation Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. @@ -23633,6 +24385,7 @@ version |versionsuffix |toolchain ``3.0.1``|``-Python-3.6.6`` |``intel/2018b`` ``3.0.2``|``-timed-pingpong`` |``gompi/2019a``, ``iimpi/2019a`` ``3.1.4``| |``gompi/2022b``, ``gompi/2023a`` +``3.1.5``| |``gompi/2023b`` ### MPICH @@ -23727,6 +24480,7 @@ version |toolchain ---------|-------------------------------------------------- ``1.3.0``|``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ``1.4.3``|``foss/2022a`` +``1.5.0``|``foss/2023a`` ### MRChem @@ -23789,6 +24543,16 @@ version |versionsuffix |toolchain ``3.0_RC2`` |``-Python-2.7.13``|``foss/2017a`` ``3.0_RC3`` |``-Python-2.7.14``|``intel/2018a`` +### MSFragger + +MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide range of datasets and applications. MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides, and glycopeptide identification (N-linked and O-linked). + +*homepage*: + +version|versionsuffix|toolchain +-------|-------------|---------- +``4.0``|``-Java-11`` |``system`` + ### msgpack-c MessagePack is an efficient binary serialization format, which lets you exchange data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves. @@ -23838,8 +24602,8 @@ Molecular structure store for testing *homepage*: version |toolchain ----------|---------------------------------------------------------------------------- -``0.2.0``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.2.1`` +---------|---------------------------------------------------------------------------------------------------------- +``0.2.0``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.1.0``, ``intel-compilers/2022.2.1`` ### MTL4 @@ -23880,8 +24644,8 @@ Electronegativity equilibration model for atomic partial charges. *homepage*: version |toolchain ----------|------------------------------- -``0.2.0``|``gfbf/2022b``, ``iimkl/2022b`` +---------|------------------------------------------------ +``0.2.0``|``gfbf/2022b``, ``iimkl/2022a``, ``iimkl/2022b`` ### multichoose @@ -23890,8 +24654,8 @@ 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/11.3.0``, ``GCCcore/9.3.0`` +---------|--------------------------------------------------------------------------------------------------------------------- +``1.0.3``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### MultilevelEstimators @@ -23913,6 +24677,16 @@ version |toolchain --------|--------------- ``3.10``|``intel/2016a`` +### multiprocess + +better multiprocessing and multithreading in python + +*homepage*: + +version |toolchain +-----------|-------------- +``0.70.15``|``gfbf/2023a`` + ### MultiQC Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. @@ -23965,10 +24739,10 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or *homepage*: 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``, ``GCCcore/12.2.0`` +``4.0.0rc1`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### MUMPS @@ -24034,7 +24808,7 @@ 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/10.3.0``, ``GCCcore/11.3.0`` +``5.1.0`` | |``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### MUSCLE3 @@ -24161,9 +24935,9 @@ Python Client for MyGene.Info services. *homepage*: version |toolchain ----------|--------------- +---------|------------------------------ ``3.1.0``|``intel/2019a`` -``3.2.2``|``foss/2022a`` +``3.2.2``|``foss/2022a``, ``foss/2022b`` ### MyMediaLite @@ -24246,7 +25020,7 @@ version |versionsuffix |toolchain ## N -[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](#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](#nf-core) - [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) - [noise](#noise) - [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 @@ -24290,7 +25064,7 @@ 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`` @@ -24299,7 +25073,7 @@ version |versionsuffix |toolchain ``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`` +``2.14``|``-mpi`` |``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2022a``, ``foss/2023a``, ``intel/2020a`` ### namedlist @@ -24484,14 +25258,14 @@ version |toolchain ### 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). +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). *homepage*: version |toolchain -----------|-------------- +----------|------------------------------ ``0.4.15``|``foss/2021b`` -``0.4.18``|``foss/2022a`` +``0.4.18``|``foss/2022a``, ``foss/2023a`` ### NASM @@ -24575,6 +25349,7 @@ version |toolchain ``3.0.0`` |``gompi/2021b``, ``gompi/2022a`` ``3.0.2`` |``gompi/2022a`` ``3.0.5`` |``gompi/2021a``, ``gompi/2022b`` +``3.0.10`` |``gompi/2023a`` ### NCCL @@ -24599,6 +25374,7 @@ version |versionsuffix |toolchain ``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`` +``2.20.5`` |``-CUDA-12.4.0`` |``GCCcore/13.2.0`` ### NCCL-tests @@ -24691,6 +25467,7 @@ version |toolchain ``5.0.6``|``intel/2019b`` ``5.1.0``|``foss/2022a`` ``5.1.3``|``foss/2021a``, ``foss/2022a`` +``5.1.9``|``intel/2022a`` ### ncolor @@ -24767,6 +25544,7 @@ Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemis version |toolchain ------------|-------------- ``20220711``|``foss/2022a`` +``20230620``|``foss/2022b`` ### NEdit @@ -24856,7 +25634,7 @@ 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`` +``4.9.2`` | |``gompi/2023a``, ``gompi/2023b``, ``iimpi/2023a``, ``iimpi/2023b`` ### netCDF-C++ @@ -24875,11 +25653,11 @@ 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``, ``gompi/2023a``, ``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``, ``gompi/2023b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a``, ``iimpi/2023b`` ### netCDF-Fortran @@ -24899,7 +25677,7 @@ 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``, ``iimpi/2023a`` +``4.6.1``| |``gompi/2023a``, ``gompi/2023b``, ``iimpi/2023a``, ``iimpi/2023b`` ### netcdf4-python @@ -24927,6 +25705,7 @@ version |versionsuffix |toolchain ``1.6.1`` | |``foss/2022a``, ``intel/2022a`` ``1.6.3`` | |``foss/2022b`` ``1.6.4`` | |``foss/2023a`` +``1.6.5`` | |``foss/2023b`` ### netloc @@ -25073,6 +25852,7 @@ version |versionsuffix |toolchain ``2.8.8``| |``gfbf/2022b`` ``3.0`` | |``gfbf/2022b`` ``3.1`` | |``gfbf/2023a`` +``3.2.1``| |``gfbf/2023b`` ### NeuroKit @@ -25151,6 +25931,17 @@ version |toolchain ----------|-------------------- ``2.1.18``|``GCC/8.2.0-2.31.1`` +### nf-core + +Python package with helper tools for the nf-core community. + +*homepage*: + +version |toolchain +----------|-------------- +``2.10`` |``foss/2022b`` +``2.13.1``|``foss/2023b`` + ### nf-core-mag The Nextflow pipeline 'mag' ported to EasyBuild/EESSI. @@ -25172,7 +25963,7 @@ version |toolchain ``3.1.3``|``foss/2020b``, ``fosscuda/2020b`` ``3.5.1``|``foss/2018b``, ``foss/2019a`` ``3.5.2``|``foss/2020a``, ``foss/2021a``, ``foss/2021b`` -``3.5.3``|``foss/2022a`` +``3.5.3``|``foss/2022a``, ``foss/2023a`` ### nghttp2 @@ -25265,9 +26056,10 @@ NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads *homepage*: version |versionsuffix |toolchain ------------|-----------------|-------------- +-----------|-----------------|------------------------------ ``0.1.1.1``|``-Python-3.7.4``|``foss/2019b`` ``0.1.2.1``| |``foss/2021b`` +``0.3.0`` | |``foss/2022b``, ``foss/2023a`` ### ngspice @@ -25312,6 +26104,7 @@ version |versionsuffix |toolchain ``3.2.1``| |``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ``3.2.2``| |``foss/2021b`` ``4.0.2``| |``foss/2022a`` +``5.2.0``| |``gfbf/2023a`` ### nichenetr @@ -25322,6 +26115,7 @@ R implementation of the NicheNet method, to predict active ligand-target links version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.1.1-20230223``|``-R-4.2.1`` |``foss/2022a`` +``2.0.4`` |``-R-4.2.2`` |``foss/2022b`` ### NIfTI @@ -25349,13 +26143,14 @@ Nilearn is a Python module for fast and easy statistical learning on NeuroImagin *homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------- -``0.5.2``| |``foss/2019a``, ``intel/2019a`` -``0.5.2``|``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` -``0.5.2``|``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` -``0.7.0``|``-Python-3.8.2`` |``foss/2020a`` -``0.7.1``| |``foss/2020b`` +version |versionsuffix |toolchain +----------|------------------|------------------------------- +``0.5.2`` | |``foss/2019a``, ``intel/2019a`` +``0.5.2`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b`` +``0.5.2`` |``-Python-3.6.3`` |``foss/2017b``, ``intel/2017b`` +``0.7.0`` |``-Python-3.8.2`` |``foss/2020a`` +``0.7.1`` | |``foss/2020b`` +``0.10.3``| |``gfbf/2023a`` ### Nim @@ -25408,6 +26203,7 @@ version |versionsuffix |toolchain ``1.0.2``|``-Python-3.6.4``|``intel/2018a`` ``1.1.3``|``-Python-3.6.6``|``foss/2018b`` ``1.4.2``|``-Python-3.7.4``|``intel/2019b`` +``1.6.0``| |``foss/2020b`` ``1.8.5``| |``foss/2021a`` ### NLMpy @@ -25432,6 +26228,7 @@ version |toolchain ``3.10.4``|``GCCcore/11.2.0`` ``3.10.5``|``GCCcore/11.3.0`` ``3.11.2``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.11.3``|``GCCcore/13.2.0`` ### NLopt @@ -25454,13 +26251,14 @@ NLTK is a leading platform for building Python programs to work with human langu *homepage*: version |versionsuffix |toolchain ----------|------------------|---------------------------------- +---------|------------------|---------------------------------------------- ``3.2.2``|``-Python-2.7.13``|``intel/2017a`` ``3.2.4``|``-Python-2.7.13``|``intel/2017a`` ``3.5`` |``-Python-3.7.4`` |``foss/2019b`` ``3.5`` |``-Python-3.8.2`` |``foss/2020a``, ``fosscuda/2020a`` ``3.6.7``| |``foss/2021a`` ``3.7`` | |``foss/2021b`` +``3.8.1``| |``foss/2022b``, ``foss/2023a``, ``foss/2023b`` ### nnU-Net @@ -25505,6 +26303,16 @@ version |toolchain ``18.17.1``|``GCCcore/12.3.0`` ``20.9.0`` |``GCCcore/13.2.0`` +### noise + +Native-code and shader implementations of Perlin noise for Python + +*homepage*: + +version |toolchain +---------|-------------- +``1.2.2``|``gfbf/2023a`` + ### Normaliz Normaliz is a open source tool for computations in affine monoids, vector configurations, rational polyhedra and rational cones. Normaliz now computes rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of QQ. @@ -25538,8 +26346,8 @@ Nose extends unittest to make testing easier. *homepage*: version |toolchain ----------|------------------ -``1.3.8``|``GCCcore/11.3.0`` +---------|-------------------------------------- +``1.3.8``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### novaSTA @@ -25671,6 +26479,7 @@ ntCard is a streaming algorithm for estimating the frequencies of k-mers in geno version |toolchain ---------|----------------------------- ``1.2.1``|``GCC/11.2.0``, ``GCC/8.3.0`` +``1.2.2``|``GCC/12.3.0`` ### ntEdit @@ -25699,9 +26508,9 @@ NTL is a high-performance, portable C++ library providing data structures and al *homepage*: version |toolchain -----------|---------------------------------------------- +----------|-------------------------------------------------------------- ``11.3.4``|``GCC/8.2.0-2.31.1`` -``11.5.1``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0`` +``11.5.1``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.2.0``, ``GCC/13.2.0`` ### NTPoly @@ -25768,6 +26577,7 @@ version |versionsuffix |toolchain ``0.54.1``|``-CUDA-11.4.1`` |``foss/2021b`` ``0.56.4``| |``foss/2022a`` ``0.56.4``|``-CUDA-11.7.0`` |``foss/2022a`` +``0.58.1``| |``foss/2022b``, ``foss/2023a`` ### numdiff @@ -25844,6 +26654,7 @@ version |versionsuffix |toolchain ``23.1`` |``-CUDA-12.0.0``|``system`` ``23.7`` |``-CUDA-12.1.1``|``system`` ``23.7`` |``-CUDA-12.2.0``|``system`` +``24.1`` |``-CUDA-12.3.0``|``system`` ### nvofbf @@ -25922,7 +26733,7 @@ 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) - [OMERO.insight](#omero.insight) - [OMERO.py](#omero.py) - [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](#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) - [OMERO.insight](#omero.insight) - [OMERO.py](#omero.py) - [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) - [OpenMEEG](#openmeeg) - [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-Java](#openslide-java) - [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 @@ -25954,9 +26765,10 @@ A package for the management of analyses and data in DNA metabarcoding. *homepage*: -version |toolchain ------------|------------------ -``3.0.1b8``|``GCCcore/10.2.0`` +version |toolchain +------------|------------------ +``3.0.1b8`` |``GCCcore/10.2.0`` +``3.0.1b26``|``GCCcore/12.3.0`` ### OCaml @@ -25968,6 +26780,7 @@ version |toolchain ----------|-------------- ``4.02.3``|``foss/2016a`` ``4.07.1``|``foss/2018b`` +``4.14.0``|``GCC/11.3.0`` ### occt @@ -25979,6 +26792,7 @@ version |toolchain -----------|------------------------------ ``7.3.0p4``|``foss/2019b`` ``7.5.0p1``|``foss/2021a``, ``foss/2022a`` +``7.8.0`` |``GCCcore/12.3.0`` ### oceanspy @@ -26120,27 +26934,30 @@ version |toolchain ----------|------------------ ``2.4.11``|``GCCcore/10.2.0`` ``2.4.21``|``GCCcore/11.3.0`` +``2.4.25``|``GCCcore/12.3.0`` ### ONNX Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring). -*homepage*: +*homepage*: version |toolchain ----------|-------------- ``1.11.0``|``foss/2021a`` +``1.15.0``|``foss/2022b`` ### ONNX-Runtime ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms. -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|----------------|-------------- ``1.10.0``| |``foss/2021a`` ``1.10.0``|``-CUDA-11.3.1``|``foss/2021a`` +``1.16.3``| |``foss/2022b`` ### ont-fast5-api @@ -26155,6 +26972,7 @@ version |versionsuffix |toolchain ``4.0.0``| |``foss/2021a`` ``4.0.2``| |``foss/2021a``, ``foss/2021b`` ``4.1.1``| |``foss/2022a``, ``foss/2022b`` +``4.1.2``| |``foss/2023a`` ### ont-guppy @@ -26203,6 +27021,7 @@ version |toolchain ``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``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.0.8``|``GCCcore/13.2.0`` ### Open-Data-Cube-Core @@ -26233,14 +27052,14 @@ Open Babel is a chemical toolbox designed to speak the many languages of chemic *homepage*: version |versionsuffix |toolchain ----------|------------------|-------------------------------- +---------|------------------|------------------------------------------------- ``2.3.2``|``-Python-2.7.11``|``foss/2016a`` ``2.4.1``|``-Python-2.7.14``|``intel/2017b`` ``2.4.1``|``-Python-2.7.15``|``intel/2018b`` ``2.4.1``|``-Python-3.6.6`` |``intel/2018b`` ``2.4.1``|``-Python-3.7.2`` |``intel/2019a`` ``3.0.0``|``-Python-3.7.4`` |``gompi/2019b`` -``3.1.1``| |``gompi/2021a``, ``gompi/2022a`` +``3.1.1``| |``gompi/2021a``, ``gompi/2022a``, ``gompi/2023a`` ``3.1.1``|``-Python-3.7.4`` |``gompi/2019b`` ``3.1.1``|``-Python-3.8.2`` |``iimpi/2020a`` @@ -26406,41 +27225,45 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: -version |versionsuffix|toolchain -----------------|-------------|------------------------------------------------- -``2.2.2`` | |``intel/2016a``, ``intel/2017a``, ``intel/2018a`` -``2.2.x`` | |``intel/2019a`` -``2.3.1`` | |``intel/2017a``, ``intel/2019b`` -``2.4.0`` | |``intel/2017a``, ``intel/2019a`` -``3.0.0`` | |``foss/2016a`` -``3.0.1`` | |``intel/2016b``, ``intel/2018a`` -``4.0`` | |``foss/2016b``, ``intel/2016b`` -``4.1`` | |``foss/2016b``, ``intel/2017a`` -``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`` -``8`` | |``foss/2020a``, ``foss/2020b`` -``8`` |``-20210316``|``foss/2020b`` -``9`` | |``foss/2021a``, ``intel/2021a`` -``10`` | |``foss/2022a``, ``foss/2023a`` -``10`` |``-20230119``|``foss/2022a`` -``11`` | |``foss/2022a`` -``v1606+`` | |``foss/2018b`` -``v1612+`` | |``foss/2018b`` -``v1712`` | |``foss/2017b``, ``intel/2017b`` -``v1806`` | |``foss/2018b`` -``v1812`` | |``foss/2018b`` -``v1906`` | |``foss/2019b`` -``v1912`` | |``foss/2019b``, ``intel/2019b`` -``v2006`` | |``foss/2020a``, ``intel/2020a`` -``v2012`` | |``foss/2020a`` -``v2106`` | |``foss/2021a`` -``v2112`` | |``foss/2020b``, ``foss/2021b`` -``v2206`` | |``foss/2022a`` +version |versionsuffix |toolchain +----------------|-------------------|------------------------------------------------- +``2.2.2`` | |``intel/2016a``, ``intel/2017a``, ``intel/2018a`` +``2.2.x`` | |``intel/2019a`` +``2.3.1`` | |``intel/2017a``, ``intel/2019b`` +``2.4.0`` | |``intel/2017a``, ``intel/2019a`` +``3.0.0`` | |``foss/2016a`` +``3.0.1`` | |``intel/2016b``, ``intel/2018a`` +``4.0`` | |``foss/2016b``, ``intel/2016b`` +``4.1`` | |``foss/2016b``, ``intel/2017a`` +``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``, ``foss/2022a`` +``7`` |``-20200508-int64``|``foss/2022a`` +``8`` | |``foss/2020a``, ``foss/2020b`` +``8`` |``-20210316`` |``foss/2020b`` +``9`` | |``foss/2021a``, ``intel/2021a`` +``10`` | |``foss/2022a``, ``foss/2023a`` +``10`` |``-20230119`` |``foss/2022a`` +``11`` | |``foss/2022a``, ``foss/2023a`` +``v1606+`` | |``foss/2018b`` +``v1612+`` | |``foss/2018b`` +``v1712`` | |``foss/2017b``, ``intel/2017b`` +``v1806`` | |``foss/2018b`` +``v1812`` | |``foss/2018b`` +``v1906`` | |``foss/2019b`` +``v1912`` | |``foss/2019b``, ``intel/2019b`` +``v2006`` | |``foss/2020a``, ``intel/2020a`` +``v2012`` | |``foss/2020a`` +``v2106`` | |``foss/2021a`` +``v2112`` | |``foss/2020b``, ``foss/2021b``, ``foss/2022a`` +``v2206`` | |``foss/2022a`` +``v2206`` |``-int64`` |``foss/2022a`` +``v2306`` | |``foss/2022b`` +``v2312`` | |``foss/2023a`` ### OpenFOAM-Extend @@ -26530,7 +27353,17 @@ version |toolchain ------------|-------------------------------------------------------------------------------- ``20190725``|``GCC/10.2.0``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` ``20210128``|``GCC/10.2.0`` -``20210811``|``GCC/12.3.0`` +``20210811``|``GCC/12.3.0``, ``intel-compilers/2023.1.0`` + +### OpenMEEG + +The OpenMEEG software is a C++ package for solving the forward problems of electroencephalography (EEG) and magnetoencephalography (MEG). + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.7``|``foss/2023a`` ### OpenMM @@ -26691,14 +27524,14 @@ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: version |versionsuffix |toolchain -----------|------------------|-------------------------------------- +----------|------------------|---------------------------------------------------------- ``2.6.2`` | |``GCCcore/8.2.0`` ``2.6.4`` |``-Python-2.7.16``|``GCCcore/8.3.0`` ``3.0.3`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` ``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``, ``GCCcore/12.3.0`` +``3.1.2`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### OpenRefine @@ -26743,6 +27576,16 @@ version |versionsuffix |toolchain ``3.4.1``| |``GCCcore/11.2.0``, ``GCCcore/8.2.0`` ``3.4.1``|``-largefiles``|``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/8.2.0`` +### OpenSlide-Java + +This is a Java binding to OpenSlide. + +*homepage*: + +version |versionsuffix|toolchain +----------|-------------|------------------ +``0.12.4``|``-Java-17`` |``GCCcore/12.3.0`` + ### openslide-python OpenSlide Python is a Python interface to the OpenSlide library. @@ -26758,7 +27601,7 @@ version |toolchain ### OpenSSL -The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. +The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. *homepage*: @@ -26781,6 +27624,7 @@ version |toolchain ``1.1.1k``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.1.1n``|``GCCcore/11.3.0`` ``1.1.1q``|``GCCcore/10.3.0`` +``3`` |``system`` ### OpenStackClient @@ -26869,6 +27713,7 @@ version |toolchain ``2.9.1`` |``foss/2021a`` ``2.10.0``|``foss/2021b`` ``3.1.0`` |``foss/2022a`` +``3.5.0`` |``foss/2023a`` ### OR-Tools @@ -26901,7 +27746,7 @@ version |versionsuffix |toolchain ``5.0.2`` | |``gompi/2021a``, ``gompi/2021b`` ``5.0.2`` |``-static`` |``gompi/2021a``, ``gompi/2021b`` ``5.0.3`` | |``gompi/2021b`` -``5.0.4`` | |``gompi/2022a`` +``5.0.4`` | |``gompi/2022a``, ``gompi/2023a`` ### ORFfinder @@ -26920,9 +27765,9 @@ A simple and not slow open reading frame (ORF) caller. *homepage*: version |toolchain ----------|---------------------------------------- +---------|-------------------------------------------------------- ``0.6.1``|``foss/2016b`` -``0.7.1``|``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.7.1``|``GCC/12.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ### OrthoFinder @@ -26963,6 +27808,7 @@ version |toolchain ``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`` +``0.108.9``|``GCC/12.3.0`` ### OSPRay @@ -27007,13 +27853,13 @@ The Open Trace Format 2 is a highly scalable, memory efficient event trace data *homepage*: version |toolchain ----------|------------------------------------------------------- +---------|---------------------------------------------------------- ``2.0`` |``foss/2016a``, ``foss/2017a`` ``2.2`` |``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``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`` +``3.0.3``|``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### OVITO @@ -27059,7 +27905,7 @@ 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) - [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) - [PFFT](#pfft) - [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) - [plotutils](#plotutils) - [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) - [primecount](#primecount) - [primecountpy](#primecountpy) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [ProBiS](#probis) - [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) - [PyAV](#pyav) - [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) - [pycubescd](#pycubescd) - [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) - [pylipid](#pylipid) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC](#pymc) - [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) - [PyPy](#pypy) - [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) - [PySINDy](#pysindy) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [PyTensor](#pytensor) - [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) - [pythermalcomfort](#pythermalcomfort) - [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) - [PyTorchVideo](#pytorchvideo) - [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) - [PAGAN2](#pagan2) - [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) - [PASA](#pasa) - [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) - [pblat](#pblat) - [pbmm2](#pbmm2) - [pbs_python](#pbs_python) - [PBSuite](#pbsuite) - [PBZIP2](#pbzip2) - [PCAngsd](#pcangsd) - [PCC](#pcc) - [PCL](#pcl) - [PCMSolver](#pcmsolver) - [PCRaster](#pcraster) - [PCRE](#pcre) - [PCRE2](#pcre2) - [PDM](#pdm) - [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) - [PFFT](#pfft) - [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) - [Philosopher](#philosopher) - [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) - [phyluce](#phyluce) - [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) - [plotutils](#plotutils) - [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) - [poppunk](#poppunk) - [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) - [primecount](#primecount) - [primecountpy](#primecountpy) - [Primer3](#primer3) - [PRINSEQ](#prinseq) - [printproto](#printproto) - [PRISMS-PF](#prisms-pf) - [ProbABEL](#probabel) - [ProBiS](#probis) - [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) - [PSASS](#psass) - [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) - [psycopg](#psycopg) - [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) - [PyAV](#pyav) - [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) - [pycubescd](#pycubescd) - [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) - [PyInstaller](#pyinstaller) - [pyiron](#pyiron) - [Pyke3](#pyke3) - [pylift](#pylift) - [Pylint](#pylint) - [pylipid](#pylipid) - [pyMannKendall](#pymannkendall) - [pymatgen](#pymatgen) - [pymatgen-db](#pymatgen-db) - [pymbar](#pymbar) - [PyMC](#pymc) - [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) - [PyPy](#pypy) - [pyqstem](#pyqstem) - [PyQt](#pyqt) - [PyQt-builder](#pyqt-builder) - [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) - [PySINDy](#pysindy) - [pyslim](#pyslim) - [pysndfx](#pysndfx) - [Pysolar](#pysolar) - [pyspoa](#pyspoa) - [pysqlite](#pysqlite) - [PyStan](#pystan) - [pysteps](#pysteps) - [pystran](#pystran) - [PyTables](#pytables) - [PyTensor](#pytensor) - [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-workflow](#pytest-workflow) - [pytest-xdist](#pytest-xdist) - [pythermalcomfort](#pythermalcomfort) - [PYTHIA](#pythia) - [Python](#python) - [Python-bundle](#python-bundle) - [Python-bundle-PyPI](#python-bundle-pypi) - [python-casacore](#python-casacore) - [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-3dunet](#pytorch-3dunet) - [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) - [PyTorchVideo](#pytorchvideo) - [PyVCF](#pyvcf) - [PyVCF3](#pyvcf3) - [pyWannier90](#pywannier90) - [PyWavelets](#pywavelets) - [PyWBGT](#pywbgt) - [pyXDF](#pyxdf) - [PyYAML](#pyyaml) - [PyZMQ](#pyzmq) ### p11-kit @@ -27133,6 +27979,16 @@ version |toolchain ``20.2.2`` |``GCC/10.2.0`` ``v20.2.2``|``iccifort/2020.1.217`` +### PAGAN2 + +PAGAN2 is a general-purpose method for the alignment of DNA, codon and amino-acid sequences as graphs. It aligns sequences either with pileup or, when related by a tree, using phylogeny-aware progressive alignment algorithm. In both cases it uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. PAGAN2 is largely compatible with PAGAN but implements new algorithms for alignment anchoring and memory handling. As a result, PAGAN2 can align sequences of several hundreds of kilobases in length. + +*homepage*: + +version |versionsuffix|toolchain +-----------------|-------------|---------- +``1.53_20230824``|``-linux64`` |``system`` + ### pagmo pagmo is a C++ scientific library for massively parallel optimization. @@ -27349,6 +28205,7 @@ version |toolchain ``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`` +``7.1.0`` |``GCCcore/13.2.0`` ### parallel @@ -27397,10 +28254,11 @@ Parallel Hashmap is built on a modified version of Abseil's flat_hash_map. Paral *homepage*: -version |toolchain ---------|------------------ -``1.33``|``GCCcore/10.3.0`` -``1.36``|``GCCcore/11.3.0`` +version |toolchain +----------|------------------ +``1.3.12``|``GCCcore/12.3.0`` +``1.33`` |``GCCcore/10.3.0`` +``1.36`` |``GCCcore/11.3.0`` ### ParallelIO @@ -27420,9 +28278,9 @@ Parameterized testing with any Python test framework *homepage*: version |toolchain ----------|------------------ +---------|-------------------------------------- ``0.8.1``|``GCCcore/10.3.0`` -``0.9.0``|``GCCcore/11.3.0`` +``0.9.0``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### paramiko @@ -27449,7 +28307,7 @@ 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`` +``2.6.2``|``GCC/12.2.0``, ``GCC/12.3.0`` ### Paraver @@ -27489,6 +28347,7 @@ version |versionsuffix |toolchain ``5.11.1``|``-CUDA-12.2.0`` |``foss/2022b`` ``5.11.1``|``-mpi`` |``foss/2022a`` ``5.11.2``| |``foss/2023a`` +``5.12.0``| |``foss/2023b`` ### Parcels @@ -27530,8 +28389,8 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -``4.0.3``|``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +---------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``4.0.3``|``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``gompi/2022b``, ``gompi/2023a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ### ParMGridGen @@ -27564,6 +28423,16 @@ version |versionsuffix |toolchain ``2.1.1``|``-Python-2.7.16``|``intel/2019b`` ``2.1.1``|``-Python-2.7.18``|``foss/2020b`` +### PASA + +PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.3``|``foss/2022b`` + ### pasta PASTA (Practical Alignment using SATe and Transitivity) @@ -27699,6 +28568,16 @@ version |toolchain ---------|-------------- ``1.8.0``|``foss/2021b`` +### pblat + +When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence. + +*homepage*: + +version |toolchain +---------|-------------- +``2.5.1``|``foss/2022b`` + ### pbmm2 A minimap2 frontend for PacBio native data formats @@ -27732,6 +28611,16 @@ version |versionsuffix |toolchain -----------|------------------|--------------- ``15.8.24``|``-Python-2.7.12``|``intel/2016b`` +### PBZIP2 + +PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be decompressed with bzip2). PBZIP2 should work on any system that has a pthreads compatible C++ compiler (such as gcc). It has been tested on: Linux, Windows (cygwin & MinGW), Solaris, Tru64/OSF1, HP-UX, OS/2, OSX, and Irix. + +*homepage*: + +version |toolchain +----------|------------------ +``1.1.13``|``GCCcore/12.3.0`` + ### PCAngsd PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations. @@ -27772,6 +28661,7 @@ An API for the Polarizable Continuum Model. version |versionsuffix |toolchain ------------|------------------|--------------- ``1.1.4`` |``-Python-2.7.11``|``intel/2016a`` +``1.2.3`` | |``iimpi/2020b`` ``1.2.3`` |``-Python-3.6.6`` |``foss/2018b`` ``1.2.3`` |``-Python-3.7.2`` |``gompi/2019a`` ``1.2.3`` |``-Python-3.7.4`` |``iimpi/2019b`` @@ -27794,7 +28684,7 @@ The PCRE library is a set of functions that implement regular expression patter *homepage*: version |toolchain ---------|---------------------------------------------------------------------------------- +--------|-------------------------------------------------------------------------------------------------- ``8.38``|``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``8.39``|``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``8.40``|``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` @@ -27802,7 +28692,7 @@ version |toolchain ``8.42``|``GCCcore/6.4.0`` ``8.43``|``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.44``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``8.45``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``8.45``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### PCRE2 @@ -27822,6 +28712,16 @@ version |toolchain ``10.40``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``10.42``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` +### PDM + +A modern Python package and dependency manager supporting the latest PEP standards. + +*homepage*: + +version |toolchain +----------|------------------ +``2.12.4``|``GCCcore/12.3.0`` + ### pdsh A high performance, parallel remote shell utility @@ -27843,6 +28743,7 @@ 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/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` +``3.25.2``|``GCCcore/13.2.0`` ### peakdetect @@ -27934,7 +28835,7 @@ 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`` +``5.38.0``| |``GCCcore/13.2.0``, ``system`` ### perl-app-cpanminus @@ -28011,6 +28912,7 @@ version |versionsuffix |toolchain ``3.17.4``| |``foss/2022a`` ``3.18.4``| |``intel/2021b`` ``3.19.2``| |``foss/2022b`` +``3.20.3``| |``foss/2023a`` ### petsc4py @@ -28124,8 +29026,8 @@ The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-indep *homepage*: version |toolchain ----------|-------------------------------------- -``5.2.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +---------|---------------------------------------------------------- +``5.2.2``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/13.2.0`` ### PHANOTATE @@ -28199,6 +29101,16 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``1.1.20``|``-Python-3.7.4``|``foss/2019b`` +### Philosopher + +Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery. + +*homepage*: + +version |toolchain +---------|-------------- +``5.0.0``|``GCC/11.3.0`` + ### PhiPack The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. @@ -28228,17 +29140,19 @@ The phonemizer allows simple phonemization of words and texts in many languages. version |versionsuffix |toolchain ---------|-----------------|--------------- ``2.2.1``|``-Python-3.8.2``|``gompi/2020a`` +``3.2.1``| |``gfbf/2023a`` ### phono3py -phono3py calculates phonon-phonon interaction and related properties using the supercell approach. +A simulation package of phonon-phonon interaction related properties. -*homepage*: +*homepage*: version |versionsuffix |toolchain -------------|------------------|------------------------------- ``1.12.5.35``|``-Python-2.7.14``|``intel/2017b`` ``1.12.7.55``|``-Python-2.7.14``|``foss/2018a``, ``intel/2018a`` +``2.7.0`` | |``foss/2023a`` ### phonopy @@ -28288,9 +29202,9 @@ PHYLIP is a free package of programs for inferring phylogenies. *homepage*: version |toolchain ----------|------------------------------------------------------------------------- +---------|----------------------------------------------------------------------------------------- ``3.696``|``foss/2016a``, ``intel/2016a`` -``3.697``|``GCC/6.4.0-2.28``, ``GCC/9.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``3.697``|``GCC/12.3.0``, ``GCC/6.4.0-2.28``, ``GCC/9.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ### PhyloBayes-MPI @@ -28334,6 +29248,16 @@ version |versionsuffix |toolchain ``3.0.2``| |``foss/2021a`` ``3.0.3``| |``foss/2022a`` +### phyluce + +phyluce is a software package for working with data generated from sequence capture of UCE (ultra-conserved element) loci, as first published in [BCF2012]. Specifically, phyluce is a suite of programs to: 1) assemble raw sequence reads from Illumina platforms into contigs 2) determine which contigs represent UCE loci 3) filter potentially paralagous UCE loci 4) generate different sets of UCE loci across taxa of interest + +*homepage*: + +version |toolchain +---------|-------------- +``1.7.3``|``foss/2023a`` + ### PhyML Phylogenetic estimation using (Maximum) Likelihood @@ -28490,6 +29414,7 @@ version |versionsuffix |toolchain ``9.2.0`` | |``GCCcore/10.2.0`` ``9.4.0`` | |``GCCcore/12.2.0`` ``10.0.0``| |``GCCcore/12.3.0`` +``10.2.0``| |``GCCcore/13.2.0`` ### Pillow-SIMD @@ -28508,7 +29433,7 @@ 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`` +``9.5.0`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### Pilon @@ -28566,6 +29491,7 @@ version |versionsuffix |toolchain ``0.19.2``| |``GCCcore/11.2.0`` ``0.20.1``| |``GCCcore/10.3.0`` ``0.22`` | |``GCCcore/11.3.0`` +``0.23`` | |``GCCcore/12.3.0`` ### pip @@ -28699,7 +29625,7 @@ 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`` @@ -28716,7 +29642,7 @@ 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``, ``GCCcore/12.3.0`` +``1.5.5``|``-python`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### PLAMS @@ -28831,7 +29757,7 @@ version |toolchain ``2.00a2.3_x86_64`` |``system`` ``2.00a3.1`` |``GCC/11.2.0`` ``2.00a3.6`` |``GCC/11.3.0`` -``2.00a3.7`` |``foss/2022a`` +``2.00a3.7`` |``foss/2022a``, ``gfbf/2023a`` ### plinkliftover @@ -28923,6 +29849,7 @@ version |toolchain ``5.12.0``|``GCCcore/11.3.0`` ``5.13.1``|``GCCcore/12.2.0`` ``5.16.0``|``GCCcore/12.3.0`` +``5.18.0``|``GCCcore/13.2.0`` ### plotutils @@ -28985,8 +29912,8 @@ PLY is yet another implementation of lex and yacc for Python. *homepage*: version |versionsuffix |toolchain ---------|-----------------|------------------ -``3.11``| |``GCCcore/12.2.0`` +--------|-----------------|-------------------------------------- +``3.11``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``3.11``|``-Python-3.6.4``|``foss/2018a`` ``3.11``|``-Python-3.7.4``|``GCCcore/8.3.0`` @@ -29020,10 +29947,12 @@ PMT is a high-level software library capable of collecting power consumptio *homepage*: -version |toolchain ----------|-------------------------------------- -``1.1.0``|``GCCcore/11.3.0`` -``1.2.0``|``GCCcore/11.3.0``, ``GCCcore/12.3.0`` +version |versionsuffix |toolchain +---------|----------------|-------------------------------------- +``1.1.0``| |``GCCcore/11.3.0`` +``1.2.0``| |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` +``1.2.0``|``-CUDA-11.7.0``|``GCCcore/11.3.0`` +``1.2.0``|``-CUDA-12.1.1``|``GCCcore/12.3.0`` ### pmx @@ -29056,15 +29985,17 @@ PoCL is a portable open source (MIT-licensed) implementation of the OpenCL stan *homepage*: -version|toolchain --------|---------------------------------------------------------- -``1.2``|``GCC/7.3.0-2.30`` -``1.3``|``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` -``1.4``|``GCC/8.3.0``, ``gcccuda/2019b`` -``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`` +version|versionsuffix |toolchain +-------|----------------|---------------------------------------------------------- +``1.2``| |``GCC/7.3.0-2.30`` +``1.3``| |``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` +``1.4``| |``GCC/8.3.0``, ``gcccuda/2019b`` +``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`` +``1.8``|``-CUDA-11.7.0``|``GCC/11.3.0`` +``4.0``| |``GCC/12.3.0`` +``4.0``|``-CUDA-12.1.1``|``GCC/12.3.0`` ### pod5-file-format @@ -29088,6 +30019,7 @@ version |versionsuffix |toolchain ``1.2.2``| |``GCCcore/11.3.0`` ``1.5.1``| |``GCCcore/12.3.0`` ``1.6.1``| |``GCCcore/13.2.0`` +``1.7.1``| |``GCCcore/12.3.0`` ### polars @@ -29149,6 +30081,16 @@ version |toolchain ``22.12.0``|``GCC/11.3.0`` ``23.09.0``|``GCC/12.3.0`` +### poppunk + +PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages. + +*homepage*: + +version |toolchain +---------|-------------- +``2.6.0``|``foss/2022a`` + ### popscle A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools @@ -29257,7 +30199,7 @@ version |versionsuffix |toolchain ``13.4`` | |``GCCcore/11.2.0`` ``14.4`` | |``GCCcore/11.3.0`` ``15.2`` | |``GCCcore/12.2.0`` -``16.1`` | |``GCCcore/12.3.0`` +``16.1`` | |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### POT @@ -29362,8 +30304,8 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: version |toolchain -----------|---------------------------------------------------------------------------------------------- -``170427``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/9.3.0``, ``intel/2018a`` +----------|-------------------------------------------------------------------------------------------------------------- +``170427``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/12.3.0``, ``GCC/9.3.0``, ``intel/2018a`` ### PRC @@ -29420,6 +30362,7 @@ version |versionsuffix|toolchain ------------------|-------------|-------------- ``1.0.0-20200718``|``-R-4.1.2`` |``foss/2021b`` ``1.0.0-20230113``|``-R-4.2.1`` |``foss/2022a`` +``1.0.0-20230501``|``-R-4.3.2`` |``foss/2023a`` ### pretty-yaml @@ -29526,9 +30469,9 @@ 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/12.2.0``, ``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/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ### ProFit @@ -29561,6 +30504,7 @@ version |toolchain ``9.0.0``|``GCCcore/11.3.0`` ``9.1.1``|``GCCcore/12.2.0`` ``9.2.0``|``GCCcore/12.3.0`` +``9.3.1``|``GCCcore/13.2.0`` ### ProjectQ @@ -29593,12 +30537,13 @@ prompt_toolkit is a Python library for building powerful interactive command lin *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------- +----------|------------------|-------------------------------------- ``1.0.3`` |``-Python-2.7.11``|``foss/2016a`` ``1.0.3`` |``-Python-3.5.1`` |``foss/2016a`` ``1.0.6`` |``-Python-2.7.12``|``foss/2016b``, ``intel/2016b`` ``1.0.6`` |``-Python-3.5.2`` |``intel/2016b`` ``1.0.13``|``-Python-2.7.12``|``intel/2016b`` +``3.0.36``| |``GCCcore/12.2.0``, ``GCCcore/13.2.0`` ### proovread @@ -29669,6 +30614,7 @@ version |toolchain ``3.21.9`` |``GCCcore/10.3.0`` ``23.0`` |``GCCcore/12.2.0`` ``24.0`` |``GCCcore/12.3.0`` +``25.3`` |``GCCcore/13.2.0`` ### protobuf-python @@ -29698,6 +30644,7 @@ version |versionsuffix |toolchain ``3.19.4``| |``GCCcore/11.3.0`` ``4.23.0``| |``GCCcore/12.2.0`` ``4.24.0``| |``GCCcore/12.3.0`` +``4.25.3``| |``GCCcore/13.2.0`` ### protozero @@ -29723,6 +30670,16 @@ version |toolchain ``2.3.3`` |``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``2.3.5`` |``GCCcore/11.3.0``, ``GCCcore/12.3.0`` +### PSASS + +PSASS (Pooled Sequencing Analysis for Sex Signal) is a software to compare pooled sequencing datasets from two groups (usually two sexes). Results from PSASS can be easily visualized using the sgtr R package. PSASS is integrated in a Snakemake workflow to perform all required steps starting from a genome and reads files. + +*homepage*: + +version |toolchain +---------|-------------- +``3.1.0``|``GCC/12.3.0`` + ### pscom ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. @@ -29787,9 +30744,10 @@ This software package infers population size history from a diploid sequence usi *homepage*: -version |toolchain ----------|------------------------------ -``0.6.5``|``foss/2016a``, ``foss/2018a`` +version |toolchain +------------------|------------------------------ +``0.6.5`` |``foss/2016a``, ``foss/2018a`` +``0.6.5_20221121``|``GCC/12.3.0`` ### psmpi @@ -29857,6 +30815,7 @@ pstoedit translates PostScript and PDF graphics into other vector formats version |toolchain --------|------------------------------------ ``3.70``|``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``3.78``|``GCC/11.3.0`` ### psutil @@ -29877,6 +30836,16 @@ version |versionsuffix |toolchain ``5.9.4``| |``GCCcore/11.2.0`` ``5.9.5``| |``GCCcore/12.2.0`` +### psycopg + +Psycopg is the most popular PostgreSQL adapter for the Python programming language. + +*homepage*: + +version |toolchain +----------|-------------------------------------- +``3.1.18``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` + ### psycopg2 Psycopg is the most popular PostgreSQL adapter for the Python programming language. @@ -29890,6 +30859,7 @@ version |versionsuffix |toolchain ``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`` +``2.9.9``| |``GCCcore/12.3.0`` ### ptemcee @@ -29952,6 +30922,7 @@ version |toolchain ---------|-------------- ``2.5.1``|``foss/2021a`` ``2.7.0``|``foss/2022b`` +``2.8.0``|``foss/2023a`` ### purge_dups @@ -30022,10 +30993,10 @@ py-cpuinfo gets CPU info with pure Python. *homepage*: version |toolchain ----------|---------------------------------------------------------- +---------|-------------------------------------------------------------------------------------------------- ``5.0.0``|``system`` ``8.0.0``|``GCCcore/11.2.0`` -``9.0.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``9.0.0``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### py3Dmol @@ -30102,9 +31073,9 @@ PyBerny is an optimizer of molecular geometries with respect to the total energy *homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- +---------|-----------------|------------------------------ ``0.6.2``|``-Python-3.8.2``|``intel/2020a`` -``0.6.3``| |``foss/2022a`` +``0.6.3``| |``foss/2022a``, ``foss/2022b`` ### pyBigWig @@ -30224,8 +31195,8 @@ PyCheMPS2 is a python interface to CheMPS2, for compilation without MPI. CheMPS2 *homepage*: version |toolchain -----------|-------------- -``1.8.12``|``foss/2022a`` +----------|------------------------------ +``1.8.12``|``foss/2022a``, ``foss/2022b`` ### Pychopper @@ -30287,9 +31258,10 @@ pycodestyle is a tool to check your Python code against some of the style conven *homepage*: -version |versionsuffix |toolchain ----------|-----------------|--------------- -``2.5.0``|``-Python-3.6.4``|``intel/2018a`` +version |versionsuffix |toolchain +----------|-----------------|--------------- +``2.5.0`` |``-Python-3.6.4``|``intel/2018a`` +``2.11.1``| |``foss/2022a`` ### PyCogent @@ -30365,11 +31337,14 @@ Data validation and settings management using Python type hinting. *homepage*: -version |versionsuffix |toolchain -----------|-----------------|------------------ -``1.6.1`` |``-Python-3.7.4``|``GCCcore/8.3.0`` -``1.10.2``| |``GCCcore/11.2.0`` -``1.10.4``| |``GCCcore/11.3.0`` +version |versionsuffix |toolchain +-----------|-----------------|-------------------------------------- +``1.6.1`` |``-Python-3.7.4``|``GCCcore/8.3.0`` +``1.10.2`` | |``GCCcore/11.2.0`` +``1.10.4`` | |``GCCcore/11.3.0`` +``1.10.13``| |``GCCcore/12.3.0`` +``2.5.3`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.6.4`` | |``GCCcore/13.2.0`` ### PyDatastream @@ -30396,6 +31371,7 @@ version |versionsuffix |toolchain ``2.1.2``|``-Python-3.8.2`` |``GCCcore/9.3.0`` ``2.2.2``| |``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2.3.0``| |``GCCcore/11.3.0`` +``2.4.4``| |``GCCcore/12.3.0`` ### pydicom-seg @@ -30428,6 +31404,7 @@ version |toolchain ---------|------------------------------------------------------------------------------ ``1.4.1``|``GCCcore/9.3.0``, ``foss/2019b`` ``1.4.2``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.0``|``GCCcore/12.3.0`` ### pyEGA3 @@ -30483,13 +31460,14 @@ pyfaidx: efficient pythonic random access to fasta subsequences *homepage*: version |versionsuffix |toolchain ------------|-----------------|------------------ +-----------|-----------------|-------------------------------------- ``0.5.9.5``| |``GCCcore/10.2.0`` ``0.5.9.5``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``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`` +``0.8.1.1``| |``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### pyfasta @@ -30568,13 +31546,14 @@ version |versionsuffix |toolchain ### PyFrag -PyFrag 2019 resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring of the entire computational process along with the extraction and plotting of relevant information from large amounts of data; and 3) the analysis and presentation of these data in a clear and informative way. This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2019 +The PyFrag program is specially designed to facilitate the analysis of reaction mechanism in a more efficient and user-friendly way. PyFrag resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring of the entire computational process along with the extraction and plotting of relevant information from large amounts of data; and 3) the analysis and presentation of these data in a clear and informative way. This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2023 *homepage*: -version |versionsuffix|toolchain ------------------|-------------|--------------- -``2019-20220216``|``-ASA`` |``intel/2020b`` +version |versionsuffix|toolchain +---------------------|-------------|--------------- +``2019-20220216`` |``-ASA`` |``intel/2020b`` +``2023-dev.20240220``|``-ASA`` |``intel/2022a`` ### pygame @@ -30755,6 +31734,16 @@ version |toolchain ---------|-------------- ``1.3.1``|``foss/2021a`` +### PyInstaller + +PyInstaller bundles a Python application and all its dependencies into a single package. The user can run the packaged app without installing a Python interpreter or any modules. + +*homepage*: + +version |toolchain +---------|------------------ +``6.3.0``|``GCCcore/12.3.0`` + ### pyiron An integrated development environment (IDE) for computational materials science. @@ -30837,6 +31826,7 @@ version |versionsuffix |toolchain ``2017.10.16``|``-Python-3.6.3`` |``intel/2017b`` ``2022.0.4`` | |``foss/2020b`` ``2023.3.10`` | |``foss/2022a`` +``2023.12.18``| |``foss/2023a`` ### pymatgen-db @@ -30980,6 +31970,9 @@ version |versionsuffix |toolchain ``2021.1.2`` | |``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2021.2.13``| |``foss/2021b`` ``2021.2.13``|``-CUDA-11.4.1`` |``foss/2021b`` +``2023.1.4`` | |``foss/2022a``, ``foss/2023a`` +``2023.1.4`` |``-CUDA-11.7.0`` |``foss/2022a`` +``2023.1.4`` |``-CUDA-12.1.1`` |``foss/2023a`` ### PyOpenGL @@ -30997,6 +31990,7 @@ version |versionsuffix |toolchain ``3.1.3b2``|``-Python-2.7.15``|``foss/2018b`` ``3.1.5`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` ``3.1.6`` | |``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.1.7`` | |``GCCcore/12.3.0`` ### pyparsing @@ -31008,6 +32002,7 @@ version |versionsuffix |toolchain ---------|------------------|------------------ ``2.4.6``|``-Python-2.7.16``|``GCCcore/8.3.0`` ``3.0.9``| |``GCCcore/11.3.0`` +``3.1.1``| |``GCCcore/12.3.0`` ### pyperf @@ -31116,28 +32111,39 @@ version |versionsuffix |toolchain ``4.12.1``|``-Python-2.7.14``|``foss/2018a`` ``4.12.3``|``-Python-2.7.15``|``fosscuda/2018b`` +### PyQt-builder + +PyQt-builder is the PEP 517 compliant build system for PyQt and projects that extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules. + +*homepage*: + +version |toolchain +----------|------------------ +``1.15.4``|``GCCcore/12.3.0`` + ### PyQt5 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. *homepage*: -version |versionsuffix |toolchain -----------|------------------|---------------------------------------------------------- -``5.7`` |``-Python-2.7.11``|``foss/2016a`` -``5.7.1`` |``-Python-2.7.12``|``intel/2016b`` -``5.8.2`` |``-Python-2.7.13``|``intel/2017a`` -``5.9.2`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.9.2`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` -``5.11.3``|``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` -``5.12.1``|``-Python-2.7.15``|``GCCcore/8.2.0`` -``5.12.1``|``-Python-3.7.2`` |``GCCcore/8.2.0`` -``5.13.2``|``-Python-3.7.4`` |``GCCcore/8.3.0`` -``5.15.1``| |``GCCcore/10.2.0`` -``5.15.1``|``-Python-3.8.2`` |``GCCcore/9.3.0`` -``5.15.4``| |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.15.5``| |``GCCcore/11.3.0`` -``5.15.7``| |``GCCcore/12.2.0`` +version |versionsuffix |toolchain +-----------|------------------|---------------------------------------------------------- +``5.7`` |``-Python-2.7.11``|``foss/2016a`` +``5.7.1`` |``-Python-2.7.12``|``intel/2016b`` +``5.8.2`` |``-Python-2.7.13``|``intel/2017a`` +``5.9.2`` |``-Python-2.7.14``|``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.9.2`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` +``5.11.3`` |``-Python-3.6.6`` |``foss/2018b``, ``intel/2018b`` +``5.12.1`` |``-Python-2.7.15``|``GCCcore/8.2.0`` +``5.12.1`` |``-Python-3.7.2`` |``GCCcore/8.2.0`` +``5.13.2`` |``-Python-3.7.4`` |``GCCcore/8.3.0`` +``5.15.1`` | |``GCCcore/10.2.0`` +``5.15.1`` |``-Python-3.8.2`` |``GCCcore/9.3.0`` +``5.15.4`` | |``GCCcore/10.2.0``, ``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`` ### PyQtGraph @@ -31219,6 +32225,7 @@ version |versionsuffix |toolchain ``1.5.2``| |``fosscuda/2020b`` ``1.8.0``|``-CUDA-11.3.1``|``foss/2021a`` ``1.8.4``| |``foss/2022a`` +``1.8.4``|``-CUDA-11.7.0``|``foss/2022a`` ### Pyro4 @@ -31273,6 +32280,7 @@ version |versionsuffix |toolchain ``0.19.1`` | |``GCC/11.3.0`` ``0.20.0`` | |``GCC/11.3.0`` ``0.21.0`` | |``GCC/12.2.0`` +``0.22.0`` | |``GCC/12.3.0`` ### pysamstats @@ -31311,10 +32319,11 @@ pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Singl *homepage*: -version |versionsuffix |toolchain -----------|-----------------|------------------------------- -``0.10.3``|``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` -``0.12.1``| |``foss/2022a`` +version |versionsuffix |toolchain +-------------------|-----------------|------------------------------- +``0.10.3`` |``-Python-3.8.2``|``foss/2020a``, ``intel/2020a`` +``0.12.1`` | |``foss/2022a`` +``0.12.1-20240311``| |``foss/2023a`` ### PySCF @@ -31327,6 +32336,7 @@ version |versionsuffix |toolchain ``1.6.3``|``-Python-3.7.2``|``foss/2019a`` ``1.7.6``| |``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` ``2.1.1``| |``foss/2022a`` +``2.4.0``| |``foss/2022b`` ### pysheds @@ -31413,6 +32423,7 @@ 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`` +``0.2.1``| |``GCC/12.3.0`` ### pysqlite @@ -31483,6 +32494,7 @@ version |versionsuffix |toolchain ``3.6.1`` |``-Python-3.7.4`` |``foss/2019b``, ``fosscuda/2019b`` ``3.6.1`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ``3.8.0`` | |``foss/2022a``, ``foss/2022b`` +``3.9.2`` | |``foss/2023b`` ### PyTensor @@ -31554,8 +32566,8 @@ Runs tests multiple times to expose flakiness. *homepage*: version |toolchain ----------|-------------------------------------- -``1.1.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +---------|------------------------------------------------------------------------------ +``1.1.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### pytest-rerunfailures @@ -31567,6 +32579,7 @@ version |toolchain --------|-------------------------------------- ``11.1``|``GCCcore/11.3.0`` ``12.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``14.0``|``GCCcore/13.2.0`` ### pytest-shard @@ -31575,8 +32588,19 @@ pytest plugin to support parallelism across multiple machines. Shards tests bas *homepage*: version |toolchain ----------|-------------------------------------- -``0.1.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +---------|------------------------------------------------------------------------------ +``0.1.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` + +### pytest-workflow + +Configure workflow/pipeline tests using yaml files. pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by using YAML files for the test configuration. Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, pytest-workflow makes testing easy. pytest-workflow is build on top of the pytest test framework. + +*homepage*: + +version |toolchain +---------|------------------ +``2.0.1``|``GCCcore/12.2.0`` +``2.1.0``|``GCCcore/13.2.0`` ### pytest-xdist @@ -31684,6 +32708,16 @@ version |toolchain ``2023.06``|``GCCcore/12.3.0`` ``2023.10``|``GCCcore/13.2.0`` +### python-casacore + +Python-casacore is a set of Python bindings for casacore, a c++ library used in radio astronomy. Python-casacore replaces the old pyrap. + +*homepage*: + +version |toolchain +---------|-------------- +``3.5.2``|``foss/2023b`` + ### python-docx python-docx is a Python library for creating and updating Microsoft Word (.docx) files @@ -31720,6 +32754,7 @@ version |versionsuffix |toolchain ``0.9.8`` | |``foss/2021b`` ``0.10.3`` | |``foss/2022a`` ``0.10.6`` | |``foss/2022b`` +``0.11.4`` | |``foss/2023a`` ### python-irodsclient @@ -31730,6 +32765,7 @@ A python API for iRODS version |toolchain ---------|-------------------------------------- ``1.1.4``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.0.0``|``GCCcore/12.3.0`` ### python-isal @@ -31742,6 +32778,7 @@ 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``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.6.1`` |``GCCcore/13.2.0`` ### python-Levenshtein @@ -31764,6 +32801,7 @@ LibSBML Python API. version |toolchain ----------|-------------- ``5.19.7``|``foss/2021a`` +``5.20.2``|``foss/2023b`` ### python-louvain @@ -31801,7 +32839,7 @@ 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`` +``1.3.4`` | |``foss/2022b``, ``foss/2023a`` ### python-telegram-bot @@ -31834,6 +32872,7 @@ version |toolchain ``2.0.2``|``GCCcore/10.2.0`` ``3.1.0``|``GCCcore/11.3.0`` ``3.2.0``|``GCCcore/12.2.0`` +``3.4.1``|``GCCcore/12.3.0`` ### pythran @@ -31852,7 +32891,7 @@ Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTo *homepage*: version |versionsuffix |toolchain -----------|-----------------------------|---------------------------------------------- +----------|-----------------------------|-------------------------------------------------------------- ``0.3.1`` |``-Python-2.7.14`` |``fosscuda/2017b`` ``0.3.1`` |``-Python-3.6.3`` |``fosscuda/2017b`` ``0.3.1`` |``-Python-3.6.4`` |``intel/2018a`` @@ -31885,7 +32924,18 @@ version |versionsuffix |toolchain ``1.13.1``| |``foss/2022a``, ``foss/2022b`` ``1.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` ``2.0.1`` | |``foss/2022a``, ``foss/2022b`` -``2.1.2`` | |``foss/2022a``, ``foss/2022b`` +``2.1.2`` | |``foss/2022a``, ``foss/2022b``, ``foss/2023a``, ``foss/2023b`` +``2.1.2`` |``-CUDA-12.1.1`` |``foss/2023a`` + +### pytorch-3dunet + +PyTorch implementation of 3D U-Net and its variants: - UNet3D: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation - ResidualUNet3D: Residual 3D U-Net based on Superhuman Accuracy on the SNEMI3D Connectomics Challenge - ResidualUNetSE3D: Similar to ResidualUNet3D with the addition of Squeeze and Excitation blocks based on Deep Learning Semantic Segmentation for High- Resolution Medical Volumes. Original squeeze and excite paper: Squeeze-and- Excitation Networks The code allows for training the U-Net for both: semantic segmentation (binary and multi-class) and regression problems (e.g. de-noising, learning deconvolutions). + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``1.6.0``|``-CUDA-11.7.0``|``foss/2022a`` ### PyTorch-bundle @@ -31921,6 +32971,7 @@ version |versionsuffix |toolchain ``1.6.3``| |``foss/2020b``, ``fosscuda/2020b`` ``1.6.3``|``-Python-3.7.4-PyTorch-1.8.1``|``fosscuda/2019b`` ``2.0.1``|``-PyTorch-1.9.0`` |``fosscuda/2020b`` +``2.1.0``|``-PyTorch-1.12.0`` |``foss/2022a`` ``2.1.0``|``-PyTorch-1.12.0-CUDA-11.7.0``|``foss/2022a`` ``2.1.0``|``-PyTorch-1.12.1-CUDA-11.3.1``|``foss/2021a`` @@ -31935,6 +32986,7 @@ version |versionsuffix |toolchain ``0.4.9`` |``-CUDA-11.3.1``|``foss/2021a`` ``0.4.12``| |``foss/2022a`` ``0.4.12``|``-CUDA-11.7.0``|``foss/2022a`` +``0.4.13``| |``foss/2023a`` ### PyTorch-Image-Models @@ -31961,6 +33013,9 @@ version |versionsuffix |toolchain ``1.7.7``|``-CUDA-11.7.0``|``foss/2022a`` ``1.8.4``| |``foss/2022a`` ``1.8.4``|``-CUDA-11.7.0``|``foss/2022a`` +``2.1.2``| |``foss/2022b`` +``2.2.1``| |``foss/2023a`` +``2.2.1``|``-CUDA-12.1.1``|``foss/2023a`` ### PyTorch3D @@ -32034,6 +33089,17 @@ version |toolchain ---------|------------------------------ ``1.0.0``|``foss/2021b``, ``foss/2022a`` +### pyXDF + +Python package for working with XDF files. + +*homepage*: + +version |toolchain +----------|-------------- +``1.16.3``|``foss/2021a`` +``1.16.5``|``gfbf/2023a`` + ### PyYAML PyYAML is a YAML parser and emitter for the Python programming language. @@ -32088,12 +33154,23 @@ version |versionsuffix |toolchain ``24.0.1``| |``GCCcore/11.3.0`` ``25.1.0``| |``GCCcore/12.2.0`` ``25.1.1``| |``GCCcore/12.3.0`` +``25.1.2``| |``GCCcore/13.2.0`` ## Q -[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) - [Qt6](#qt6) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [QuickTree](#quicktree) - [Quip](#quip) - [Quorum](#quorum) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) +[q2-krona](#q2-krona) - [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) - [Qt6](#qt6) - [Qtconsole](#qtconsole) - [QtKeychain](#qtkeychain) - [QTLtools](#qtltools) - [qtop](#qtop) - [QtPy](#qtpy) - [Qualimap](#qualimap) - [Quandl](#quandl) - [QuantumESPRESSO](#quantumespresso) - [QUAST](#quast) - [QuaZIP](#quazip) - [QuickFF](#quickff) - [QuickPIC](#quickpic) - [QuickTree](#quicktree) - [Quip](#quip) - [Quorum](#quorum) - [QuPath](#qupath) - [QuTiP](#qutip) - [Qwt](#qwt) - [QwtPolar](#qwtpolar) + + +### q2-krona + +QIIME2 plugin for creating Krona plots +*homepage*: + +version |toolchain +------------|------------------ +``20220124``|``GCCcore/11.3.0`` ### Q6 @@ -32136,9 +33213,9 @@ A python service for easy execution of many tasks inside a single allocation. *homepage*: version |toolchain -----------|------------------------------ +----------|---------------------------------------------- ``0.12.3``|``foss/2021a`` -``0.13.1``|``foss/2022a``, ``gfbf/2022b`` +``0.13.1``|``foss/2022a``, ``gfbf/2022b``, ``gfbf/2023b`` ### qcint @@ -32224,7 +33301,7 @@ 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``, ``GCCcore/12.3.0`` +``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``, ``GCCcore/13.2.0`` ### QIIME @@ -32254,6 +33331,7 @@ version |toolchain ``2022.8`` |``system`` ``2022.11`` |``system`` ``2023.5.1``|``foss/2022a`` +``2023.7.0``|``foss/2022a`` ### Qiskit @@ -32367,6 +33445,7 @@ version |toolchain ``5.15.5`` |``GCCcore/11.3.0`` ``5.15.7`` |``GCCcore/12.2.0`` ``5.15.10``|``GCCcore/12.3.0`` +``5.15.13``|``GCCcore/13.2.0`` ### Qt5Webkit @@ -32388,6 +33467,7 @@ Qt is a comprehensive cross-platform C++ application framework. version |toolchain ---------|------------------ ``6.5.2``|``GCCcore/12.3.0`` +``6.6.3``|``GCCcore/13.2.0`` ### Qtconsole @@ -32401,6 +33481,7 @@ version |versionsuffix |toolchain ``5.0.2``| |``GCCcore/10.2.0`` ``5.3.2``| |``GCCcore/11.2.0`` ``5.4.0``| |``GCCcore/11.3.0`` +``5.5.1``| |``GCCcore/12.3.0`` ### QtKeychain @@ -32446,6 +33527,7 @@ version |versionsuffix |toolchain ``1.9.0``|``-Python-3.7.4``|``GCCcore/8.3.0`` ``2.2.1``| |``GCCcore/11.2.0`` ``2.3.0``| |``GCCcore/11.3.0`` +``2.4.1``| |``GCCcore/12.3.0`` ### Qualimap @@ -32495,6 +33577,7 @@ version |versionsuffix|toolchain ``7.0`` | |``foss/2021b``, ``intel/2021b`` ``7.1`` | |``foss/2022a``, ``intel/2022a`` ``7.2`` | |``foss/2022b``, ``foss/2023a``, ``intel/2022b`` +``7.3`` | |``foss/2023a``, ``intel/2023a`` ### QUAST @@ -32577,6 +33660,16 @@ version |toolchain ---------|--------------- ``1.1.1``|``intel/2017a`` +### QuPath + +QuPath is open source software for bioimage analysis. QuPath is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|------------------ +``0.5.0``|``-Java-17`` |``GCCcore/12.3.0`` + ### QuTiP QuTiP is open-source software for simulating the dynamics of open quantum systems. @@ -32595,12 +33688,12 @@ The Qwt library contains GUI Components and utility classes which are primarily *homepage*: version |toolchain ----------|---------------------------------------------------- +---------|---------------------------------------------------------- ``6.1.2``|``intel/2016a`` ``6.1.3``|``foss/2016b``, ``intel/2016b`` ``6.1.4``|``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``6.1.5``|``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``6.2.0``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.2.0`` ### QwtPolar @@ -32615,7 +33708,7 @@ version |toolchain ## R -[R](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-bundle-CRAN](#r-bundle-cran) - [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) - [Raptor](#raptor) - [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) - [RCall](#rcall) - [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) - [ResistanceGA](#resistancega) - [resolos](#resolos) - [Restrander](#restrander) - [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](#r) - [R-bundle-Bioconductor](#r-bundle-bioconductor) - [R-bundle-CRAN](#r-bundle-cran) - [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) - [radian](#radian) - [RaGOO](#ragoo) - [Ragout](#ragout) - [RagTag](#ragtag) - [rampart](#rampart) - [randfold](#randfold) - [randrproto](#randrproto) - [rapidcsv](#rapidcsv) - [RapidJSON](#rapidjson) - [rapidNJ](#rapidnj) - [rapidtide](#rapidtide) - [RAPSearch2](#rapsearch2) - [Raptor](#raptor) - [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) - [RCall](#rcall) - [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) - [remake](#remake) - [ReMatCh](#rematch) - [REMORA](#remora) - [renderproto](#renderproto) - [RepastHPC](#repasthpc) - [RepeatMasker](#repeatmasker) - [RepeatModeler](#repeatmodeler) - [RepeatScout](#repeatscout) - [request](#request) - [requests](#requests) - [RERconverge](#rerconverge) - [ResistanceGA](#resistancega) - [resolos](#resolos) - [Restrander](#restrander) - [rethinking](#rethinking) - [retworkx](#retworkx) - [RevBayes](#revbayes) - [RFdiffusion](#rfdiffusion) - [rgdal](#rgdal) - [rgeos](#rgeos) - [Rgurobi](#rgurobi) - [rhdf5](#rhdf5) - [RHEIA](#rheia) - [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 @@ -32654,6 +33747,7 @@ version |versionsuffix |toolchain ``4.2.1``| |``foss/2022a`` ``4.2.2``| |``foss/2022b`` ``4.3.2``| |``gfbf/2023a`` +``4.3.3``| |``gfbf/2023b`` ### R-bundle-Bioconductor @@ -32680,6 +33774,7 @@ version |versionsuffix|toolchain ``3.15``|``-R-4.2.0`` |``foss/2021b`` ``3.15``|``-R-4.2.1`` |``foss/2022a`` ``3.16``|``-R-4.2.2`` |``foss/2022b`` +``3.18``|``-R-4.3.2`` |``foss/2023a`` ### R-bundle-CRAN @@ -32772,13 +33867,13 @@ Ultrafast consensus module for raw de novo genome assembly of long uncorrected r *homepage*: version |toolchain -----------|-------------------------------------- +----------|------------------------------------------------------------------------------ ``1.3.2`` |``GCCcore/8.2.0`` ``1.4.7`` |``GCCcore/8.2.0``, ``gcccuda/2019b`` ``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``, ``GCCcore/11.3.0`` +``1.5.0`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ### radeontop @@ -32790,6 +33885,16 @@ version|toolchain -------|------------------ ``1.3``|``GCCcore/10.3.0`` +### radian + +radian is an alternative console for the R program with multiline editing and rich syntax highlight. + +*homepage*: + +version |toolchain +---------|-------------- +``0.6.9``|``foss/2022b`` + ### RaGOO A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome @@ -32871,8 +33976,8 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: version |toolchain -------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------- -``1.1.0`` |``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`` +------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +``1.1.0`` |``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/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.1.0-20230928``|``GCCcore/12.3.0`` ### rapidNJ @@ -32950,6 +34055,7 @@ version |versionsuffix |toolchain ``1.2.10``| |``foss/2021b`` ``1.3.4`` | |``foss/2022a`` ``1.3.8`` | |``foss/2022b`` +``1.3.9`` | |``foss/2023a`` ### rasterstats @@ -33074,7 +34180,7 @@ 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 ----------|-------------|---------- @@ -33083,6 +34189,8 @@ version |versionsuffix|toolchain ``1.56.0``|``-amd64`` |``system`` ``1.57.0``| |``system`` ``1.63.1``|``-amd64`` |``system`` +``1.65.2``| |``system`` +``1.66.0``| |``system`` ### Rcorrector @@ -33172,6 +34280,7 @@ version |toolchain ``2022-06-01``|``GCCcore/11.3.0`` ``2023-03-01``|``GCCcore/12.2.0`` ``2023-08-01``|``GCCcore/12.3.0`` +``2024-03-01``|``GCCcore/13.2.0`` ### re2c @@ -33251,6 +34360,8 @@ version |toolchain ---------|------------------------------ ``6.2.6``|``GCC/10.3.0``, ``GCC/11.2.0`` ``7.0.8``|``GCC/11.3.0`` +``7.2.3``|``GCCcore/12.3.0`` +``7.2.4``|``GCCcore/13.2.0`` ### redis-py @@ -33259,10 +34370,11 @@ The Python interface to the Redis key-value store. *homepage*: version |toolchain ----------|-------------- +---------|------------------ ``4.3.1``|``foss/2021a`` ``4.3.3``|``foss/2021b`` ``4.5.1``|``foss/2022a`` +``5.0.1``|``GCCcore/12.3.0`` ### Redundans @@ -33360,6 +34472,16 @@ version |versionsuffix |toolchain ``3.0.4`` | |``foss/2017b``, ``intel/2017b`` ``3.0_beta.2018.08.02``| |``fosscuda/2018a``, ``intel/2018a`` +### remake + +remake is an enhanced version of GNU Make that adds improved error reporting, better tracing, profiling and a debugger + +*homepage*: + +version |toolchain +---------------|------------------ +``4.3+dbg-1.6``|``GCCcore/11.3.0`` + ### ReMatCh Reads mapping against target sequences, checking mapping and consensus sequences production @@ -33501,6 +34623,16 @@ version |toolchain ------------|------------------ ``20230713``|``GCCcore/12.2.0`` +### rethinking + +R package that contains tools for conducting both quick quadratic approximation of the posterior distribution as well as Hamiltonian Monte Carlo. + +*homepage*: + +version |versionsuffix|toolchain +-----------------|-------------|-------------- +``2.40-20230914``|``-R-4.3.2`` |``foss/2023a`` + ### retworkx retworkx is a general purpose graph library for python3 written in Rust to take advantage of the performance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current) networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for any python application. The project was originally started to build a faster directed graph to use as the underlying data structure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usage in Qiskit and other applications. @@ -33585,6 +34717,16 @@ version |versionsuffix|toolchain ``2.16.0``|``-R-3.2.3`` |``intel/2016a`` ``2.18.0``|``-R-3.3.1`` |``intel/2016b`` +### RHEIA + +Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems + +*homepage*: + +version |toolchain +---------|-------------- +``1.1.6``|``foss/2022a`` + ### RheoTool RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows. @@ -33628,9 +34770,9 @@ version |versionsuffix|toolchain ### rioxarray -geospatial xarray extension powered by rasterio +Geospatial xarray extension powered by rasterio -*homepage*: +*homepage*: version |versionsuffix |toolchain ----------|-----------------|--------------- @@ -33639,6 +34781,7 @@ version |versionsuffix |toolchain ``0.1.1`` |``-Python-3.8.2``|``foss/2020a`` ``0.11.1``| |``foss/2021b`` ``0.14.0``| |``foss/2022a`` +``0.15.0``| |``foss/2023a`` ### ripunzip @@ -33671,6 +34814,7 @@ Rivet toolkit (Robust Independent Validation of Experiment and Theory) To use y version |versionsuffix |toolchain ---------|-----------------|--------------- ``3.1.7``|``-HepMC3-3.2.5``|``gompi/2022a`` +``3.1.9``|``-HepMC3-3.2.6``|``gompi/2023a`` ### rjags @@ -33727,13 +34871,14 @@ version |toolchain ### rMATS-turbo -rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). +rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io). *homepage*: version |toolchain ---------|-------------- ``4.1.1``|``foss/2020b`` +``4.2.0``|``gfbf/2023a`` ### RMBlast @@ -33760,6 +34905,7 @@ version |toolchain ---------|-------------- ``1.2.3``|``GCC/8.3.0`` ``1.4.3``|``GCC/11.2.0`` +``2.0.1``|``GCC/12.3.0`` ### RNA-SeQC @@ -33901,6 +35047,7 @@ version |toolchain ---------|------------------ ``4.5.0``|``GCCcore/11.2.0`` ``5.4.4``|``GCCcore/11.3.0`` +``5.6.0``|``GCCcore/11.3.0`` ### rocminfo @@ -34032,14 +35179,15 @@ version |toolchain rpy2 is an interface to R running embedded in a Python process. -*homepage*: +*homepage*: -version |versionsuffix |toolchain ----------|------------------|------------------------------ -``2.7.9``|``-Python-2.7.12``|``foss/2016b`` -``2.8.2``|``-Python-2.7.13``|``intel/2017a`` -``3.2.6``|``-Python-3.7.4`` |``foss/2019b`` -``3.4.5``| |``foss/2021a``, ``foss/2021b`` +version |versionsuffix |toolchain +----------|------------------|------------------------------ +``2.7.9`` |``-Python-2.7.12``|``foss/2016b`` +``2.8.2`` |``-Python-2.7.13``|``intel/2017a`` +``3.2.6`` |``-Python-3.7.4`` |``foss/2019b`` +``3.4.5`` | |``foss/2021a``, ``foss/2021b`` +``3.5.15``| |``foss/2023a`` ### RQGIS3 @@ -34148,6 +35296,7 @@ version |toolchain -----------|------------------------------------------------------------------------------ ``0.17.21``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``0.17.32``|``GCCcore/12.3.0`` +``0.18.6`` |``GCCcore/13.2.0`` ### Ruby @@ -34172,6 +35321,7 @@ version |toolchain ``3.0.3``|``GCCcore/11.3.0`` ``3.0.5``|``GCCcore/11.3.0`` ``3.2.2``|``GCCcore/12.2.0`` +``3.3.0``|``GCCcore/12.3.0`` ### Ruby-Tk @@ -34229,6 +35379,8 @@ version |toolchain ``1.65.0``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.70.0``|``GCCcore/12.3.0`` ``1.73.0``|``GCCcore/13.2.0`` +``1.75.0``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.76.0``|``GCCcore/13.2.0`` ### rustworkx @@ -34243,7 +35395,7 @@ version |toolchain ## S -[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) - [scCODA](#sccoda) - [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-build-core](#scikit-build-core) - [scikit-cuda](#scikit-cuda) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-lego](#scikit-lego) - [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) - [scrublet](#scrublet) - [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) - [SEACells](#seacells) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [segmentation-models-pytorch](#segmentation-models-pytorch) - [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) - [simanneal](#simanneal) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [Simstrat](#simstrat) - [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-ESA](#snap-esa) - [SNAP-ESA-python](#snap-esa-python) - [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++) - [solo](#solo) - [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) - [SPEI](#spei) - [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) - [starparser](#starparser) - [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) - [SUPPA](#suppa) - [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) - [SYMMETRICA](#symmetrica) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synapseclient](#synapseclient) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) +[S-Lang](#s-lang) - [s3fs](#s3fs) - [S4](#s4) - [Sabre](#sabre) - [safestringlib](#safestringlib) - [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) - [scCODA](#sccoda) - [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-build-core](#scikit-build-core) - [scikit-cuda](#scikit-cuda) - [scikit-extremes](#scikit-extremes) - [scikit-image](#scikit-image) - [scikit-learn](#scikit-learn) - [scikit-lego](#scikit-lego) - [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) - [scrublet](#scrublet) - [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) - [SEACells](#seacells) - [SearchGUI](#searchgui) - [SeaView](#seaview) - [SECAPR](#secapr) - [Seeder](#seeder) - [segemehl](#segemehl) - [segment-anything](#segment-anything) - [segmentation-models](#segmentation-models) - [segmentation-models-pytorch](#segmentation-models-pytorch) - [SeisSol](#seissol) - [SelEstim](#selestim) - [SELFIES](#selfies) - [SemiBin](#semibin) - [semla](#semla) - [Sentence-Transformers](#sentence-transformers) - [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) - [simanneal](#simanneal) - [simint](#simint) - [SimNIBS](#simnibs) - [SimPEG](#simpeg) - [SIMPLE](#simple) - [Simple-DFTD3](#simple-dftd3) - [SimpleElastix](#simpleelastix) - [SimpleITK](#simpleitk) - [simpy](#simpy) - [Simstrat](#simstrat) - [SimVascular](#simvascular) - [SingleM](#singlem) - [Singular](#singular) - [sinto](#sinto) - [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) - [sktime](#sktime) - [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-ESA](#snap-esa) - [SNAP-ESA-python](#snap-esa-python) - [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++) - [solo](#solo) - [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) - [SPEI](#spei) - [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) - [SQLAlchemy](#sqlalchemy) - [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) - [starparser](#starparser) - [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) - [SUPPA](#suppa) - [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) - [SYMMETRICA](#symmetrica) - [SYMPHONY](#symphony) - [sympy](#sympy) - [synapseclient](#synapseclient) - [synthcity](#synthcity) - [SyRI](#syri) - [sysbench](#sysbench) - [Szip](#szip) ### S-Lang @@ -34256,6 +35408,16 @@ version |toolchain ---------|------------- ``2.3.0``|``GCC/4.9.2`` +### s3fs + +S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3.. + +*homepage*: + +version |toolchain +-------------|-------------- +``2023.12.2``|``foss/2023a`` + ### S4 S4 stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell’s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA, also called the Fourier Modal Method (FMM)) and the S-matrix algorithm. @@ -34276,6 +35438,16 @@ version |toolchain --------------|-------------- ``2013-09-28``|``GCC/12.2.0`` +### safestringlib + +The Secure Development Lifecycle (SDL) recommends banning certain C Library functions because they directly contribute to security vulnerabilities such as buffer overflows. However routines for the manipulation of strings and memory buffers are common in software and firmware, and are essential to accomplish certain programming tasks. Safer replacements for these functions that avoid or prevent serious security vulnerabilities (e.g. buffer overflows, string format attacks, conversion overflows/underflows, etc.) are available in the SafeString Library. + +*homepage*: + +version |toolchain +------------|---------------------------- +``20240228``|``intel-compilers/2023.1.0`` + ### 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. @@ -34339,6 +35511,7 @@ version |versionsuffix |toolchain ``1.3.0`` | |``gompi/2020a`` ``1.4.0`` | |``GCC/11.2.0``, ``gompi/2020b`` ``1.9.0`` | |``GCC/11.3.0`` +``1.10.1``| |``GCC/12.2.0`` ### SALMON-TDDFT @@ -34362,6 +35535,7 @@ version |toolchain ``0.7.1``|``system`` ``0.8.0``|``GCC/10.2.0`` ``0.8.2``|``GCC/10.3.0`` +``1.0.1``|``GCC/11.3.0`` ### samblaster @@ -34415,7 +35589,7 @@ version |versionsuffix |toolchain ----------|-----------------|--------------------------------------------------------------------------------------------------------------------------------------- ``0.1.17``| |``intel/2017a`` ``0.1.19``| |``GCC/10.3.0``, ``foss/2016a``, ``foss/2016b`` -``0.1.20``| |``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` +``0.1.20``| |``GCC/12.3.0``, ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` ``1.2`` | |``foss/2016b`` ``1.3`` | |``foss/2016a``, ``intel/2016a`` ``1.3.1`` | |``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -34430,7 +35604,7 @@ version |versionsuffix |toolchain ``1.10`` | |``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` | |``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` ``1.12`` | |``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -``1.13`` | |``GCC/10.3.0``, ``GCC/11.3.0`` +``1.13`` | |``GCC/10.3.0``, ``GCC/11.3.0``, ``GCC/12.3.0`` ``1.14`` | |``GCC/11.2.0`` ``1.15`` | |``GCC/11.2.0`` ``1.15.1``| |``GCC/11.2.0``, ``GCC/11.3.0`` @@ -34499,6 +35673,7 @@ version |versionsuffix |toolchain ``9.7.0.4`` |``-Java-1.7.0_79`` |``system`` ``9.7.0.21``|``-Java-1.8.0_162``|``system`` ``9.9.1.7`` |``-Java-13`` |``system`` +``12.4`` |``-Java-21`` |``system`` ### SBCL @@ -34511,6 +35686,7 @@ version |toolchain ``2.0.9`` |``GCCcore/9.3.0`` ``2.2.1`` |``GCCcore/10.3.0`` ``2.3.11``|``GCCcore/11.3.0`` +``2.4.1`` |``GCCcore/12.3.0`` ### sbt @@ -34532,7 +35708,7 @@ 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``, ``foss/2022b`` +``1.0.4``|``foss/2022a``, ``foss/2022b``, ``foss/2023a`` ### ScaLAPACK @@ -34595,6 +35771,7 @@ version |toolchain ``1.5.13``|``GCCcore/11.2.0`` ``1.5.20``|``GCCcore/11.3.0`` ``1.5.26``|``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.5.35``|``GCCcore/13.2.0`` ### scanpy @@ -34608,6 +35785,7 @@ version |toolchain ``1.8.1``|``foss/2020b``, ``foss/2021a`` ``1.8.2``|``foss/2021b`` ``1.9.1``|``foss/2021b``, ``foss/2022a`` +``1.9.8``|``foss/2023a`` ### scArches @@ -34627,8 +35805,8 @@ scCODA allows for identification of compositional changes in high-throughput seq *homepage*: version |toolchain ----------|-------------- -``0.1.9``|``foss/2021a`` +---------|------------------------------ +``0.1.9``|``foss/2021a``, ``foss/2023a`` ### sceasy @@ -34650,6 +35828,7 @@ version |versionsuffix|toolchain ---------|-------------|-------------- ``1.2.4``|``-R-4.1.0`` |``foss/2021a`` ``1.3.0``|``-R-4.2.1`` |``foss/2022a`` +``1.3.0``|``-R-4.3.2`` |``foss/2023a`` ### scGeneFit @@ -34715,6 +35894,7 @@ version |toolchain ---------|-------------- ``1.1.1``|``foss/2022a`` ``1.1.3``|``foss/2021a`` +``1.1.4``|``foss/2023a`` ### scib-metrics @@ -34769,6 +35949,7 @@ version |versionsuffix |toolchain ---------|-----------------|-------------------------------------------------------------- ``0.5.6``|``-Python-3.8.2``|``foss/2020a`` ``0.5.7``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``0.5.9``| |``foss/2023a`` ### scikit-build @@ -34805,6 +35986,16 @@ version |versionsuffix |toolchain ---------|-----------------|------------------ ``0.5.3``|``-Python-3.7.4``|``fosscuda/2019b`` +### scikit-extremes + +scikit-extremes is a basic statistical package to perform univariate extreme value calculations using Python + +*homepage*: + +version |toolchain +-------------|-------------- +``2022.4.10``|``foss/2022a`` + ### scikit-image scikit-image is a collection of algorithms for image processing. @@ -34874,7 +36065,9 @@ version |versionsuffix |toolchain ``1.0.2`` | |``foss/2021b`` ``1.1.2`` | |``foss/2022a``, ``intel/2022a`` ``1.2.1`` | |``gfbf/2022b`` -``1.3.1`` | |``gfbf/2023a`` +``1.3.1`` | |``gfbf/2023a``, ``iimkl/2023a`` +``1.3.2`` | |``gfbf/2023b`` +``1.4.0`` | |``gfbf/2023b`` ### scikit-lego @@ -34885,6 +36078,7 @@ We love scikit learn but very often we find ourselves writing custom transformer version |toolchain ----------|-------------- ``0.6.16``|``foss/2022a`` +``0.7.4`` |``foss/2023a`` ### scikit-misc @@ -34895,6 +36089,7 @@ Miscellaneous tools for data analysis and scientific computing version |toolchain ---------|------------------------------ ``0.1.4``|``foss/2021a``, ``foss/2022a`` +``0.3.1``|``foss/2023a`` ### scikit-multilearn @@ -34993,7 +36188,7 @@ 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`` +``2023.07``| |``gfbf/2023a``, ``iimkl/2023a`` ``2023.11``| |``gfbf/2023.09``, ``gfbf/2023b`` ### SCnorm @@ -35046,6 +36241,7 @@ version |versionsuffix |toolchain ``4.2.0`` | |``GCCcore/11.2.0`` ``4.4.0`` | |``GCCcore/11.3.0`` ``4.5.2`` | |``GCCcore/12.3.0`` +``4.6.0`` | |``GCCcore/13.2.0`` ### SCOOP @@ -35091,6 +36287,8 @@ version |versionsuffix |toolchain ``8.1`` |``-CUDA-12.0.0``|``gompi/2022b`` ``8.1`` |``-CUDA-12.1.1``|``gompi/2023a`` ``8.3`` | |``gompi/2022b`` +``8.4`` | |``gompi/2023b`` +``8.4`` |``-CUDA-12.4.0``|``gompi/2023b`` ### SCOTCH @@ -35108,6 +36306,7 @@ 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`` +``7.0.1`` |``-int64`` |``gompi/2022a`` ``7.0.3`` | |``gompi/2022b``, ``gompi/2023a`` ### scp @@ -35162,6 +36361,7 @@ version |versionsuffix |toolchain ----------|-----------------|-------------- ``0.1.24``|``-Python-3.7.4``|``foss/2019b`` ``0.2.3`` | |``foss/2021a`` +``0.3.1`` | |``foss/2023a`` ### scvi-tools @@ -35300,6 +36500,7 @@ version |versionsuffix |toolchain ``0.11.2``| |``foss/2021a``, ``foss/2021b`` ``0.12.1``| |``foss/2022a`` ``0.12.2``| |``foss/2022b`` +``0.13.2``| |``gfbf/2023a`` ### SEACells @@ -35423,6 +36624,37 @@ version |toolchain ---------|-------------- ``2.1.1``|``GCC/11.2.0`` +### SemiBin + +SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``2.0.2``| |``foss/2022a`` +``2.0.2``|``-CUDA-11.7.0``|``foss/2022a`` + +### semla + +R interface to the Apache Arrow C++ library + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``1.1.6``|``-R-4.3.2`` |``foss/2023a`` + +### Sentence-Transformers + +Sentence Transformers provides an easy method to compute dense vector representations for sentences, paragraphs, and images + +*homepage*: + +version |toolchain +---------|-------------- +``2.2.2``|``foss/2022b`` + ### SentencePiece Unsupervised text tokenizer for Neural Network-based text generation. @@ -35435,6 +36667,7 @@ version |versionsuffix |toolchain ``0.1.94``|``-Python-3.8.2``|``GCC/9.3.0`` ``0.1.96``| |``GCC/10.2.0``, ``GCC/10.3.0`` ``0.1.97``| |``GCC/11.3.0`` +``0.1.99``| |``GCC/12.2.0`` ### sentinelsat @@ -35534,8 +36767,8 @@ C++ interface to HTSlib, BWA-MEM and Fermi. *homepage*: version |toolchain ----------|------------------------------------------------------------- -``1.2.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +---------|----------------------------------------------------------------------------- +``1.2.0``|``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/12.3.0``, ``GCC/9.3.0`` ### Seqmagick @@ -35547,6 +36780,7 @@ version |versionsuffix |toolchain ---------|------------------|-------------- ``0.6.1``|``-Python-2.7.11``|``foss/2016a`` ``0.6.2``|``-Python-2.7.15``|``foss/2018b`` +``0.8.6``| |``foss/2023a`` ### SeqPrep @@ -35568,7 +36802,7 @@ 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`` +``1.4``|``GCC/12.2.0``, ``GCC/12.3.0`` ### Serf @@ -35623,6 +36857,7 @@ version |versionsuffix|toolchain ``4.3.0`` |``-R-4.1.2`` |``foss/2021b`` ``4.3.0`` |``-R-4.2.1`` |``foss/2022a`` ``4.4.0`` |``-R-4.2.2`` |``foss/2022b`` +``5.0.1`` |``-R-4.2.2`` |``foss/2022b`` ### SeuratData @@ -36070,6 +37305,16 @@ version |toolchain ``4.1.2`` |``GCC/8.2.0-2.31.1``, ``system`` ``4.3.2p10``|``gfbf/2022a`` +### sinto + +Sinto is a toolkit for processing aligned single-cell data. + +*homepage*: + +version |toolchain +---------|-------------- +``0.7.4``|``foss/2021a`` + ### SiNVICT SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples obtained by ultra-deep sequencing. @@ -36087,14 +37332,14 @@ 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``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``1.7.7``|``-tools`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### SIP @@ -36112,6 +37357,7 @@ version |versionsuffix |toolchain ``4.19.8`` |``-Python-2.7.14``|``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``4.19.8`` |``-Python-3.6.4`` |``foss/2018a``, ``intel/2018a`` ``4.19.13``|``-Python-2.7.15``|``fosscuda/2018b`` +``6.8.1`` | |``GCCcore/12.3.0`` ### siscone @@ -36122,6 +37368,7 @@ Hadron Seedless Infrared-Safe Cone jet algorithm version |toolchain ---------|------------------ ``3.0.5``|``GCCcore/11.3.0`` +``3.0.6``|``GCCcore/12.3.0`` ### SISSO @@ -36206,6 +37453,17 @@ version |versionsuffix |toolchain ----------|-------------------------------|-------------- ``0.11.0``|``-PyTorch-1.10.0`` |``foss/2021a`` ``0.11.0``|``-PyTorch-1.10.0-CUDA-11.3.1``|``foss/2021a`` +``0.15.0``|``-PyTorch-2.1.2`` |``foss/2023a`` + +### sktime + +sktime is a library for time series analysis in Python. It provides a unified interface for multiple time series learning tasks. Currently, this includes time series classification, regression, clustering, annotation, and forecasting. It comes with time series algorithms and scikit-learn compatible tools to build, tune and validate time series models. + +*homepage*: + +version |toolchain +----------|-------------- +``0.25.0``|``gfbf/2023a`` ### SlamDunk @@ -36245,6 +37503,7 @@ version |versionsuffix |toolchain ``3.15.1``| |``foss/2021a`` ``3.17.2``| |``foss/2022a`` ``3.18.2``| |``intel/2021b`` +``3.20.1``| |``foss/2023a`` ### slepc4py @@ -36379,8 +37638,8 @@ smith-waterman-gotoh alignment algorithm. *homepage*: version |toolchain -------------|------------------------------------------------------------------------------------------------- -``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +------------|--------------------------------------------------------------------------------------------------------------------- +``20160702``|``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### Smoldyn @@ -36443,6 +37702,7 @@ version |versionsuffix |toolchain ``7.18.2``| |``foss/2021b`` ``7.22.0``| |``foss/2022a`` ``7.32.3``| |``foss/2022b`` +``8.4.2`` | |``foss/2023a`` ### SNAP @@ -36495,9 +37755,10 @@ SNAPE-pooled computes the probability distribution for the frequency of the mino *homepage*: -version|toolchain --------|-------------- -``r32``|``foss/2016a`` +version |toolchain +------------|-------------- +``20150707``|``GCC/11.3.0`` +``r32`` |``foss/2016a`` ### snaphu @@ -36523,7 +37784,7 @@ version |toolchain ``1.1.7`` |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` ``1.1.8`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``1.1.9`` |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` -``1.1.10``|``GCCcore/12.3.0`` +``1.1.10``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### Sniffles @@ -36614,6 +37875,7 @@ SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo f version |toolchain ---------|--------------- ``1.0.4``|``intel/2017a`` +``1.0.5``|``GCC/12.3.0`` ### SOAPdenovo2 @@ -36686,8 +37948,8 @@ Sonic is a simple algorithm for speeding up or slowing down speech. However, it *homepage*: version |toolchain -------------|--------------- -``20180202``|``gompi/2020a`` +------------|------------------------------- +``20180202``|``gfbf/2023a``, ``gompi/2020a`` ### SoPlex @@ -36810,7 +38072,7 @@ 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`` +``3.15.4``| |``GCC/12.2.0``, ``GCC/12.3.0`` ``3.15.5``| |``GCC/11.3.0`` ### spaln @@ -36856,6 +38118,7 @@ version |versionsuffix |toolchain ``3.2.1``| |``foss/2021b`` ``3.3.1``| |``foss/2022a`` ``3.5.0``| |``foss/2023a`` +``3.5.1``|``-Java-17`` |``foss/2023a`` ### sparse-neighbors-search @@ -36877,7 +38140,7 @@ version |toolchain ---------|------------------------------------------------------------------------------------------------------------------------------ ``2.0.2``|``foss/2016a`` ``2.0.3``|``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.4``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``2.0.4``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### SpatialDE @@ -36911,6 +38174,7 @@ 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`` +``1.12.0``|``GCCcore/13.2.0`` ### SpectrA @@ -36919,9 +38183,9 @@ Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. *homepage*: version |toolchain ----------|-------------------------------------- +---------|---------------------------------------------------------- ``1.0.0``|``GCC/10.2.0`` -``1.0.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.0.1``|``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0`` ### spectral.methods @@ -36941,8 +38205,8 @@ The Edinburgh Speech Tools Library is a collection of C++ class, functions and r *homepage*: <['http://festvox.org/festival/']> version |toolchain ----------|----------------- -``2.5.0``|``GCCcore/9.3.0`` +---------|------------------------------------- +``2.5.0``|``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ### SPEI @@ -36980,7 +38244,7 @@ version |toolchain ### spglib-python -Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. +Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. *homepage*: @@ -36999,7 +38263,7 @@ version |versionsuffix |toolchain ``1.16.3`` | |``foss/2021b``, ``intel/2021b`` ``2.0.0`` | |``foss/2022a``, ``intel/2022a`` ``2.0.2`` | |``gfbf/2022b`` -``2.1.0`` | |``gfbf/2023a`` +``2.1.0`` | |``gfbf/2023a``, ``iimkl/2023a`` ### Sphinx @@ -37126,6 +38390,7 @@ version |toolchain ``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``, ``GCC/11.3.0``, ``GCC/12.2.0`` +``4.1.0``|``GCC/12.3.0`` ### SPOOLES @@ -37134,8 +38399,8 @@ SPOOLES is a library for solving sparse real and complex linear systems of equa *homepage*: version|toolchain --------|-------------------------------- -``2.2``|``gompi/2021a``, ``gompi/2022b`` +-------|------------------------------------------------- +``2.2``|``gompi/2021a``, ``gompi/2022b``, ``gompi/2023a`` ### SPOTPY @@ -37171,6 +38436,17 @@ version |versionsuffix |toolchain ``4.1.5``|``-Python-3.7.2`` |``foss/2019a`` ``4.1.5``|``-Python-3.8.2`` |``foss/2020a`` +### SQLAlchemy + +SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language. + +*homepage*: + +version |toolchain +----------|-------------------------------------- +``2.0.25``|``GCCcore/12.3.0`` +``2.0.29``|``GCCcore/12.2.0``, ``GCCcore/13.2.0`` + ### SQLite SQLite: SQL Database Engine in a C Library @@ -37248,6 +38524,7 @@ version |versionsuffix |toolchain ``3.0.0`` |``-centos_linux64``|``system`` ``3.0.3`` | |``gompi/2022a`` ``3.0.5`` | |``gompi/2021a`` +``3.0.10`` | |``gompi/2023a`` ### sradownloader @@ -37321,8 +38598,8 @@ SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Si *homepage*: version |toolchain ----------|----------------------------------------------------------------------------- -``1.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +---------|------------------------------------------------------------------------------------------------- +``1.1`` |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0`` ``1.2.4``|``GCCcore/10.3.0`` ### STACEY @@ -37345,6 +38622,7 @@ version |versionsuffix|toolchain ----------|-------------|---------- ``2.3.3`` |``-x86_64`` |``system`` ``2.11.1``|``-x86_64`` |``system`` +``2.13.1``|``-x86_64`` |``system`` ### Stacks @@ -37437,6 +38715,7 @@ version |toolchain ``2.7.10a_alpha_220601``|``GCC/10.3.0`` ``2.7.10b`` |``GCC/11.3.0``, ``GCC/12.2.0`` ``2.7.11a`` |``GCC/12.2.0``, ``GCC/12.3.0`` +``2.7.11b`` |``GCC/12.3.0`` ### STAR-CCM+ @@ -37549,6 +38828,7 @@ version |versionsuffix |toolchain ``0.12.2``| |``foss/2021a`` ``0.13.1``| |``foss/2021b``, ``foss/2022a``, ``intel/2021b`` ``0.14.0``| |``gfbf/2022b`` +``0.14.1``| |``gfbf/2023a``, ``gfbf/2023b`` ### STEAK @@ -37834,16 +39114,17 @@ SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers *homepage*: -version |toolchain ----------|---------------------------------------------------------------------------------------------------------------------------------- -``2.6.2``|``intel/2016b``, ``intel/2018b`` -``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`` -``6.6.0``|``foss/2022b``, ``foss/2023a`` +version |versionsuffix |toolchain +---------|----------------|---------------------------------------------------------------------------------------------------------------------------------- +``2.6.2``| |``intel/2016b``, ``intel/2018b`` +``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`` +``6.6.0``| |``foss/2022b``, ``foss/2023a`` +``6.6.0``|``-CUDA-12.1.1``|``foss/2023a`` ### SunPy @@ -37879,7 +39160,7 @@ 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`` +``8.1.2``| |``foss/2022b``, ``foss/2023a`` ### supermagic @@ -37919,8 +39200,8 @@ Toolset for SV simulation, comparison and filtering *homepage*: version |toolchain ----------------------|-------------- -``1.0.7-19-ged1ca51``|``GCC/11.2.0`` +---------------------|------------------------------ +``1.0.7-19-ged1ca51``|``GCC/11.2.0``, ``GCC/12.2.0`` ### SVclone @@ -38122,7 +39403,7 @@ SymPy is a Python library for symbolic mathematics. It aims to become a full-fe *homepage*: version |versionsuffix |toolchain -----------|------------------|------------------------------- +----------|------------------|---------------------------------------------- ``1.0`` |``-Python-2.7.11``|``foss/2016a``, ``intel/2016a`` ``1.3`` |``-Python-2.7.14``|``intel/2018a`` ``1.3`` |``-Python-2.7.15``|``foss/2018b`` @@ -38136,7 +39417,7 @@ version |versionsuffix |toolchain ``1.9`` | |``foss/2021b``, ``intel/2021b`` ``1.10.1``| |``foss/2022a``, ``intel/2022a`` ``1.11.1``| |``foss/2022a``, ``intel/2022a`` -``1.12`` | |``gfbf/2022b``, ``gfbf/2023a`` +``1.12`` | |``gfbf/2022b``, ``gfbf/2023a``, ``gfbf/2023b`` ### synapseclient @@ -38187,12 +39468,12 @@ Szip compression software, providing lossless compression of scientific data version |toolchain ---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``2.1`` |``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1``|``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/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1``|``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/13.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ## T -[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) - [Triton](#triton) - [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](#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) - [tiny-cuda-nn](#tiny-cuda-nn) - [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) - [tox](#tox) - [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) - [Triton](#triton) - [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 @@ -38225,7 +39506,7 @@ 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`` +``1.1.2``|``GCC/11.3.0``, ``GCC/12.3.0`` ### taco @@ -38294,11 +39575,12 @@ TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry a *homepage*: version |versionsuffix |toolchain ----------|------------------|--------------- +---------|------------------|---------------------------------------------- ``1.0.9``|``-Python-2.7.11``|``intel/2016a`` ``1.2.4``|``-Python-2.7.14``|``intel/2017b`` +``1.2.6``| |``foss/2020b``, ``foss/2021a``, ``foss/2021b`` ``1.2.6``|``-Python-3.7.2`` |``intel/2019a`` -``1.2.6``|``-Python-3.8.2`` |``intel/2020a`` +``1.2.6``|``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` ### tantan @@ -38505,6 +39787,7 @@ version |toolchain ----------|-------------- ``2.8.0`` |``foss/2021a`` ``2.10.0``|``foss/2022a`` +``2.15.1``|``gfbf/2023a`` ### tensorboardX @@ -38512,12 +39795,13 @@ Tensorboard for PyTorch. *homepage*: -version |versionsuffix |toolchain ----------|------------------|---------------------------------- -``2.0`` |``-Python-3.7.4`` |``foss/2019b`` -``2.1`` |``-PyTorch-1.7.1``|``fosscuda/2020b`` -``2.2`` |``-PyTorch-1.7.1``|``foss/2020b``, ``fosscuda/2020b`` -``2.5.1``| |``foss/2022a`` +version |versionsuffix |toolchain +-----------|------------------|---------------------------------- +``2.0`` |``-Python-3.7.4`` |``foss/2019b`` +``2.1`` |``-PyTorch-1.7.1``|``fosscuda/2020b`` +``2.2`` |``-PyTorch-1.7.1``|``foss/2020b``, ``fosscuda/2020b`` +``2.5.1`` | |``foss/2022a`` +``2.6.2.2``| |``foss/2022b``, ``foss/2023a`` ### TensorFlow @@ -38636,6 +39920,7 @@ version |versionsuffix |toolchain ``0.16.0``| |``foss/2021b`` ``0.19.0``| |``foss/2022a`` ``0.19.0``|``-CUDA-11.7.0`` |``foss/2022a`` +``0.20.0``| |``foss/2023a`` ### TensorRT @@ -38750,6 +40035,7 @@ version |toolchain ``6.7`` |``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.8`` |``GCCcore/11.2.0`` ``7.0.2``|``GCCcore/11.3.0`` +``7.1`` |``GCCcore/12.3.0`` ### texlive @@ -38762,7 +40048,7 @@ version |toolchain ``20200406``|``GCCcore/8.3.0`` ``20210324``|``GCC/10.3.0``, ``GCC/11.2.0`` ``20220321``|``GCC/11.2.0`` -``20230313``|``GCC/11.3.0`` +``20230313``|``GCC/11.3.0``, ``GCC/12.3.0`` ### Text-CSV @@ -38925,6 +40211,7 @@ timm is a library containing SOTA computer vision models, layers, utilities, opt version |versionsuffix |toolchain ----------|----------------|-------------- ``0.6.13``|``-CUDA-11.7.0``|``foss/2022a`` +``0.9.7`` |``-CUDA-11.7.0``|``foss/2022a`` ### TINKER @@ -38938,6 +40225,16 @@ version |toolchain ``8.7.2``|``foss/2019b`` ``8.8.1``|``foss/2020a`` +### tiny-cuda-nn + +is a small, self-contained framework for training and querying neural networks. Most notably, it contains a lightning fast "fully fused" multi-layer perceptron (technical paper), a versatile multiresolution hash encoding (technical paper), as well as support for various other input encodings, losses, and optimizers. + +*homepage*: + +version|versionsuffix |toolchain +-------|----------------|-------------- +``1.6``|``-CUDA-11.7.0``|``foss/2022a`` + ### TinyDB TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server. @@ -39101,8 +40398,8 @@ A Tcl/Tk widget for OpenGL rendering. *homepage*: version|toolchain --------|--------------------------------------------------------- -``2.0``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +-------|----------------------------------------------------------------------------- +``2.0``|``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` ### toil @@ -39280,6 +40577,8 @@ version |versionsuffix |toolchain ``0.12.0``|``-PyTorch-1.11.0-CUDA-11.3.1`` |``foss/2021a`` ``0.13.1``| |``foss/2022a`` ``0.13.1``|``-CUDA-11.7.0`` |``foss/2022a`` +``0.14.1``| |``foss/2022b`` +``0.16.0``| |``foss/2023a`` ### tornado @@ -39303,6 +40602,16 @@ version |versionsuffix |toolchain ``8.11.0-2``|``-linux-x86-64``|``system`` ``8.12.0-0``|``-linux-x86-64``|``system`` +### tox + +tox aims to automate and standardize testing in Python + +*homepage*: + +version |toolchain +----------|-------------------------------------- +``3.25.1``|``GCCcore/10.2.0``, ``GCCcore/11.3.0`` + ### tqdm A fast, extensible progress bar for Python and CLI @@ -39327,6 +40636,7 @@ version |versionsuffix |toolchain ``4.64.0``| |``GCCcore/11.3.0`` ``4.64.1``| |``GCCcore/12.2.0`` ``4.66.1``| |``GCCcore/12.3.0`` +``4.66.2``| |``GCCcore/13.2.0`` ### Tracer @@ -39503,8 +40813,8 @@ A tool for automated alignment trimming in large-scale phylogenetic analyses *homepage*: version |toolchain ----------|-------------------------------------------------------------------------------------------------------------------- -``1.4.1``|``GCC/8.2.0-2.31.1``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0``, ``intel/2018a`` +---------|---------------------------------------------------------------------------------------------------------------------------------------- +``1.4.1``|``GCC/8.2.0-2.31.1``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.3.0``, ``GCCcore/9.3.0``, ``intel/2018a`` ### trimesh @@ -39586,6 +40896,7 @@ version |versionsuffix |toolchain ``2.2.1``|``-Python-2.7.15``|``foss/2019a`` ``3.0.0``|``-Python-3.8.2`` |``foss/2020a`` ``3.1.1``| |``foss/2022a`` +``3.2.0``| |``foss/2023a`` ### TRIQS-cthyb @@ -39598,6 +40909,7 @@ version |versionsuffix |toolchain ``2.2.0``|``-Python-2.7.15``|``foss/2019a`` ``3.0.0``|``-Python-3.8.2`` |``foss/2020a`` ``3.1.0``| |``foss/2022a`` +``3.2.1``| |``foss/2023a`` ### TRIQS-dft_tools @@ -39610,6 +40922,7 @@ version |versionsuffix |toolchain ``2.2.0``|``-Python-2.7.15``|``foss/2019a`` ``3.0.0``|``-Python-3.8.2`` |``foss/2020a`` ``3.1.0``| |``foss/2022a`` +``3.2.0``| |``foss/2023a`` ### TRIQS-tprf @@ -39622,6 +40935,7 @@ version |versionsuffix |toolchain ``2.2.0``|``-Python-2.7.15``|``foss/2019a`` ``3.0.0``|``-Python-3.8.2`` |``foss/2020a`` ``3.1.1``| |``foss/2022a`` +``3.2.1``| |``foss/2023a`` ### Triton @@ -39795,12 +41109,12 @@ version|toolchain ### typing-extensions -Typing Extensions - Backported and Experimental Type Hints for Python +Typing Extensions – Backported and Experimental Type Hints for Python *homepage*: version |versionsuffix |toolchain -------------|-----------------|------------------ +------------|-----------------|-------------------------------------- ``3.7.4.3`` | |``GCCcore/10.2.0`` ``3.7.4.3`` |``-Python-3.7.4``|``GCCcore/8.3.0`` ``3.7.4.3`` |``-Python-3.8.2``|``GCCcore/9.3.0`` @@ -39808,6 +41122,8 @@ version |versionsuffix |toolchain ``3.10.0.2``| |``GCCcore/11.2.0`` ``4.3.0`` | |``GCCcore/11.3.0`` ``4.4.0`` | |``GCCcore/10.3.0`` +``4.9.0`` | |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``4.10.0`` | |``GCCcore/13.2.0`` ## U @@ -39855,26 +41171,27 @@ Unified Communication X An open-source production grade communication framework *homepage*: -version |versionsuffix |toolchain -------------|----------------|------------------------------------------------------- -``1.3.1`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.5.0`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.5.0rc1``|``-hpcx`` |``GCCcore/8.2.0`` -``1.5.1`` | |``GCCcore/8.2.0`` -``1.6.1`` | |``GCCcore/8.3.0`` -``1.8.0`` | |``GCCcore/9.3.0`` -``1.8.0`` |``-CUDA-11.0.2``|``GCCcore/9.3.0`` -``1.9.0`` | |``GCCcore/10.2.0`` -``1.9.0`` |``-CUDA-11.1.1``|``GCCcore/10.2.0`` -``1.9.0`` |``-CUDA-11.2.1``|``GCCcore/10.2.0`` -``1.10.0`` | |``GCCcore/10.3.0`` -``1.11.0`` | |``GCCcore/11.2.0`` -``1.11.2`` | |``GCCcore/11.2.0`` -``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`` -``1.15.0`` | |``GCCcore/13.2.0`` +version |versionsuffix |toolchain +--------------|----------------|-------------------------------------------------------------------------------------------------- +``1.3.1`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.5.0`` | |``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.5.0rc1`` |``-hpcx`` |``GCCcore/8.2.0`` +``1.5.1`` | |``GCCcore/8.2.0`` +``1.6.1`` | |``GCCcore/8.3.0`` +``1.8.0`` | |``GCCcore/9.3.0`` +``1.8.0`` |``-CUDA-11.0.2``|``GCCcore/9.3.0`` +``1.9.0`` | |``GCCcore/10.2.0`` +``1.9.0`` |``-CUDA-11.1.1``|``GCCcore/10.2.0`` +``1.9.0`` |``-CUDA-11.2.1``|``GCCcore/10.2.0`` +``1.10.0`` | |``GCCcore/10.3.0`` +``1.11.0`` | |``GCCcore/11.2.0`` +``1.11.2`` | |``GCCcore/11.2.0`` +``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`` +``1.15.0`` | |``GCCcore/13.2.0`` +``1.16.0-rc4``| |``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### UCX-CUDA @@ -39891,7 +41208,7 @@ version |versionsuffix |toolchain ``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`` -``1.15.0``|``-CUDA-12.3.0``|``GCCcore/13.2.0`` +``1.15.0``|``-CUDA-12.4.0``|``GCCcore/13.2.0`` ### ucx-py @@ -39936,7 +41253,7 @@ version |toolchain ``2.2.24``|``intel/2017a`` ``2.2.25``|``foss/2017b``, ``intel/2017b`` ``2.2.26``|``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``2.2.28``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``2.2.28``|``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/13.2.0`` ### UFL @@ -39969,6 +41286,7 @@ version |toolchain ---------|-------------------------------------------------------------- ``0.4.6``|``foss/2020b``, ``fosscuda/2020b`` ``0.5.3``|``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``0.5.5``|``foss/2023a`` ### UMI-tools @@ -39981,6 +41299,7 @@ version |versionsuffix |toolchain ``1.0.0``|``-Python-3.6.6``|``foss/2018b`` ``1.0.1``|``-Python-3.7.4``|``foss/2019b`` ``1.0.1``|``-Python-3.8.2``|``foss/2020a`` +``1.1.4``| |``foss/2023a`` ### umi4cPackage @@ -40019,8 +41338,8 @@ Transparent calculations with uncertainties on the quantities involved (aka erro *homepage*: version |toolchain ----------|-------------- -``3.1.7``|``foss/2021b`` +---------|------------------------------ +``3.1.7``|``foss/2021b``, ``foss/2023a`` ### uncertainty-calibration @@ -40229,7 +41548,7 @@ version |toolchain ## V -[V8](#v8) - [vaeda](#vaeda) - [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) - [VSCode](#vscode) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) +[V8](#v8) - [vaeda](#vaeda) - [Vala](#vala) - [Valgrind](#valgrind) - [Vamb](#vamb) - [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) - [VSCode](#vscode) - [VSEARCH](#vsearch) - [vt](#vt) - [VTK](#vtk) - [VTune](#vtune) - [VV](#vv) - [VXL](#vxl) ### V8 @@ -40261,9 +41580,10 @@ Vala is a programming language using modern high level abstractions without impo *homepage*: -version |toolchain -----------|------------------ -``0.52.4``|``GCCcore/10.3.0`` +version |toolchain +-----------|------------------ +``0.52.4`` |``GCCcore/10.3.0`` +``0.56.14``|``GCCcore/12.3.0`` ### Valgrind @@ -40283,6 +41603,16 @@ version |toolchain ``3.20.0``|``gompi/2022a`` ``3.21.0``|``gompi/2022b``, ``gompi/2023a`` +### Vamb + +Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation. + +*homepage*: + +version |versionsuffix |toolchain +---------|----------------|-------------- +``3.0.9``|``-CUDA-11.5.2``|``foss/2021b`` + ### Vampir The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. @@ -40422,6 +41752,7 @@ version |versionsuffix |toolchain ``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`` +``1.0.9``|``-R-4.3.2`` |``gfbf/2023a`` ### vcfnp @@ -40486,8 +41817,8 @@ Sequence assembler for very short reads *homepage*: version |versionsuffix |toolchain -----------|----------------|------------------------------------------------------------- -``1.2.10``|``-mt-kmer_191``|``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +----------|----------------|----------------------------------------------------------------------------- +``1.2.10``|``-mt-kmer_191``|``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2023a`` ``1.2.10``|``-mt-kmer_37`` |``intel/2017a`` ### VEP @@ -40506,6 +41837,7 @@ version |versionsuffix |toolchain ``103.1``| |``GCC/10.2.0`` ``105`` | |``GCC/11.2.0`` ``107`` | |``GCC/11.3.0`` +``111`` | |``GCC/12.2.0`` ### verifyBamID @@ -40567,6 +41899,7 @@ version |versionsuffix |toolchain ``8.1.1209``|``-Python-3.7.2`` |``GCCcore/8.2.0`` ``9.0.0950``| |``GCCcore/11.3.0`` ``9.0.1434``| |``GCCcore/12.2.0`` +``9.1.0004``| |``GCCcore/12.3.0`` ### VirSorter @@ -40652,7 +41985,7 @@ VisPy is a high-performance interactive 2D/3D data visualization library levera version |toolchain ----------|------------------------------- ``0.6.6`` |``foss/2020b``, ``intel/2020b`` -``0.12.2``|``foss/2022a`` +``0.12.2``|``foss/2022a``, ``gfbf/2023a`` ### vitessce-python @@ -40726,8 +42059,8 @@ 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/11.3.0``, ``GCCcore/12.2.0``, ``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/12.2.0``, ``GCCcore/12.3.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` ### vsc-base @@ -40806,6 +42139,7 @@ version |versionsuffix |toolchain ``5.2.11`` | |``system`` ``5.3.0`` | |``system`` ``5.3.1`` | |``system`` +``5.4.0`` | |``system`` ### vsc-mympirun-scoop @@ -40962,8 +42296,8 @@ Widely applicable Lattics-Boltzmann from Erlangen is a block-structured high-pe *homepage*: version|toolchain --------|-------------- -``6.1``|``foss/2021a`` +-------|------------------------------ +``6.1``|``foss/2021a``, ``foss/2022b`` ### wandb @@ -40985,13 +42319,13 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: version |versionsuffix|toolchain ------------|-------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-----------|-------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ``1.2`` | |``intel/2016.02-GCC-4.9`` ``2.0.1`` | |``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``2.0.1.1``|``-abinit`` |``intel/2018b`` ``2.1.0`` | |``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` | |``intel/2018b`` -``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``gomkl/2021a``, ``gomkl/2023a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2023a`` +``3.1.0`` | |``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``foss/2023a``, ``gomkl/2021a``, ``gomkl/2023a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intel/2022b``, ``intel/2023a`` ### WannierTools @@ -41033,8 +42367,8 @@ The FITS "World Coordinate System" (WCS) standard defines keywords and usage tha *homepage*: version |toolchain ---------|------------------------------ -``7.11``|``GCC/11.2.0``, ``GCC/11.3.0`` +--------|---------------------------------------------- +``7.11``|``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/13.2.0`` ### WCT @@ -41112,6 +42446,7 @@ The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that t version |toolchain ---------|------------------ ``2.3.3``|``GCCcore/11.3.0`` +``2.3.4``|``GCCcore/12.3.0`` ### wget @@ -41128,6 +42463,7 @@ version |toolchain ``1.21.1``|``GCCcore/10.3.0`` ``1.21.2``|``GCCcore/11.2.0`` ``1.21.3``|``GCCcore/11.3.0`` +``1.21.4``|``GCCcore/13.2.0`` ### wgsim @@ -41163,6 +42499,8 @@ version|toolchain ``1.1``|``foss/2020b``, ``foss/2021a`` ``1.4``|``foss/2021b`` ``1.7``|``foss/2022a`` +``2.1``|``foss/2022b`` +``2.2``|``foss/2023a`` ### wheel @@ -41195,6 +42533,7 @@ version |toolchain ``19.1``|``intel/2019a`` ``19.2``|``intel/2020b`` ``21.1``|``intel/2021a``, ``intel/2021b`` +``23.2``|``intel/2021b`` ### WildMagic @@ -41339,10 +42678,11 @@ A collection of diagnostic and interpolation routines for use with output from *homepage*: -version |versionsuffix |toolchain ----------|-----------------|--------------- -``1.2.0``|``-Python-3.6.4``|``intel/2018a`` -``1.3.1``|``-Python-3.6.6``|``intel/2018b`` +version |versionsuffix |toolchain +-----------|-----------------|--------------- +``1.2.0`` |``-Python-3.6.4``|``intel/2018a`` +``1.3.1`` |``-Python-3.6.6``|``intel/2018b`` +``1.3.4.1``| |``foss/2023a`` ### WSClean @@ -41351,8 +42691,8 @@ WSClean (w-stacking clean) is a fast generic widefield imager. It implements sev *homepage*: version|toolchain --------|-------------- -``3.4``|``foss/2022a`` +-------|------------------------------ +``3.4``|``foss/2022a``, ``foss/2023b`` ### wtdbg2 @@ -41415,7 +42755,7 @@ version |toolchain ## X -[X11](#x11) - [x13as](#x13as) - [x264](#x264) - [x265](#x265) - [XALT](#xalt) - [xarray](#xarray) - [XBeach](#xbeach) - [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) - [XOOPIC](#xoopic) - [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) - [XBeach](#xbeach) - [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) - [XOOPIC](#xoopic) - [xorg-macros](#xorg-macros) - [xpdf](#xpdf) - [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 @@ -41636,9 +42976,9 @@ XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on *homepage*: version |versionsuffix |toolchain -------------|------------------|---------------------------------------------------------- +------------|------------------|------------------------------------------------------------------------------ ``2.1.0`` | |``GCCcore/9.3.0`` -``2.1.1`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``2.1.1`` | |``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``20180122``|``-Python-2.7.14``|``intel/2017b`` ``20190127``|``-Python-3.7.2`` |``foss/2019a`` @@ -41659,9 +42999,9 @@ XCrySDen is a crystalline and molecular structure visualisation program aiming a *homepage*: version |toolchain -----------|-------------------------------------------------------------------------------- +----------|------------------------------------------------------------------------------------------------- ``1.5.60``|``intel/2019a`` -``1.6.2`` |``foss/2019b``, ``foss/2020b``, ``foss/2022a``, ``intel/2019b``, ``intel/2022a`` +``1.6.2`` |``foss/2019b``, ``foss/2020b``, ``foss/2022a``, ``intel/2019b``, ``intel/2021b``, ``intel/2022a`` ### xdotool @@ -41686,6 +43026,7 @@ version |toolchain ``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/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/12.3.0`` +``3.2.5``|``GCCcore/13.2.0`` ### xESMF @@ -41783,6 +43124,7 @@ version |toolchain ``3.0.8``|``GCCcore/11.3.0`` ``3.1.2``|``GCCcore/12.2.0`` ``3.1.3``|``GCCcore/12.3.0`` +``3.1.9``|``GCCcore/13.2.0`` ### XMDS2 @@ -41845,6 +43187,7 @@ version |versionsuffix |toolchain ``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`` +``2.0209``| |``GCCcore/12.3.0`` ### XML-Parser @@ -41931,6 +43274,16 @@ version |toolchain ``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``, ``GCCcore/13.2.0`` +### xpdf + +Xpdf was first released in 1995. It was written, and is still developed, by Derek Noonburg. Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source. + +*homepage*: + +version |toolchain +--------|------------------ +``4.04``|``GCCcore/12.3.0`` + ### XPLOR-NIH A System for X-ray Crystallography and NMR @@ -42002,7 +43355,7 @@ version |versionsuffix |toolchain ``6.5.0`` | |``foss/2021b`` ``6.5.1`` | |``foss/2022a`` ``6.6.0`` | |``foss/2022a``, ``intel/2022a`` -``6.6.1`` | |``foss/2023a`` +``6.6.1`` | |``gfbf/2023a`` ### xtensor @@ -42063,6 +43416,7 @@ version |toolchain ---------|---------------------------------------------------------- ``0.8.0``|``GCCcore/11.2.0`` ``0.8.1``|``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``0.8.2``|``GCCcore/12.3.0`` ### XZ @@ -42086,7 +43440,7 @@ version |versionsuffix |toolchain ## Y -[YACS](#yacs) - [Yade](#yade) - [yaff](#yaff) - [Yambo](#yambo) - [yaml-cpp](#yaml-cpp) - [YANK](#yank) - [YAPS](#yaps) - [Yasm](#yasm) - [YAXT](#yaxt) - [Yices](#yices) - [YODA](#yoda) +[YACS](#yacs) - [Yade](#yade) - [yaff](#yaff) - [Yambo](#yambo) - [yaml-cpp](#yaml-cpp) - [YANK](#yank) - [YAPS](#yaps) - [Yasm](#yasm) - [YAXT](#yaxt) - [Yices](#yices) - [YODA](#yoda) - [yt](#yt) ### YACS @@ -42128,7 +43482,7 @@ version |versionsuffix |toolchain ``1.4.5`` |``-Python-2.7.15`` |``intel/2018b`` ``1.5.0`` |``-Python-2.7.15`` |``intel/2018b`` ``1.5.0`` |``-Python-3.7.2`` |``intel/2019a`` -``1.6.0`` | |``foss/2020b`` +``1.6.0`` | |``foss/2020b``, ``foss/2023a`` ``1.6.0`` |``-Python-3.7.2`` |``intel/2019a`` ``1.6.0`` |``-Python-3.7.4`` |``foss/2019b``, ``intel/2019b`` ``1.6.0`` |``-Python-3.8.2`` |``foss/2020a``, ``intel/2020a`` @@ -42202,6 +43556,7 @@ version |toolchain ``0.9.1`` |``gompi/2021a`` ``0.9.2`` |``iimpi/2021b`` ``0.9.2.1``|``gompi/2021b`` +``0.10.0`` |``gompi/2022b`` ### Yices @@ -42212,6 +43567,7 @@ Yices 2 is an SMT solver that decides the satisfiability of formulas containing version |toolchain ---------|------------------ ``2.6.2``|``GCCcore/10.2.0`` +``2.6.4``|``GCCcore/12.2.0`` ### YODA @@ -42222,11 +43578,22 @@ Yet more Objects for (High Energy Physics) Data Analysis version |toolchain ---------|-------------- ``1.9.7``|``GCC/11.3.0`` +``1.9.9``|``GCC/12.3.0`` + +### yt + +yt is an open-source, permissively-licensed python package for analyzing and visualizing volumetric data. + +*homepage*: + +version |toolchain +---------|-------------- +``4.3.0``|``foss/2022a`` ## Z -[Z3](#z3) - [zarr](#zarr) - [ZeroMQ](#zeromq) - [zeus-mcmc](#zeus-mcmc) - [zfp](#zfp) - [Zgoubi](#zgoubi) - [ZIMPL](#zimpl) - [zingeR](#zinger) - [Zip](#zip) - [zlib](#zlib) - [zlib-ng](#zlib-ng) - [zlibbioc](#zlibbioc) - [Zopfli](#zopfli) - [ZPAQ](#zpaq) - [zsh](#zsh) - [zstd](#zstd) +[Z3](#z3) - [zarr](#zarr) - [Zeo++](#zeo++) - [ZeroMQ](#zeromq) - [zeus-mcmc](#zeus-mcmc) - [zfp](#zfp) - [Zgoubi](#zgoubi) - [ZIMPL](#zimpl) - [zingeR](#zinger) - [Zip](#zip) - [zlib](#zlib) - [zlib-ng](#zlib-ng) - [zlibbioc](#zlibbioc) - [Zopfli](#zopfli) - [ZPAQ](#zpaq) - [zsh](#zsh) - [zstd](#zstd) - [zUMIs](#zumis) ### Z3 @@ -42250,7 +43617,7 @@ version |versionsuffix |toolchain ``4.10.2``|``-Python-3.10.4``|``GCCcore/11.3.0`` ``4.12.2``| |``GCCcore/12.2.0``, ``GCCcore/12.3.0`` ``4.12.2``|``-Python-3.10.8``|``GCCcore/12.2.0`` -``4.12.2``|``-Python-3.11.3``|``GCCcore/12.3.0`` +``4.13.0``| |``GCCcore/13.2.0`` ### zarr @@ -42267,6 +43634,16 @@ version |versionsuffix |toolchain ``2.13.3``| |``foss/2021b``, ``foss/2022a`` ``2.16.0``| |``foss/2022b`` +### Zeo++ + +Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. + +*homepage*: + +version|toolchain +-------|---------------------------- +``0.3``|``intel-compilers/2023.1.0`` + ### ZeroMQ ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. @@ -42433,3 +43810,13 @@ version |toolchain ``1.5.0``|``GCCcore/11.2.0`` ``1.5.2``|``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ``1.5.5``|``GCCcore/12.3.0``, ``GCCcore/13.2.0`` + +### zUMIs + +A fast and flexible pipeline to process RNA sequencing data with UMIs. + +*homepage*: + +version |versionsuffix|toolchain +---------|-------------|-------------- +``2.9.7``|``-R-4.3.2`` |``foss/2023a`` diff --git a/mkdocs.yml b/mkdocs.yml index 0f79fc30c..3350aca15 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -157,7 +157,7 @@ extra: provider: google property: G-BLVCH6991S easybuild: - version: 4.9.0 + version: 4.9.1 # add links in bottom right social: - icon: fontawesome/brands/twitter @@ -196,9 +196,11 @@ plugins: - index.md # necessary for search to work - search - # redirects for original EasyBuild documentation to avoid broken URLs - redirects: redirect_maps: + # redirect removed pages to sensible alternative + easybuild-v5/proposed-changes/: easybuild-v5/index.md + # redirects for original EasyBuild documentation to avoid broken URLs en/latest/Archived-easyconfigs.html: archived-easyconfigs.md en/latest/Backup_modules.html: backup-modules.md en/latest/Changelog.html: changelog-docs.md