From a90b12b5600ed44dc2093ed6d56811fdf7cdea3a Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 13 Nov 2020 12:15:29 +0000 Subject: [PATCH 1/6] Fix ``run_tests.sh`` invocation --- planemo/galaxy/test/structures.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/galaxy/test/structures.py b/planemo/galaxy/test/structures.py index 8273ac72e..97c93bbae 100644 --- a/planemo/galaxy/test/structures.py +++ b/planemo/galaxy/test/structures.py @@ -39,7 +39,7 @@ def __init__( def build(self): xunit_report_file = self.xunit_report_file sd_report_file = self.structured_report_file - cmd = "sh run_tests.sh $COMMON_STARTUP_ARGS --report_file %s" % shlex_quote(self.html_report_file) + cmd = "./run_tests.sh $COMMON_STARTUP_ARGS --report_file %s" % shlex_quote(self.html_report_file) if xunit_report_file: cmd += " --xunit_report_file %s" % shlex_quote(xunit_report_file) if sd_report_file: From 4682840fd6c7b6e3e9bad4330aa1088949c3d131 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 13 Nov 2020 12:17:11 +0000 Subject: [PATCH 2/6] Do not use mutable argument defaults --- planemo/galaxy/test/actions.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/planemo/galaxy/test/actions.py b/planemo/galaxy/test/actions.py index fabe84d0e..45c91f8b6 100644 --- a/planemo/galaxy/test/actions.py +++ b/planemo/galaxy/test/actions.py @@ -127,13 +127,15 @@ def run_in_config(ctx, config, run=run_galaxy_command, test_data_target_dir=None ) -def handle_reports_and_summary(ctx, structured_data, exit_code=None, kwds={}): +def handle_reports_and_summary(ctx, structured_data, exit_code=None, kwds=None): """Produce reports and print summary, return 0 if tests passed. If ``exit_code`` is set - use underlying test source for return code and test success determination, otherwise infer from supplied test data. """ + if kwds is None: + kwds = {} handle_reports(ctx, structured_data, kwds) summary_exit_code = _handle_summary( structured_data, From 9be60bfba404245b60012068f6df576e9cf5c5f5 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 23 Nov 2020 16:48:33 +0000 Subject: [PATCH 3/6] Drop support for Python 3.5, add support for Python 3.9 --- .circleci/config.yml | 10 +++++----- CONTRIBUTING.rst | 10 +++++----- planemo/options.py | 2 +- setup.py | 6 +++--- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1f7284f4a..605d1afef 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -5,7 +5,7 @@ jobs: tox-env: type: string docker: - - image: circleci/python:3.5-node + - image: circleci/python:3.6-node steps: - checkout - run: git submodule sync @@ -19,7 +19,7 @@ workflows: matrix: parameters: tox-env: - - "py35-diagnostic-unit-servebasic-gx-dev" - - "py35-unit-nonredundant-noclientbuild-noshed-gx-2005" - - "py35-unit-nonredundant-noclientbuild-noshed-gx-dev" - - "py35-unit-nonredundant-noclientbuild-noshed" + - "py36-diagnostic-unit-servebasic-gx-dev" + - "py36-unit-nonredundant-noclientbuild-noshed-gx-2005" + - "py36-unit-nonredundant-noclientbuild-noshed-gx-dev" + - "py36-unit-nonredundant-noclientbuild-noshed" diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 085e650bc..77593f70a 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -106,7 +106,7 @@ Before you submit a pull request, check that it meets these guidelines: 1. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring. -2. The pull request should work for Python >=3.5. Check +2. The pull request should work for Python >=3.6. Check https://travis-ci.org/galaxyproject/planemo/pull_requests and make sure that the tests pass for all supported Python versions. @@ -118,7 +118,7 @@ To run a subset of tests:: % make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py' This will use Tox_ to run the specified tests using Python 3.7. ``ENV`` here -can be used to specify different Python version (e.g. ``py35`` or +can be used to specify different Python version (e.g. ``py36`` or ``py37``). Even more granularity is also possible by specifying specific test methods.:: @@ -148,7 +148,7 @@ Tox_ is a tool to automate testing across different Python versions. The testing environment. Planemo defines the following environments: ``py37-lint`` - Lint the planemo code using Python 3.7.. + Lint the planemo code using Python 3.7. ``py37-lint_docs`` Lint the docs reStructuredText. @@ -156,8 +156,8 @@ testing environment. Planemo defines the following environments: ``py37-lint_docstrings`` Lint the project Python docstrings (doesn't pass currently). -``py35-unit-quick`` - Run the fastest unit tests (with least external dependencies) on Python 3.5. +``py36-unit-quick`` + Run the fastest unit tests (with least external dependencies) on Python 3.6. ``py36-unit-nonredundant-noclientbuild-gx-2005`` Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05. diff --git a/planemo/options.py b/planemo/options.py index 9a4175036..c17e6fe2c 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -159,7 +159,7 @@ def galaxy_python_version(): '--galaxy_python_version', use_global_config=True, default=None, - type=click.Choice(['3', '3.5', '3.6', '3.7', '3.8']), + type=click.Choice(['3', '3.6', '3.7', '3.8', '3.9']), help="Python version to start Galaxy under", ) diff --git a/setup.py b/setup.py index 83ff04ac3..315d89501 100644 --- a/setup.py +++ b/setup.py @@ -10,8 +10,8 @@ except ImportError: from distutils.core import setup -if sys.version_info < (3, 5): - sys.stderr.write("ERROR: planemo requires at least Python Version 3.5\n") +if sys.version_info < (3, 6): + sys.stderr.write("ERROR: planemo requires at least Python Version 3.6\n") sys.exit(1) # Allow installer to turn off dependency on lxml by setting the environment variable @@ -123,10 +123,10 @@ def get_var(var_name): 'Topic :: Software Development :: Testing', 'Natural Language :: English', "Programming Language :: Python :: 3", - 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', ], test_suite=TEST_DIR, tests_require=test_requirements From 0d71db4a2894508c0437db68f9efe0cc8d8bbd0e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 23 Nov 2020 19:27:45 +0000 Subject: [PATCH 4/6] Use `yaml.safe_load()` --- tests/test_cmd_dockstore_init.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_cmd_dockstore_init.py b/tests/test_cmd_dockstore_init.py index b12a86d66..e2bfcba2a 100644 --- a/tests/test_cmd_dockstore_init.py +++ b/tests/test_cmd_dockstore_init.py @@ -16,7 +16,7 @@ def test_plain_init(self): self._check_exit_code(init_cmd) assert os.path.exists(".dockstore.yml") with open(".dockstore.yml", "r") as f: - dockstore_config = yaml.load(f) + dockstore_config = yaml.safe_load(f) assert str(dockstore_config["version"]) == "1.2" assert "workflows" in dockstore_config assert len(dockstore_config["workflows"]) == 1 From e7edb69ed771b414864b85b80827c6ed02813367 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 23 Nov 2020 16:52:51 +0000 Subject: [PATCH 5/6] Rebuild docs --- docs/commands.rst | 7 ++- docs/commands/ci_find_repos.rst | 6 +- docs/commands/ci_find_tools.rst | 3 + docs/commands/clone.rst | 5 +- docs/commands/conda_build.rst | 3 + docs/commands/conda_env.rst | 3 + docs/commands/conda_init.rst | 3 + docs/commands/conda_install.rst | 6 ++ docs/commands/conda_lint.rst | 1 + docs/commands/conda_search.rst | 3 + docs/commands/container_register.rst | 9 +++ docs/commands/create_alias.rst | 26 ++++++++ docs/commands/database_create.rst | 8 +++ docs/commands/database_delete.rst | 8 +++ docs/commands/database_list.rst | 8 +++ docs/commands/delete_alias.rst | 26 ++++++++ docs/commands/docker_build.rst | 3 + docs/commands/docker_shell.rst | 5 ++ docs/commands/lint.rst | 5 ++ docs/commands/list_alias.rst | 25 ++++++++ docs/commands/list_invocations.rst | 25 ++++++++ docs/commands/list_repos.rst | 2 + docs/commands/mull.rst | 5 ++ docs/commands/mulled_init.rst | 3 + docs/commands/normalize.rst | 3 + docs/commands/profile_create.rst | 14 +++++ docs/commands/profile_delete.rst | 8 +++ docs/commands/pull_request.rst | 5 +- docs/commands/run.rst | 57 +++++++++++++++-- docs/commands/serve.rst | 49 +++++++++++++-- docs/commands/share_test.rst | 5 +- docs/commands/shed_create.rst | 9 +++ docs/commands/shed_diff.rst | 10 +++ docs/commands/shed_init.rst | 5 ++ docs/commands/shed_lint.rst | 5 ++ docs/commands/shed_serve.rst | 56 +++++++++++++++-- docs/commands/shed_test.rst | 39 ++++++++++-- docs/commands/shed_update.rst | 12 ++++ docs/commands/shed_upload.rst | 12 ++++ docs/commands/test.rst | 64 ++++++++++++++++++-- docs/commands/test_reports.rst | 3 + docs/commands/tool_init.rst | 9 +++ docs/commands/training_fill_data_library.rst | 3 + docs/commands/training_generate_from_wf.rst | 50 +++++++++++++-- docs/commands/training_init.rst | 51 ++++++++++++++-- docs/commands/workflow_convert.rst | 49 +++++++++++++-- docs/commands/workflow_edit.rst | 49 +++++++++++++-- docs/commands/workflow_job_init.rst | 2 +- docs/commands/workflow_lint.rst | 1 + docs/commands/workflow_test_init.rst | 9 ++- docs/commands/workflow_upload.rst | 25 ++++++++ docs/installation.rst | 2 +- docs/planemo.commands.rst | 39 ++++++++++++ docs/planemo.conda_verify.rst | 1 - docs/planemo.cwl.rst | 1 - docs/planemo.database.rst | 1 - docs/planemo.engine.rst | 1 - docs/planemo.galaxy.rst | 1 - docs/planemo.galaxy.test.rst | 1 - docs/planemo.linters.rst | 1 - docs/planemo.reports.rst | 1 - docs/planemo.rst | 1 - docs/planemo.shed.rst | 1 - docs/planemo.shed2tap.rst | 1 - docs/planemo.test.rst | 1 - docs/planemo.training.rst | 1 - docs/planemo.xml.rst | 1 - 67 files changed, 788 insertions(+), 69 deletions(-) create mode 100644 docs/commands/create_alias.rst create mode 100644 docs/commands/delete_alias.rst create mode 100644 docs/commands/list_alias.rst create mode 100644 docs/commands/list_invocations.rst create mode 100644 docs/commands/workflow_upload.rst diff --git a/docs/commands.rst b/docs/commands.rst index f9875bf83..e21daece3 100644 --- a/docs/commands.rst +++ b/docs/commands.rst @@ -18,14 +18,18 @@ documentation describes these commands. .. include:: commands/conda_search.rst .. include:: commands/config_init.rst .. include:: commands/container_register.rst +.. include:: commands/create_alias.rst .. include:: commands/database_create.rst .. include:: commands/database_delete.rst .. include:: commands/database_list.rst +.. include:: commands/delete_alias.rst .. include:: commands/docker_build.rst .. include:: commands/docker_shell.rst .. include:: commands/dockstore_init.rst .. include:: commands/docs.rst .. include:: commands/lint.rst +.. include:: commands/list_alias.rst +.. include:: commands/list_invocations.rst .. include:: commands/list_repos.rst .. include:: commands/merge_test_reports.rst .. include:: commands/mull.rst @@ -62,4 +66,5 @@ documentation describes these commands. .. include:: commands/workflow_edit.rst .. include:: commands/workflow_job_init.rst .. include:: commands/workflow_lint.rst -.. include:: commands/workflow_test_init.rst \ No newline at end of file +.. include:: commands/workflow_test_init.rst +.. include:: commands/workflow_upload.rst \ No newline at end of file diff --git a/docs/commands/ci_find_repos.rst b/docs/commands/ci_find_repos.rst index a5010d36f..9eca951a0 100644 --- a/docs/commands/ci_find_repos.rst +++ b/docs/commands/ci_find_repos.rst @@ -14,8 +14,8 @@ This section is auto-generated from the help text for the planemo command Find all shed repositories in one or more directories. -Currently, a shed repository is considered a directory with a .shed.yml -file. +Currently, a repository is considered any directory with a .shed.yml +or .dockstore.yml file. **Options**:: @@ -25,9 +25,11 @@ file. --changed_in_commit_range TEXT Exclude paths unchanged in git commit range. --chunk_count INTEGER Split output into chunks of this many item and print --chunk such group. + --chunk INTEGER When output is split into --chunk_count groups, output the group 0-indexedby this option. + --output TEXT File to output to, or - for standard output. --help Show this message and exit. diff --git a/docs/commands/ci_find_tools.rst b/docs/commands/ci_find_tools.rst index f162b79e3..2dbbfa418 100644 --- a/docs/commands/ci_find_tools.rst +++ b/docs/commands/ci_find_tools.rst @@ -25,11 +25,14 @@ operations over for continuous integration operations. --changed_in_commit_range TEXT Exclude paths unchanged in git commit range. --chunk_count INTEGER Split output into chunks of this many item and print --chunk such group. + --chunk INTEGER When output is split into --chunk_count groups, output the group 0-indexedby this option. + --output TEXT File to output to, or - for standard output. --group_tools Group tools of the same repository on a single line. + --help Show this message and exit. diff --git a/docs/commands/clone.rst b/docs/commands/clone.rst index f252522a9..78dd15d4f 100644 --- a/docs/commands/clone.rst +++ b/docs/commands/clone.rst @@ -27,8 +27,9 @@ repository to allow a subsequent pull request to fix a problem with bwa. $ git commit -m "Fix bwa problem." $ planemo pull_request -m "Fix bwa problem." -These changes do require that a github username and password are -specified in ~/.planemo.yml. +These changes do require that a github access token is +specified in ~/.planemo.yml. An access token can be generated by going +to https://github.com/settings/tokens. **Options**:: diff --git a/docs/commands/conda_build.rst b/docs/commands/conda_build.rst index 532372122..e8ffb6871 100644 --- a/docs/commands/conda_build.rst +++ b/docs/commands/conda_build.rst @@ -18,12 +18,15 @@ Perform conda build with Planemo's conda. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --help Show this message and exit. diff --git a/docs/commands/conda_env.rst b/docs/commands/conda_env.rst index 83a07bc03..8a3b551e4 100644 --- a/docs/commands/conda_env.rst +++ b/docs/commands/conda_env.rst @@ -32,12 +32,15 @@ tool. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --help Show this message and exit. diff --git a/docs/commands/conda_init.rst b/docs/commands/conda_init.rst index c8b87bbca..70ee6167a 100644 --- a/docs/commands/conda_init.rst +++ b/docs/commands/conda_init.rst @@ -29,12 +29,15 @@ if Conda is already installed. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --help Show this message and exit. diff --git a/docs/commands/conda_install.rst b/docs/commands/conda_install.rst index 3cf7fea78..4e07912e2 100644 --- a/docs/commands/conda_install.rst +++ b/docs/commands/conda_install.rst @@ -18,24 +18,30 @@ Install conda packages for tool requirements. -r, --recursive Recursively perform command for subdirectories. + --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --global Install Conda dependencies globally instead of in requirement specific environments packaged for tools. If the Conda bin directory is on your PATH, tools may still use binaries but this is more designed for interactive testing and debugging. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --help Show this message and exit. diff --git a/docs/commands/conda_lint.rst b/docs/commands/conda_lint.rst index 2ae5fd24f..414ae11e7 100644 --- a/docs/commands/conda_lint.rst +++ b/docs/commands/conda_lint.rst @@ -25,5 +25,6 @@ https://github.com/ContinuumIO/anaconda-verify. --fail_level [warn|error] -r, --recursive Recursively perform command for nested conda directories. + --help Show this message and exit. diff --git a/docs/commands/conda_search.rst b/docs/commands/conda_search.rst index f4eb7df64..6496fda95 100644 --- a/docs/commands/conda_search.rst +++ b/docs/commands/conda_search.rst @@ -21,12 +21,15 @@ Implicitly adds channels Planemo is configured with. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --help Show this message and exit. diff --git a/docs/commands/container_register.rst b/docs/commands/container_register.rst index d029d8d1b..7cc288443 100644 --- a/docs/commands/container_register.rst +++ b/docs/commands/container_register.rst @@ -24,28 +24,37 @@ so that a container can be created and registered for these tools. -r, --recursive Recursively perform command for subdirectories. + --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. + --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --output_directory DIRECTORY Container registration directory (defaults to ~/.planemo/multi-package-containers. + -m, --message TEXT Commit and pull request message template for registration interactions. + --pull_request / --no_pull_request Fork and create a pull request against BioContainers/multi-package-containers for these changes. + --force_push / --no_force_push Force push branch for pull request in case it already exists. + --help Show this message and exit. diff --git a/docs/commands/create_alias.rst b/docs/commands/create_alias.rst new file mode 100644 index 000000000..925a785dc --- /dev/null +++ b/docs/commands/create_alias.rst @@ -0,0 +1,26 @@ + +``create_alias`` command +====================================== + +This section is auto-generated from the help text for the planemo command +``create_alias``. This help message can be generated with ``planemo create_alias +--help``. + +**Usage**:: + + planemo create_alias [OPTIONS] OBJ + +**Help** + + +Add an alias for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile. + +**Options**:: + + + --alias TEXT Name of an alias. + --profile TEXT Name of profile (created with the profile_create command) to + use with this command. [required] + + --help Show this message and exit. + diff --git a/docs/commands/database_create.rst b/docs/commands/database_create.rst index 6563075ea..1ac638d48 100644 --- a/docs/commands/database_create.rst +++ b/docs/commands/database_create.rst @@ -69,21 +69,29 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --help Show this message and exit. diff --git a/docs/commands/database_delete.rst b/docs/commands/database_delete.rst index 68dba6ff4..e379928e0 100644 --- a/docs/commands/database_delete.rst +++ b/docs/commands/database_delete.rst @@ -69,21 +69,29 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --help Show this message and exit. diff --git a/docs/commands/database_list.rst b/docs/commands/database_list.rst index c5b748650..aa33d332e 100644 --- a/docs/commands/database_list.rst +++ b/docs/commands/database_list.rst @@ -69,21 +69,29 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --help Show this message and exit. diff --git a/docs/commands/delete_alias.rst b/docs/commands/delete_alias.rst new file mode 100644 index 000000000..37351f3ac --- /dev/null +++ b/docs/commands/delete_alias.rst @@ -0,0 +1,26 @@ + +``delete_alias`` command +====================================== + +This section is auto-generated from the help text for the planemo command +``delete_alias``. This help message can be generated with ``planemo delete_alias +--help``. + +**Usage**:: + + planemo delete_alias [OPTIONS] + +**Help** + + +List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile. + +**Options**:: + + + --alias TEXT Name of an alias. [required] + --profile TEXT Name of profile (created with the profile_create command) to + use with this command. [required] + + --help Show this message and exit. + diff --git a/docs/commands/docker_build.rst b/docs/commands/docker_build.rst index ee4ccf4e2..f1aca827f 100644 --- a/docs/commands/docker_build.rst +++ b/docs/commands/docker_build.rst @@ -38,11 +38,14 @@ This can optionally also cache the images. --docker_image_cache TEXT --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --help Show this message and exit. diff --git a/docs/commands/docker_shell.rst b/docs/commands/docker_shell.rst index cd8f1cfc7..1c1408bc5 100644 --- a/docs/commands/docker_shell.rst +++ b/docs/commands/docker_shell.rst @@ -30,15 +30,20 @@ generates - so be sure to wrap this in $(...) to launch the subshell. --from_tag Treat the tool's Docker container identifier as a locally cached tag. + --shell TEXT Shell to launch in container (defaults to /bin/bash). + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --help Show this message and exit. diff --git a/docs/commands/lint.rst b/docs/commands/lint.rst index 4db5093e4..d35574938 100644 --- a/docs/commands/lint.rst +++ b/docs/commands/lint.rst @@ -23,17 +23,22 @@ Check for common errors and best practices. (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. + --xsd / --no_xsd Include tool XSD validation in linting process. + -r, --recursive Recursively perform command for subdirectories. + --urls Check validity of URLs in XML files --doi Check validity of DOIs in XML files --conda_requirements Check tool requirements for availability in best practice Conda channels. + --biocontainer, --biocontainers Check best practice BioContainer namespaces for a container definition applicable for this tool. + --help Show this message and exit. diff --git a/docs/commands/list_alias.rst b/docs/commands/list_alias.rst new file mode 100644 index 000000000..cbf827cd3 --- /dev/null +++ b/docs/commands/list_alias.rst @@ -0,0 +1,25 @@ + +``list_alias`` command +====================================== + +This section is auto-generated from the help text for the planemo command +``list_alias``. This help message can be generated with ``planemo list_alias +--help``. + +**Usage**:: + + planemo list_alias [OPTIONS] + +**Help** + + +List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile. + +**Options**:: + + + --profile TEXT Name of profile (created with the profile_create command) to + use with this command. [required] + + --help Show this message and exit. + diff --git a/docs/commands/list_invocations.rst b/docs/commands/list_invocations.rst new file mode 100644 index 000000000..e8161027d --- /dev/null +++ b/docs/commands/list_invocations.rst @@ -0,0 +1,25 @@ + +``list_invocations`` command +====================================== + +This section is auto-generated from the help text for the planemo command +``list_invocations``. This help message can be generated with ``planemo list_invocations +--help``. + +**Usage**:: + + planemo list_invocations [OPTIONS] WORKFLOW_ID + +**Help** + + +Get a list of invocations for a particular workflow ID or alias. + +**Options**:: + + + --profile TEXT Name of profile (created with the profile_create command) to + use with this command. [required] + + --help Show this message and exit. + diff --git a/docs/commands/list_repos.rst b/docs/commands/list_repos.rst index 3d536ce25..3c8b919e3 100644 --- a/docs/commands/list_repos.rst +++ b/docs/commands/list_repos.rst @@ -25,9 +25,11 @@ file. --changed_in_commit_range TEXT Exclude paths unchanged in git commit range. --chunk_count INTEGER Split output into chunks of this many item and print --chunk such group. + --chunk INTEGER When output is split into --chunk_count groups, output the group 0-indexedby this option. + --output TEXT File to output to, or - for standard output. --help Show this message and exit. diff --git a/docs/commands/mull.rst b/docs/commands/mull.rst index d103f483f..aa4a25e60 100644 --- a/docs/commands/mull.rst +++ b/docs/commands/mull.rst @@ -29,20 +29,25 @@ target tool(s). -r, --recursive Recursively perform command for subdirectories. + --mulled_conda_version TEXT Install a specific version of Conda before running the command, by default the version that comes with the continuumio miniconda3 image will be used under Linux and under Mac OS X Conda will be upgraded to to work around a bug in 4.2. + --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. + --mulled_command TEXT Mulled action to perform for targets - this defaults to 'build-and-test'. + --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --help Show this message and exit. diff --git a/docs/commands/mulled_init.rst b/docs/commands/mulled_init.rst index d1b7e1bc7..23e026fc9 100644 --- a/docs/commands/mulled_init.rst +++ b/docs/commands/mulled_init.rst @@ -25,11 +25,14 @@ be pre-installed in an environment using this command. comes with the continuumio miniconda3 image will be used under Linux and under Mac OS X Conda will be upgraded to to work around a bug in 4.2. + --mulled_namespace TEXT Build a mulled image with the specified namespace - defaults to biocontainers. Galaxy currently only recognizes images with the namespace biocontainers. + --mulled_command TEXT Mulled action to perform for targets - this defaults to 'build-and-test'. + --help Show this message and exit. diff --git a/docs/commands/normalize.rst b/docs/commands/normalize.rst index 7746510ee..d314017e3 100644 --- a/docs/commands/normalize.rst +++ b/docs/commands/normalize.rst @@ -39,11 +39,14 @@ the tool development best practices outlined on the Galaxy wiki. --expand_macros Expand macros while normalizing tool XML - useful to see how macros are evaluated. + --skip_reorder Planemo will reorder top-level tool blocks according to tool development best practices as part of this command, this flag will disable that behavior. + --skip_reindent Planemo will reindent the XML according to tool development best practices as part of this command, this flag will disable that behavior. + --help Show this message and exit. diff --git a/docs/commands/profile_create.rst b/docs/commands/profile_create.rst index 0623a7871..f4aab33ff 100644 --- a/docs/commands/profile_create.rst +++ b/docs/commands/profile_create.rst @@ -28,26 +28,40 @@ Create a profile. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + + --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy + engine. + + --galaxy_user_key TEXT User key to use with external Galaxy engine. + --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --help Show this message and exit. diff --git a/docs/commands/profile_delete.rst b/docs/commands/profile_delete.rst index 1b9baef08..f8dae258e 100644 --- a/docs/commands/profile_delete.rst +++ b/docs/commands/profile_delete.rst @@ -28,21 +28,29 @@ Delete a profile. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --help Show this message and exit. diff --git a/docs/commands/pull_request.rst b/docs/commands/pull_request.rst index 36d871a5f..c220216c8 100644 --- a/docs/commands/pull_request.rst +++ b/docs/commands/pull_request.rst @@ -26,8 +26,9 @@ repository to allow a subsequent pull request to fix a problem with bwa. $ git commit -m "Fix bwa problem." $ planemo pull_request -m "Fix bwa problem." -These changes do require that a github username and password are -specified in ~/.planemo.yml. +These changes do require that a github access token is +specified in ~/.planemo.yml. An access token can be generated by going +to https://github.com/settings/tokens. **Options**:: diff --git a/docs/commands/run.rst b/docs/commands/run.rst index 43906bee2..44efa204d 100644 --- a/docs/commands/run.rst +++ b/docs/commands/run.rst @@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command **Usage**:: - planemo run [OPTIONS] TOOL_URI JOB_PATH + planemo run [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH **Help** @@ -23,45 +23,58 @@ Planemo command for running tools and jobs. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -71,42 +84,55 @@ Planemo command for running tools and jobs. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -119,16 +145,22 @@ Planemo command for running tools and jobs. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -138,55 +170,70 @@ Planemo command for running tools and jobs. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --cwl Configure Galaxy for use with CWL tool. (this option is experimental and will be replaced when and if CWL support is merged into Galaxy). + --cwl_galaxy_root DIRECTORY Root of development galaxy directory to execute command with (must be branch of Galaxy with CWL support, this option is experimental and will be replaced with --galaxy_root when and if CWL support is merged into Galaxy. + --output_directory, --outdir DIRECTORY Where to store outputs of a 'run' task. --output_json FILE Where to store JSON dictionary describing outputs of a 'run' task. + --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy] Select an engine to run or test artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container or the CWL reference implementation 'cwltool' and 'toil' be selected. + --non_strict_cwl Disable strict validation of CWL. --no-container, --no_container If cwltool engine is used, disable Docker container usage. + --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --install_tool_dependencies / --no_install_tool_dependencies Turn on installation of tool dependencies using classic toolshed packages. + --install_resolver_dependencies / --no_install_resolver_dependencies Skip installing tool dependencies through resolver (e.g. conda). + --install_repository_dependencies / --no_install_repository_dependencies Skip installing the repository dependencies. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. + --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. + --history_name TEXT Name to give a Galaxy history, if one is + created. + --help Show this message and exit. diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst index 90427e4bb..6dd95ad2b 100644 --- a/docs/commands/serve.rst +++ b/docs/commands/serve.rst @@ -39,45 +39,58 @@ Galaxy instance. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -87,53 +100,68 @@ Galaxy instance. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -146,16 +174,22 @@ Galaxy instance. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -165,30 +199,37 @@ Galaxy instance. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --cwl Configure Galaxy for use with CWL tool. (this option is experimental and will be replaced when and if CWL support is merged into Galaxy). + --cwl_galaxy_root DIRECTORY Root of development galaxy directory to execute command with (must be branch of Galaxy with CWL support, this option is experimental and will be replaced with --galaxy_root when and if CWL support is merged into Galaxy. + --help Show this message and exit. diff --git a/docs/commands/share_test.rst b/docs/commands/share_test.rst index 89d9a3a87..7aa0b0644 100644 --- a/docs/commands/share_test.rst +++ b/docs/commands/share_test.rst @@ -20,8 +20,9 @@ produce sharable URL. The sharable URL can be used to share an HTML version of the report that can be easily embedded in pull requests or commit messages. -Requires a ~/.planemo.yml with Github 'username' and 'password' -defined in a 'github' section of that configuration file. +Requires a ~/.planemo.yml with a Github access token +defined in a 'github' section of that configuration file. An access +token can be generated by going to https://github.com/settings/tokens. **Options**:: diff --git a/docs/commands/shed_create.rst b/docs/commands/shed_create.rst index 6c6c12eac..f79ea9b78 100644 --- a/docs/commands/shed_create.rst +++ b/docs/commands/shed_create.rst @@ -21,28 +21,37 @@ This will read the settings from the ``.shed.yml`` file. -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + -m, --message TEXT Commit message for tool shed upload. --skip_upload Skip upload contents as part of operation, only update metadata. + --help Show this message and exit. diff --git a/docs/commands/shed_diff.rst b/docs/commands/shed_diff.rst index 0e9390849..d4ad8cf84 100644 --- a/docs/commands/shed_diff.rst +++ b/docs/commands/shed_diff.rst @@ -48,32 +48,42 @@ uploaded to the repository. -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + -o, --output PATH Send diff output to specified file. --shed_target_source TEXT Source Tool Shed to diff against (will ignore local project info specified). To compare the main Tool Shed against the test, set this to testtoolshed. + --raw Do not attempt smart diff of XML to filter out attributes populated by the Tool Shed. + --report_xunit PATH Output an XUnit report, useful for CI testing --help Show this message and exit. diff --git a/docs/commands/shed_init.rst b/docs/commands/shed_init.rst index 1a966bb0f..40f488828 100644 --- a/docs/commands/shed_init.rst +++ b/docs/commands/shed_init.rst @@ -23,18 +23,23 @@ to manage repositories in a Galaxy Tool Shed. --from_workflow PATH Attempt to generate repository dependencies from specified workflow. + --description TEXT Specify repository description for .shed.yml. --long_description TEXT Specify repository long_description for .shed.yml. + --remote_repository_url TEXT Specify repository remote_repository_url for .shed.yml. + --homepage_url TEXT Specify repository homepage_url for .shed.yml. --category [Assembly|ChIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Graphics|Imaging|Machine Learning|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Statistics|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services] Specify repository category for .shed.yml (may specify multiple). + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + -f, --force Overwrite existing files if present. --help Show this message and exit. diff --git a/docs/commands/shed_lint.rst b/docs/commands/shed_lint.rst index 99ef7d450..ec575a799 100644 --- a/docs/commands/shed_lint.rst +++ b/docs/commands/shed_lint.rst @@ -29,18 +29,23 @@ help text for mentioned URLs and checks those. -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --report_level [all|warn|error] --fail_level [warn|error] --tools Lint tools discovered in the process of linting repositories. + --xsd / --no_xsd Include tool XSD validation in linting process. + --ensure_metadata Ensure .shed.yml files contain enough metadata for each repository to allow automated creation and/or updates. + --urls Check validity of URLs in XML files --help Show this message and exit. diff --git a/docs/commands/shed_serve.rst b/docs/commands/shed_serve.rst index f548d5904..8342cb614 100644 --- a/docs/commands/shed_serve.rst +++ b/docs/commands/shed_serve.rst @@ -25,67 +25,88 @@ logged into and explored interactively. -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -95,53 +116,68 @@ logged into and explored interactively. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -154,16 +190,22 @@ logged into and explored interactively. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -173,23 +215,29 @@ logged into and explored interactively. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --skip_dependencies Do not install shed dependencies as part of repository installation. + --help Show this message and exit. diff --git a/docs/commands/shed_test.rst b/docs/commands/shed_test.rst index 2767ce307..f198199fc 100644 --- a/docs/commands/shed_test.rst +++ b/docs/commands/shed_test.rst @@ -26,97 +26,128 @@ This command requires the target to be version 15.07 or newer. -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) + --paste_test_data_paths / --no_paste_test_data_paths By default Planemo will use or not use Galaxy's path paste option to load test data into a history based on the engine type it is targeting. This can override the logic to explicitly enable or disable path pasting. + --test_output PATH Output test report (HTML - for humans) defaults to tool_test_output.html. + --test_output_text PATH Output test report (Basic text - for display in CI) + --test_output_markdown PATH Output test report (Markdown style - for humans & computers) + --test_output_xunit PATH Output test report (xunit style - for CI systems + --test_output_junit PATH Output test report (jUnit style - for CI systems + --test_output_json PATH Output test report (planemo json) defaults to tool_test_output.json. + --job_output_files DIRECTORY Write job outputs to specified directory. --summary [none|minimal|compact] Summary style printed to planemo's standard output (see output reports for more complete summary). Set to 'none' to disable completely. + --skip_dependencies Do not install shed dependencies as part of repository installation. + --help Show this message and exit. diff --git a/docs/commands/shed_update.rst b/docs/commands/shed_update.rst index b77535bb6..d79e236ab 100644 --- a/docs/commands/shed_update.rst +++ b/docs/commands/shed_update.rst @@ -50,36 +50,48 @@ the repository doesn't define complete metadata in a ``.shed.yml``. --report_xunit PATH Output an XUnit report, useful for CI testing -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + -m, --message TEXT Commit message for tool shed upload. --force_repository_creation If a repository cannot be found for the specified user/repo name pair, then automatically create the repository in the toolshed. + --check_diff Skip uploading if the shed_diff detects there would be no 'difference' (only attributes populated by the shed would be updated.) + --skip_upload Skip upload contents as part of operation, only update metadata. + --skip_metadata Skip metadata update as part of operation, only upload new contents. + --help Show this message and exit. diff --git a/docs/commands/shed_upload.rst b/docs/commands/shed_upload.rst index 65bb0e458..7ea82e028 100644 --- a/docs/commands/shed_upload.rst +++ b/docs/commands/shed_upload.rst @@ -34,37 +34,49 @@ metadata (to handle metadata changes in ``.shed.yml`` files). -r, --recursive Recursively perform command for nested repository directories. + --fail_fast If multiple repositories are specified and an error occurs stop immediately instead of processing remaining repositories. + --owner TEXT Tool Shed repository owner (username). --name TEXT Tool Shed repository name (defaults to the inferred tool directory name). + --shed_email TEXT E-mail for Tool Shed auth (required unless shed_key is specified). + --shed_key TEXT API key for Tool Shed access. An API key is required unless e-mail and password is specified. This key can be specified with either --shed_key or --shed_key_from_env. + --shed_key_from_env TEXT Environment variable to read API key for Tool Shed access from. + --shed_password TEXT Password for Tool Shed auth (required unless shed_key is specified). + -t, --shed_target TEXT Tool Shed to target (this can be 'toolshed', 'testtoolshed', 'local' (alias for http://localhost:9009/), an arbitrary url or mappings defined ~/.planemo.yml. + -m, --message TEXT Commit message for tool shed upload. --force_repository_creation If a repository cannot be found for the specified user/repo name pair, then automatically create the repository in the toolshed. + --check_diff Skip uploading if the shed_diff detects there would be no 'difference' (only attributes populated by the shed would be updated.) + --tar_only Produce tar file for upload but do not publish to a tool shed. + --tar FILE Specify a pre-existing tar file instead of automatically building one as part of this command. + --help Show this message and exit. diff --git a/docs/commands/test.rst b/docs/commands/test.rst index c95583b7e..656b090db 100644 --- a/docs/commands/test.rst +++ b/docs/commands/test.rst @@ -47,92 +47,117 @@ please careful and do not try this against production Galaxy instances. tests failed so this file must have been produced with the same set of tool ids previously. + --polling_backoff INTEGER Poll resources with an increasing interval between requests. Useful when testing against remote and/or production instances to limit generated traffic. - --history_name TEXT Name for history (if a history is generated as - part of testing.) + --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -145,16 +170,22 @@ please careful and do not try this against production Galaxy instances. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -164,68 +195,89 @@ please careful and do not try this against production Galaxy instances. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) + --paste_test_data_paths / --no_paste_test_data_paths By default Planemo will use or not use Galaxy's path paste option to load test data into a history based on the engine type it is targeting. This can override the logic to explicitly enable or disable path pasting. + --test_output PATH Output test report (HTML - for humans) defaults to tool_test_output.html. + --test_output_text PATH Output test report (Basic text - for display in CI) + --test_output_markdown PATH Output test report (Markdown style - for humans & computers) + --test_output_xunit PATH Output test report (xunit style - for CI systems + --test_output_junit PATH Output test report (jUnit style - for CI systems + --test_output_json PATH Output test report (planemo json) defaults to tool_test_output.json. + --job_output_files DIRECTORY Write job outputs to specified directory. --summary [none|minimal|compact] Summary style printed to planemo's standard output (see output reports for more complete summary). Set to 'none' to disable completely. + --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy] Select an engine to run or test artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container or the CWL reference implementation 'cwltool' and 'toil' be selected. + --non_strict_cwl Disable strict validation of CWL. --no-container, --no_container If cwltool engine is used, disable Docker container usage. + --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --install_tool_dependencies / --no_install_tool_dependencies Turn on installation of tool dependencies using classic toolshed packages. + --install_resolver_dependencies / --no_install_resolver_dependencies Skip installing tool dependencies through resolver (e.g. conda). + --install_repository_dependencies / --no_install_repository_dependencies Skip installing the repository dependencies. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. + --galaxy_admin_key TEXT Admin key to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. + --history_name TEXT Name to give a Galaxy history, if one is + created. + --help Show this message and exit. diff --git a/docs/commands/test_reports.rst b/docs/commands/test_reports.rst index 8a89bfc03..d71a2f364 100644 --- a/docs/commands/test_reports.rst +++ b/docs/commands/test_reports.rst @@ -22,10 +22,13 @@ from the structured test output (tool_test_output.json). --test_output PATH Output test report (HTML - for humans) defaults to tool_test_output.html. + --test_output_text PATH Output test report (Basic text - for display in CI) + --test_output_markdown PATH Output test report (Markdown style - for humans & computers) + --test_output_xunit PATH Output test report (xunit style - for CI systems --test_output_junit PATH Output test report (jUnit style - for CI systems --help Show this message and exit. diff --git a/docs/commands/tool_init.rst b/docs/commands/tool_init.rst index 37bae86e7..d32536915 100644 --- a/docs/commands/tool_init.rst +++ b/docs/commands/tool_init.rst @@ -24,31 +24,40 @@ Generate tool outline from given arguments. -d, --description TEXT Short description for new tool (user facing) -c, --command TEXT Command potentially including cheetah variables ()(e.g. 'seqtk seq -a $input > $output') + --example_command TEXT Example to command with paths to build Cheetah template from (e.g. 'seqtk seq -a 2.fastq > 2.fasta'). Option cannot be used with --command, should be used --example_input and --example_output. + --example_input TEXT For use with --example_command, replace input file (e.g. 2.fastq with a data input parameter). + --example_output TEXT For use with --example_command, replace input file (e.g. 2.fastq with a tool output). + --named_output TEXT Create a named output for use with command block for example specify --named_output=output1.bam and then use '-o $output1' in your command block. + --input TEXT An input description (e.g. input.fasta) --output TEXT An output location (e.g. output.bam), the Galaxy datatype is inferred from the extension. + --help_text TEXT Help text (reStructuredText) --help_from_command TEXT Auto populate help from supplied command. --doi TEXT Supply a DOI (http://www.doi.org/) easing citation of the tool for Galxy users (e.g. 10.1101/014043). + --cite_url TEXT Supply a URL for citation. --test_case For use with --example_commmand, generate a tool test case from the supplied example. + --macros Generate a macros.xml for reuse across many tools. --version_command TEXT Command to print version (e.g. 'seqtk --version') --requirement TEXT Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68'). + --container TEXT Add a Docker image identifier for this tool. --cwl Build a CWL tool instead of a Galaxy tool. --help Show this message and exit. diff --git a/docs/commands/training_fill_data_library.rst b/docs/commands/training_fill_data_library.rst index f9d141429..36c173aa7 100644 --- a/docs/commands/training_fill_data_library.rst +++ b/docs/commands/training_fill_data_library.rst @@ -18,10 +18,13 @@ Build training template from workflow. --topic_name TEXT Name (directory name) of the topic to create or in which a tutorial should be created or updates [required] + --tutorial_name TEXT Name (directory name) of the tutorial to modify [required] + --zenodo_link TEXT Zenodo URL with the input data --datatypes PATH YAML file with the correspondance between Zenodo extension and Galaxy datatypes + --help Show this message and exit. diff --git a/docs/commands/training_generate_from_wf.rst b/docs/commands/training_generate_from_wf.rst index d36d8e0bf..d7e77c3d7 100644 --- a/docs/commands/training_generate_from_wf.rst +++ b/docs/commands/training_generate_from_wf.rst @@ -19,54 +19,70 @@ Create tutorial skeleton from workflow. --topic_name TEXT Name (directory name) of the topic to create or in which a tutorial should be created or updates [required] + --tutorial_name TEXT Name (directory name) of the tutorial to modify [required] + --workflow PATH Workflow of the tutorial (locally) --galaxy_url TEXT URL of a Galaxy instance with the workflow --galaxy_api_key TEXT API key on the Galaxy instance with the workflow + --workflow_id TEXT ID of the workflow on the Galaxy instance --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -76,53 +92,68 @@ Create tutorial skeleton from workflow. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -135,16 +166,22 @@ Create tutorial skeleton from workflow. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -154,21 +191,26 @@ Create tutorial skeleton from workflow. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --help Show this message and exit. diff --git a/docs/commands/training_init.rst b/docs/commands/training_init.rst index 9bba0eb0d..c9c2cb4e3 100644 --- a/docs/commands/training_init.rst +++ b/docs/commands/training_init.rst @@ -19,12 +19,14 @@ Build training template from workflow. --topic_name TEXT Name (directory name) of the topic to create or in which a tutorial should be created or updates [required] + --topic_title TEXT Title of the topic to create --topic_summary TEXT Summary of the topic --topic_target [use|admin-dev|instructors] Target audience for the topic --tutorial_name TEXT Name (directory name) of the tutorial to create or to modify + --tutorial_title TEXT Title of the tutorial --hands_on Add hands-on for the new tutorial --slides Add slides for the new tutorial @@ -32,51 +34,66 @@ Build training template from workflow. --galaxy_url TEXT URL of a Galaxy instance with the workflow --galaxy_api_key TEXT API key on the Galaxy instance with the workflow + --workflow_id TEXT ID of the workflow on the Galaxy instance --zenodo_link TEXT Zenodo URL with the input data --datatypes PATH YAML file with the correspondance between Zenodo extension and Galaxy datatypes + --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -86,53 +103,68 @@ Build training template from workflow. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -145,16 +177,22 @@ Build training template from workflow. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -164,21 +202,26 @@ Build training template from workflow. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --help Show this message and exit. diff --git a/docs/commands/workflow_convert.rst b/docs/commands/workflow_convert.rst index d84cb2d71..2655c005e 100644 --- a/docs/commands/workflow_convert.rst +++ b/docs/commands/workflow_convert.rst @@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command **Usage**:: - planemo workflow_convert [OPTIONS] WORKFLOW_PATH + planemo workflow_convert [OPTIONS] WORKFLOW_PATH_OR_ID **Help** @@ -21,45 +21,58 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. -o, --output FILE --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -69,53 +82,68 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -128,16 +156,22 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -147,21 +181,26 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --help Show this message and exit. diff --git a/docs/commands/workflow_edit.rst b/docs/commands/workflow_edit.rst index 5c9e332c7..a7224371f 100644 --- a/docs/commands/workflow_edit.rst +++ b/docs/commands/workflow_edit.rst @@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command **Usage**:: - planemo workflow_edit [OPTIONS] WORKFLOW_PATH + planemo workflow_edit [OPTIONS] WORKFLOW_PATH_OR_ID **Help** @@ -19,45 +19,58 @@ Open a synchronized Galaxy workflow editor. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.5|3.6|3.7|3.8] + + --galaxy_python_version [3|3.6|3.7|3.8|3.9] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be linted/tested/etc... but they will be available to workflows and for interactive use. + --install_galaxy Download and configure a disposable copy of Galaxy from github. + --galaxy_branch TEXT Branch of Galaxy to target (defaults to master) if a Galaxy root isn't specified. + --galaxy_source TEXT Git source of Galaxy to target (defaults to the official galaxyproject github source if a Galaxy root isn't specified. + --skip_venv Do not create or source a virtualenv - environment for Galaxy, this should be used or - instance to preserve an externally configured - virtual environment or conda environment. + environment for Galaxy, this should be used to + preserve an externally configured virtual + environment or conda environment. + --no_cache_galaxy Skip caching of Galaxy source and dependencies obtained with --install_galaxy. Not caching this results in faster downloads (no git) - so is better on throw away instances such with TravisCI. + --no_cleanup Do not cleanup temp files created for and by Galaxy. + --galaxy_email TEXT E-mail address to use when launching single- user Galaxy server. + --docker / --no_docker Run Galaxy tools in Docker if enabled. --docker_cmd TEXT Command used to launch docker (defaults to docker). + --docker_sudo / --no_docker_sudo Flag to use sudo when running docker. --docker_host TEXT Docker host to target when executing docker commands (defaults to localhost). + --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). + --job_config_file FILE Job configuration file for Galaxy to target. --tool_dependency_dir DIRECTORY Tool dependency dir for Galaxy to target. @@ -67,53 +80,68 @@ Open a synchronized Galaxy workflow editor. for security reasons set to 0.0.0.0 to bind Galaxy to all ports including potentially publicly accessible ones. + --engine [galaxy|docker_galaxy|external_galaxy] Select an engine to serve artifacts such as tools and workflows. Defaults to a local Galaxy, but running Galaxy within a Docker container. + --non_strict_cwl Disable strict validation of CWL. --docker_galaxy_image TEXT Docker image identifier for docker-galaxy- flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. + --docker_extra_volume PATH Extra path to mount if --engine docker. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). + --dependency_resolvers_config_file FILE Dependency resolver configuration for Galaxy to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. --conda_prefix DIRECTORY Conda prefix to use for conda dependency commands. + --conda_exec FILE Location of conda executable. --conda_debug Enable more verbose conda logging. --conda_channels, --conda_ensure_channels TEXT Ensure conda is configured with specified comma separated list of channels. + --conda_use_local Use locally built packages while building Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for dependency resolution. + --conda_copy_dependencies Conda dependency resolution for Galaxy will copy dependencies instead of attempting to link them. + --conda_auto_install / --no_conda_auto_install Conda dependency resolution for Galaxy will attempt to install requested but missing packages. + --conda_auto_init / --no_conda_auto_init Conda dependency resolution for Galaxy will auto install conda itself using miniconda if not availabe on conda_prefix. + --profile TEXT Name of profile (created with the profile_create command) to use with this command. + --postgres Use postgres database type. --database_type [postgres|postgres_docker|sqlite|auto] Type of database to use for profile - 'auto', @@ -126,16 +154,22 @@ Open a synchronized Galaxy workflow editor. postgres_docker is not yet persisted past when you restart the docker container launched by Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary (psql). + --postgres_database_user TEXT Postgres username for managed development databases. + --postgres_database_host TEXT Postgres host name for managed development databases. + --postgres_database_port TEXT Postgres port for managed development databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. database/files). + --database_connection TEXT Database connection string to use for Galaxy. --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. --shed_tool_path TEXT Location of shed tools directory for Galaxy. @@ -145,21 +179,26 @@ Open a synchronized Galaxy workflow editor. one user and this user is automatically logged it. Use --no_galaxy_single_user to prevent Galaxy from running this way. + --daemon Serve Galaxy process as a daemon. --pid_file FILE Location of pid file is executed with --daemon. + --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases may not prevent a workflow from successfully executing. + --skip_client_build Do not build Galaxy client when serving Galaxy. + --shed_install / --no_shed_install By default Planemo will attempt to install repositories needed for workflow testing. This may not be appropriate for production servers and so this can disabled by calling planemo with --no_shed_install. + --help Show this message and exit. diff --git a/docs/commands/workflow_job_init.rst b/docs/commands/workflow_job_init.rst index e6e4569ab..d03589a52 100644 --- a/docs/commands/workflow_job_init.rst +++ b/docs/commands/workflow_job_init.rst @@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command **Usage**:: - planemo workflow_job_init [OPTIONS] WORKFLOW_PATH + planemo workflow_job_init [OPTIONS] WORKFLOW_PATH_OR_ID **Help** diff --git a/docs/commands/workflow_lint.rst b/docs/commands/workflow_lint.rst index 604246a23..a7aeec503 100644 --- a/docs/commands/workflow_lint.rst +++ b/docs/commands/workflow_lint.rst @@ -23,5 +23,6 @@ Check workflows for syntax errors and best practices. (e.g. passing --skip 'citations,xml_order' would skip linting of citations and best- practice XML ordering. + --help Show this message and exit. diff --git a/docs/commands/workflow_test_init.rst b/docs/commands/workflow_test_init.rst index 08f18fd4b..bebaba6e2 100644 --- a/docs/commands/workflow_test_init.rst +++ b/docs/commands/workflow_test_init.rst @@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command **Usage**:: - planemo workflow_test_init [OPTIONS] WORKFLOW_PATH + planemo workflow_test_init [OPTIONS] WORKFLOW_PATH_OR_ID **Help** @@ -21,7 +21,10 @@ testing easier. **Options**:: - -f, --force Overwrite existing files if present. + -f, --force Overwrite existing files if present. -o, --output FILE - --help Show this message and exit. + --split_test / --no_split_test Write workflow job and test definitions to + separate files. + + --help Show this message and exit. diff --git a/docs/commands/workflow_upload.rst b/docs/commands/workflow_upload.rst new file mode 100644 index 000000000..b030fcc86 --- /dev/null +++ b/docs/commands/workflow_upload.rst @@ -0,0 +1,25 @@ + +``workflow_upload`` command +====================================== + +This section is auto-generated from the help text for the planemo command +``workflow_upload``. This help message can be generated with ``planemo workflow_upload +--help``. + +**Usage**:: + + planemo workflow_upload [OPTIONS] TARGET + +**Help** + +Upload workflows to github organization. +**Options**:: + + + --namespace TEXT Organization or username under which to create or update + workflow repository. Must be a valid github username or + organization + + --dry_run Don't execute action, show preview of action. + --help Show this message and exit. + diff --git a/docs/installation.rst b/docs/installation.rst index 3e00b0202..9e404b2d7 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -34,7 +34,7 @@ consider using the ``virtualenv`` argument ``-p`` to point at a non-Conda Python natively on your system or using a tool such pyenv_. ``virtualenv`` can be installed via Conda, pyenv_, or a package manager - it should make no difference. -Planemo runs on Python 2.7 and Python 3.5 or newer. Planemo can be used to run multiple versions of Galaxy, +Planemo runs on Python 3.6 or newer. Planemo can be used to run multiple versions of Galaxy, but please note that the last Galaxy release that fully supports Python 2.7 is 19.09. Conda_ (Experimental) diff --git a/docs/planemo.commands.rst b/docs/planemo.commands.rst index 16f6a1a1a..6239a23d3 100644 --- a/docs/planemo.commands.rst +++ b/docs/planemo.commands.rst @@ -92,6 +92,14 @@ planemo.commands.cmd\_container\_register module :undoc-members: :show-inheritance: +planemo.commands.cmd\_create\_alias module +------------------------------------------ + +.. automodule:: planemo.commands.cmd_create_alias + :members: + :undoc-members: + :show-inheritance: + planemo.commands.cmd\_create\_gist module ----------------------------------------- @@ -124,6 +132,14 @@ planemo.commands.cmd\_database\_list module :undoc-members: :show-inheritance: +planemo.commands.cmd\_delete\_alias module +------------------------------------------ + +.. automodule:: planemo.commands.cmd_delete_alias + :members: + :undoc-members: + :show-inheritance: + planemo.commands.cmd\_docker\_build module ------------------------------------------ @@ -164,6 +180,22 @@ planemo.commands.cmd\_lint module :undoc-members: :show-inheritance: +planemo.commands.cmd\_list\_alias module +---------------------------------------- + +.. automodule:: planemo.commands.cmd_list_alias + :members: + :undoc-members: + :show-inheritance: + +planemo.commands.cmd\_list\_invocations module +---------------------------------------------- + +.. automodule:: planemo.commands.cmd_list_invocations + :members: + :undoc-members: + :show-inheritance: + planemo.commands.cmd\_list\_repos module ---------------------------------------- @@ -476,6 +508,13 @@ planemo.commands.cmd\_workflow\_test\_init module :undoc-members: :show-inheritance: +planemo.commands.cmd\_workflow\_upload module +--------------------------------------------- + +.. automodule:: planemo.commands.cmd_workflow_upload + :members: + :undoc-members: + :show-inheritance: Module contents --------------- diff --git a/docs/planemo.conda_verify.rst b/docs/planemo.conda_verify.rst index 74619ddd2..fc3de34ac 100644 --- a/docs/planemo.conda_verify.rst +++ b/docs/planemo.conda_verify.rst @@ -28,7 +28,6 @@ planemo.conda\_verify.utils module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.cwl.rst b/docs/planemo.cwl.rst index e4749d11a..ff9f43213 100644 --- a/docs/planemo.cwl.rst +++ b/docs/planemo.cwl.rst @@ -20,7 +20,6 @@ planemo.cwl.toil module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.database.rst b/docs/planemo.database.rst index 6ae3b4f2e..7437c5868 100644 --- a/docs/planemo.database.rst +++ b/docs/planemo.database.rst @@ -36,7 +36,6 @@ planemo.database.postgres\_docker module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.engine.rst b/docs/planemo.engine.rst index a034af111..5d2130e31 100644 --- a/docs/planemo.engine.rst +++ b/docs/planemo.engine.rst @@ -52,7 +52,6 @@ planemo.engine.toil module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.galaxy.rst b/docs/planemo.galaxy.rst index 2607c668f..6c77dd5a9 100644 --- a/docs/planemo.galaxy.rst +++ b/docs/planemo.galaxy.rst @@ -84,7 +84,6 @@ planemo.galaxy.workflows module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.galaxy.test.rst b/docs/planemo.galaxy.test.rst index d87124233..8a0118db7 100644 --- a/docs/planemo.galaxy.test.rst +++ b/docs/planemo.galaxy.test.rst @@ -20,7 +20,6 @@ planemo.galaxy.test.structures module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.linters.rst b/docs/planemo.linters.rst index 3dca88b79..87f90e707 100644 --- a/docs/planemo.linters.rst +++ b/docs/planemo.linters.rst @@ -44,7 +44,6 @@ planemo.linters.xsd module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.reports.rst b/docs/planemo.reports.rst index f63e2b8ea..dddc0c88d 100644 --- a/docs/planemo.reports.rst +++ b/docs/planemo.reports.rst @@ -20,7 +20,6 @@ planemo.reports.xunit\_handler module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.rst b/docs/planemo.rst index 2311a2fc0..0b9762f7f 100644 --- a/docs/planemo.rst +++ b/docs/planemo.rst @@ -232,7 +232,6 @@ planemo.workflow\_lint module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.shed.rst b/docs/planemo.shed.rst index 5e79c2f38..15dea09f4 100644 --- a/docs/planemo.shed.rst +++ b/docs/planemo.shed.rst @@ -20,7 +20,6 @@ planemo.shed.interface module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.shed2tap.rst b/docs/planemo.shed2tap.rst index cf931a762..3694f3761 100644 --- a/docs/planemo.shed2tap.rst +++ b/docs/planemo.shed2tap.rst @@ -12,7 +12,6 @@ planemo.shed2tap.base module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.test.rst b/docs/planemo.test.rst index 20f2794cf..9f2575e7a 100644 --- a/docs/planemo.test.rst +++ b/docs/planemo.test.rst @@ -20,7 +20,6 @@ planemo.test.results module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.training.rst b/docs/planemo.training.rst index 275ddae5d..c436ec0ff 100644 --- a/docs/planemo.training.rst +++ b/docs/planemo.training.rst @@ -36,7 +36,6 @@ planemo.training.utils module :undoc-members: :show-inheritance: - Module contents --------------- diff --git a/docs/planemo.xml.rst b/docs/planemo.xml.rst index 589f6adec..2c7bea38c 100644 --- a/docs/planemo.xml.rst +++ b/docs/planemo.xml.rst @@ -20,7 +20,6 @@ planemo.xml.validation module :undoc-members: :show-inheritance: - Module contents --------------- From 730818c130bca886e5d19372ae84cfc9c90c23d1 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 24 Nov 2020 10:05:36 +0000 Subject: [PATCH 6/6] Remove Travis jobs that are already on GH workflow --- .travis.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2d41c1dbd..6034c5ecd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,10 +6,6 @@ matrix: env: TOX_ENV=py37-lint_docstrings - python: 3.7 env: TOX_ENV=py37-unit-diagnostic-serveshed - - python: 3.7 - env: TOX_ENV=py37-unit-quick - - python: 3.7 - env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-2005 - python: 3.7 env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-master - python: 3.7