├── .ci ├── autopep8.sh ├── flake8_docstrings_include_list.txt └── flake8_wrapper_docstrings.sh ├── .coveragerc ├── .editorconfig ├── .gitignore ├── .travis.yml ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── dev-requirements.txt ├── docs ├── .planemo.yml ├── Makefile ├── conduct.rst ├── conf.py ├── contributing.rst ├── developing.rst ├── galaxy.containers.rst ├── galaxy.exceptions.rst ├── galaxy.jobs.metrics.collectl.rst ├── galaxy.jobs.metrics.instrumenters.rst ├── galaxy.jobs.metrics.rst ├── galaxy.jobs.rst ├── galaxy.objectstore.rst ├── galaxy.rst ├── galaxy.tools.cwl.rst ├── galaxy.tools.deps.container_resolvers.rst ├── galaxy.tools.deps.mulled.rst ├── galaxy.tools.deps.resolvers.rst ├── galaxy.tools.deps.rst ├── galaxy.tools.linters.rst ├── galaxy.tools.locations.rst ├── galaxy.tools.parser.rst ├── galaxy.tools.rst ├── galaxy.tools.toolbox.filters.rst ├── galaxy.tools.toolbox.lineages.rst ├── galaxy.tools.toolbox.rst ├── galaxy.tools.verify.asserts.rst ├── galaxy.tools.verify.rst ├── galaxy.util.logging.rst ├── galaxy.util.path.rst ├── galaxy.util.rst ├── galaxy.web.rst ├── history.rst ├── images │ └── .gitkeep ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── readme.rst └── topics │ ├── dependency_resolution.rst │ ├── index.rst │ └── mulled.rst ├── galaxy ├── __init__.py ├── containers │ ├── __init__.py │ ├── docker.py │ ├── docker_decorators.py │ ├── docker_model.py │ └── docker_swarm.py ├── exceptions │ ├── __init__.py │ ├── error_codes.json │ └── error_codes.py ├── jobs │ ├── __init__.py │ └── metrics │ │ ├── __init__.py │ │ ├── collectl │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── processes.py │ │ ├── stats.py │ │ └── subsystems.py │ │ ├── formatting.py │ │ └── instrumenters │ │ ├── __init__.py │ │ ├── cgroup.py │ │ ├── collectl.py │ │ ├── core.py │ │ ├── cpuinfo.py │ │ ├── env.py │ │ ├── hostname.py │ │ ├── meminfo.py │ │ └── uname.py ├── objectstore │ ├── __init__.py │ ├── azure_blob.py │ ├── cloud.py │ ├── pithos.py │ ├── pulsar.py │ ├── rods.py │ ├── s3.py │ └── s3_multipart_upload.py ├── tools │ ├── __init__.py │ ├── cwl │ │ ├── __init__.py │ │ ├── cwltool_deps.py │ │ ├── parser.py │ │ ├── representation.py │ │ ├── runtime_actions.py │ │ ├── schema.py │ │ └── util.py │ ├── deps │ │ ├── __init__.py │ │ ├── brew_exts.py │ │ ├── brew_util.py │ │ ├── commands.py │ │ ├── conda_compat.py │ │ ├── conda_util.py │ │ ├── container_classes.py │ │ ├── container_resolvers │ │ │ ├── __init__.py │ │ │ ├── explicit.py │ │ │ └── mulled.py │ │ ├── containers.py │ │ ├── dependencies.py │ │ ├── docker_util.py │ │ ├── dockerfiles.py │ │ ├── installable.py │ │ ├── mulled │ │ │ ├── __init__.py │ │ │ ├── _cli.py │ │ │ ├── invfile.lua │ │ │ ├── mulled_build.py │ │ │ ├── mulled_build_channel.py │ │ │ ├── mulled_build_files.py │ │ │ ├── mulled_build_tool.py │ │ │ ├── mulled_search.py │ │ │ └── util.py │ │ ├── requirements.py │ │ ├── resolvers │ │ │ ├── __init__.py │ │ │ ├── brewed_tool_shed_packages.py │ │ │ ├── conda.py │ │ │ ├── default_conda_mapping.yml │ │ │ ├── galaxy_packages.py │ │ │ ├── homebrew.py │ │ │ ├── lmod.py │ │ │ ├── modules.py │ │ │ ├── resolver_mixins.py │ │ │ ├── tool_shed_packages.py │ │ │ └── unlinked_tool_shed_packages.py │ │ ├── singularity_util.py │ │ └── views.py │ ├── fetcher.py │ ├── hash.py │ ├── lint.py │ ├── lint_util.py │ ├── linters │ │ ├── __init__.py │ │ ├── citations.py │ │ ├── command.py │ │ ├── cwl.py │ │ ├── general.py │ │ ├── help.py │ │ ├── inputs.py │ │ ├── outputs.py │ │ ├── stdio.py │ │ ├── tests.py │ │ └── xml_order.py │ ├── loader.py │ ├── loader_directory.py │ ├── locations │ │ ├── __init__.py │ │ ├── dockstore.py │ │ ├── file.py │ │ └── http.py │ ├── parser │ │ ├── __init__.py │ │ ├── cwl.py │ │ ├── error_level.py │ │ ├── factory.py │ │ ├── interface.py │ │ ├── output_actions.py │ │ ├── output_collection_def.py │ │ ├── output_objects.py │ │ ├── util.py │ │ ├── xml.py │ │ └── yaml.py │ ├── toolbox │ │ ├── __init__.py │ │ ├── base.py │ │ ├── filters │ │ │ ├── __init__.py │ │ │ └── examples.py.sample │ │ ├── integrated_panel.py │ │ ├── lineages │ │ │ ├── __init__.py │ │ │ ├── factory.py │ │ │ └── interface.py │ │ ├── panel.py │ │ ├── parser.py │ │ ├── tags.py │ │ └── watcher.py │ ├── verify │ │ ├── __init__.py │ │ ├── asserts │ │ │ ├── __init__.py │ │ │ ├── hdf5.py │ │ │ ├── tabular.py │ │ │ ├── text.py │ │ │ └── xml.py │ │ ├── interactor.py │ │ ├── script.py │ │ └── test_data.py │ └── xsd │ │ ├── LICENSE │ │ ├── README.md │ │ ├── galaxy.jxb │ │ └── galaxy.xsd ├── util │ ├── __init__.py │ ├── aliaspickler.py │ ├── bunch.py │ ├── checkers.py │ ├── compression_utils.py │ ├── dictifiable.py │ ├── docutils_template.txt │ ├── expressions.py │ ├── facts.py │ ├── filelock.py │ ├── hash_util.py │ ├── heartbeat.py │ ├── image_util.py │ ├── inflection.py │ ├── json.py │ ├── lazy_process.py │ ├── logging │ │ ├── __init__.py │ │ └── fluent_log.py │ ├── object_wrapper.py │ ├── odict.py │ ├── oset.py │ ├── path │ │ ├── __init__.py │ │ ├── ntpath.py │ │ └── posixpath.py │ ├── plugin_config.py │ ├── properties.py │ ├── simplegraph.py │ ├── sleeper.py │ ├── sockets.py │ ├── specs.py │ ├── sqlite.py │ ├── submodules.py │ ├── tool_version.py │ ├── topsort.py │ └── xml_macros.py └── web │ └── __init__.py ├── requirements.txt ├── scripts ├── commit_version.py ├── new_version.py ├── pre-commit-lint ├── pre-commit-lint-and-test ├── print_version_for_release.py ├── test_wheel.bash └── update_bioconda.bash ├── setup.cfg ├── setup.py ├── tests ├── test_lazy_process.py ├── test_objectstore.py ├── test_sockets.py ├── test_sqlite_utils.py ├── test_topsort.py ├── test_utils.py └── tools │ ├── test_cwl_util.py │ ├── test_parsing.py │ ├── test_tool_deps.py │ ├── test_tool_loader.py │ ├── test_toolbox_filters.py │ └── test_watcher.py ├── tox.ini └── update_galaxy_utils.sh /.ci/autopep8.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.ci/autopep8.sh -------------------------------------------------------------------------------- /.ci/flake8_docstrings_include_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.ci/flake8_docstrings_include_list.txt -------------------------------------------------------------------------------- /.ci/flake8_wrapper_docstrings.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.ci/flake8_wrapper_docstrings.sh -------------------------------------------------------------------------------- /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.coveragerc -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/.travis.yml -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/CODE_OF_CONDUCT.rst -------------------------------------------------------------------------------- /CONTRIBUTING.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/CONTRIBUTING.rst -------------------------------------------------------------------------------- /HISTORY.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/HISTORY.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/Makefile -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/README.rst -------------------------------------------------------------------------------- /dev-requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/dev-requirements.txt -------------------------------------------------------------------------------- /docs/.planemo.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/.planemo.yml -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/conduct.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../CODE_OF_CONDUCT.rst 2 | -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/contributing.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../CONTRIBUTING.rst -------------------------------------------------------------------------------- /docs/developing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/developing.rst -------------------------------------------------------------------------------- /docs/galaxy.containers.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.containers.rst -------------------------------------------------------------------------------- /docs/galaxy.exceptions.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.exceptions.rst -------------------------------------------------------------------------------- /docs/galaxy.jobs.metrics.collectl.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.jobs.metrics.collectl.rst -------------------------------------------------------------------------------- /docs/galaxy.jobs.metrics.instrumenters.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.jobs.metrics.instrumenters.rst -------------------------------------------------------------------------------- /docs/galaxy.jobs.metrics.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.jobs.metrics.rst -------------------------------------------------------------------------------- /docs/galaxy.jobs.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.jobs.rst -------------------------------------------------------------------------------- /docs/galaxy.objectstore.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.objectstore.rst -------------------------------------------------------------------------------- /docs/galaxy.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.cwl.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.cwl.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.deps.container_resolvers.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.deps.container_resolvers.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.deps.mulled.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.deps.mulled.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.deps.resolvers.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.deps.resolvers.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.deps.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.deps.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.linters.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.linters.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.locations.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.locations.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.parser.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.parser.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.toolbox.filters.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.toolbox.filters.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.toolbox.lineages.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.toolbox.lineages.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.toolbox.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.toolbox.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.verify.asserts.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.verify.asserts.rst -------------------------------------------------------------------------------- /docs/galaxy.tools.verify.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.tools.verify.rst -------------------------------------------------------------------------------- /docs/galaxy.util.logging.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.util.logging.rst -------------------------------------------------------------------------------- /docs/galaxy.util.path.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.util.path.rst -------------------------------------------------------------------------------- /docs/galaxy.util.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.util.rst -------------------------------------------------------------------------------- /docs/galaxy.web.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/galaxy.web.rst -------------------------------------------------------------------------------- /docs/history.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../HISTORY.rst -------------------------------------------------------------------------------- /docs/images/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/modules.rst -------------------------------------------------------------------------------- /docs/readme.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../README.rst -------------------------------------------------------------------------------- /docs/topics/dependency_resolution.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/topics/dependency_resolution.rst -------------------------------------------------------------------------------- /docs/topics/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/topics/index.rst -------------------------------------------------------------------------------- /docs/topics/mulled.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/docs/topics/mulled.rst -------------------------------------------------------------------------------- /galaxy/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/__init__.py -------------------------------------------------------------------------------- /galaxy/containers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/containers/__init__.py -------------------------------------------------------------------------------- /galaxy/containers/docker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/containers/docker.py -------------------------------------------------------------------------------- /galaxy/containers/docker_decorators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/containers/docker_decorators.py -------------------------------------------------------------------------------- /galaxy/containers/docker_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/containers/docker_model.py -------------------------------------------------------------------------------- /galaxy/containers/docker_swarm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/containers/docker_swarm.py -------------------------------------------------------------------------------- /galaxy/exceptions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/exceptions/__init__.py -------------------------------------------------------------------------------- /galaxy/exceptions/error_codes.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/exceptions/error_codes.json -------------------------------------------------------------------------------- /galaxy/exceptions/error_codes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/exceptions/error_codes.py -------------------------------------------------------------------------------- /galaxy/jobs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /galaxy/jobs/metrics/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/__init__.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/collectl/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/collectl/__init__.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/collectl/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/collectl/cli.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/collectl/processes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/collectl/processes.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/collectl/stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/collectl/stats.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/collectl/subsystems.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/collectl/subsystems.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/formatting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/formatting.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/__init__.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/cgroup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/cgroup.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/collectl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/collectl.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/core.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/cpuinfo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/cpuinfo.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/env.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/env.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/hostname.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/hostname.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/meminfo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/meminfo.py -------------------------------------------------------------------------------- /galaxy/jobs/metrics/instrumenters/uname.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/jobs/metrics/instrumenters/uname.py -------------------------------------------------------------------------------- /galaxy/objectstore/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/__init__.py -------------------------------------------------------------------------------- /galaxy/objectstore/azure_blob.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/azure_blob.py -------------------------------------------------------------------------------- /galaxy/objectstore/cloud.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/cloud.py -------------------------------------------------------------------------------- /galaxy/objectstore/pithos.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/pithos.py -------------------------------------------------------------------------------- /galaxy/objectstore/pulsar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/pulsar.py -------------------------------------------------------------------------------- /galaxy/objectstore/rods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/rods.py -------------------------------------------------------------------------------- /galaxy/objectstore/s3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/s3.py -------------------------------------------------------------------------------- /galaxy/objectstore/s3_multipart_upload.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/objectstore/s3_multipart_upload.py -------------------------------------------------------------------------------- /galaxy/tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /galaxy/tools/cwl/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/cwltool_deps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/cwltool_deps.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/parser.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/representation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/representation.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/runtime_actions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/runtime_actions.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/schema.py -------------------------------------------------------------------------------- /galaxy/tools/cwl/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/cwl/util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/deps/brew_exts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/brew_exts.py -------------------------------------------------------------------------------- /galaxy/tools/deps/brew_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/brew_util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/commands.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/commands.py -------------------------------------------------------------------------------- /galaxy/tools/deps/conda_compat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/conda_compat.py -------------------------------------------------------------------------------- /galaxy/tools/deps/conda_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/conda_util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/container_classes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/container_classes.py -------------------------------------------------------------------------------- /galaxy/tools/deps/container_resolvers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/container_resolvers/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/deps/container_resolvers/explicit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/container_resolvers/explicit.py -------------------------------------------------------------------------------- /galaxy/tools/deps/container_resolvers/mulled.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/container_resolvers/mulled.py -------------------------------------------------------------------------------- /galaxy/tools/deps/containers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/containers.py -------------------------------------------------------------------------------- /galaxy/tools/deps/dependencies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/dependencies.py -------------------------------------------------------------------------------- /galaxy/tools/deps/docker_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/docker_util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/dockerfiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/dockerfiles.py -------------------------------------------------------------------------------- /galaxy/tools/deps/installable.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/installable.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/_cli.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/invfile.lua: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/invfile.lua -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/mulled_build.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/mulled_build.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/mulled_build_channel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/mulled_build_channel.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/mulled_build_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/mulled_build_files.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/mulled_build_tool.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/mulled_build_tool.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/mulled_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/mulled_search.py -------------------------------------------------------------------------------- /galaxy/tools/deps/mulled/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/mulled/util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/requirements.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/requirements.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/conda.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/conda.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/default_conda_mapping.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/default_conda_mapping.yml -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/galaxy_packages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/galaxy_packages.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/homebrew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/homebrew.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/lmod.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/lmod.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/modules.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/resolver_mixins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/resolver_mixins.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/tool_shed_packages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/tool_shed_packages.py -------------------------------------------------------------------------------- /galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py -------------------------------------------------------------------------------- /galaxy/tools/deps/singularity_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/singularity_util.py -------------------------------------------------------------------------------- /galaxy/tools/deps/views.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/deps/views.py -------------------------------------------------------------------------------- /galaxy/tools/fetcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/fetcher.py -------------------------------------------------------------------------------- /galaxy/tools/hash.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/hash.py -------------------------------------------------------------------------------- /galaxy/tools/lint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/lint.py -------------------------------------------------------------------------------- /galaxy/tools/lint_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/lint_util.py -------------------------------------------------------------------------------- /galaxy/tools/linters/__init__.py: -------------------------------------------------------------------------------- 1 | """This package contains linting functions for Galaxy tools.""" 2 | -------------------------------------------------------------------------------- /galaxy/tools/linters/citations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/citations.py -------------------------------------------------------------------------------- /galaxy/tools/linters/command.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/command.py -------------------------------------------------------------------------------- /galaxy/tools/linters/cwl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/cwl.py -------------------------------------------------------------------------------- /galaxy/tools/linters/general.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/general.py -------------------------------------------------------------------------------- /galaxy/tools/linters/help.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/help.py -------------------------------------------------------------------------------- /galaxy/tools/linters/inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/inputs.py -------------------------------------------------------------------------------- /galaxy/tools/linters/outputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/outputs.py -------------------------------------------------------------------------------- /galaxy/tools/linters/stdio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/stdio.py -------------------------------------------------------------------------------- /galaxy/tools/linters/tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/tests.py -------------------------------------------------------------------------------- /galaxy/tools/linters/xml_order.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/linters/xml_order.py -------------------------------------------------------------------------------- /galaxy/tools/loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/loader.py -------------------------------------------------------------------------------- /galaxy/tools/loader_directory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/loader_directory.py -------------------------------------------------------------------------------- /galaxy/tools/locations/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/locations/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/locations/dockstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/locations/dockstore.py -------------------------------------------------------------------------------- /galaxy/tools/locations/file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/locations/file.py -------------------------------------------------------------------------------- /galaxy/tools/locations/http.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/locations/http.py -------------------------------------------------------------------------------- /galaxy/tools/parser/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/parser/cwl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/cwl.py -------------------------------------------------------------------------------- /galaxy/tools/parser/error_level.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/error_level.py -------------------------------------------------------------------------------- /galaxy/tools/parser/factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/factory.py -------------------------------------------------------------------------------- /galaxy/tools/parser/interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/interface.py -------------------------------------------------------------------------------- /galaxy/tools/parser/output_actions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/output_actions.py -------------------------------------------------------------------------------- /galaxy/tools/parser/output_collection_def.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/output_collection_def.py -------------------------------------------------------------------------------- /galaxy/tools/parser/output_objects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/output_objects.py -------------------------------------------------------------------------------- /galaxy/tools/parser/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/util.py -------------------------------------------------------------------------------- /galaxy/tools/parser/xml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/xml.py -------------------------------------------------------------------------------- /galaxy/tools/parser/yaml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/parser/yaml.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/base.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/filters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/filters/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/filters/examples.py.sample: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/filters/examples.py.sample -------------------------------------------------------------------------------- /galaxy/tools/toolbox/integrated_panel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/integrated_panel.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/lineages/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/lineages/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/lineages/factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/lineages/factory.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/lineages/interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/lineages/interface.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/panel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/panel.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/parser.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/tags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/tags.py -------------------------------------------------------------------------------- /galaxy/tools/toolbox/watcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/toolbox/watcher.py -------------------------------------------------------------------------------- /galaxy/tools/verify/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/verify/asserts/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/asserts/__init__.py -------------------------------------------------------------------------------- /galaxy/tools/verify/asserts/hdf5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/asserts/hdf5.py -------------------------------------------------------------------------------- /galaxy/tools/verify/asserts/tabular.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/asserts/tabular.py -------------------------------------------------------------------------------- /galaxy/tools/verify/asserts/text.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/asserts/text.py -------------------------------------------------------------------------------- /galaxy/tools/verify/asserts/xml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/asserts/xml.py -------------------------------------------------------------------------------- /galaxy/tools/verify/interactor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/interactor.py -------------------------------------------------------------------------------- /galaxy/tools/verify/script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/script.py -------------------------------------------------------------------------------- /galaxy/tools/verify/test_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/verify/test_data.py -------------------------------------------------------------------------------- /galaxy/tools/xsd/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/xsd/LICENSE -------------------------------------------------------------------------------- /galaxy/tools/xsd/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/xsd/README.md -------------------------------------------------------------------------------- /galaxy/tools/xsd/galaxy.jxb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/xsd/galaxy.jxb -------------------------------------------------------------------------------- /galaxy/tools/xsd/galaxy.xsd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/tools/xsd/galaxy.xsd -------------------------------------------------------------------------------- /galaxy/util/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/__init__.py -------------------------------------------------------------------------------- /galaxy/util/aliaspickler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/aliaspickler.py -------------------------------------------------------------------------------- /galaxy/util/bunch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/bunch.py -------------------------------------------------------------------------------- /galaxy/util/checkers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/checkers.py -------------------------------------------------------------------------------- /galaxy/util/compression_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/compression_utils.py -------------------------------------------------------------------------------- /galaxy/util/dictifiable.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/dictifiable.py -------------------------------------------------------------------------------- /galaxy/util/docutils_template.txt: -------------------------------------------------------------------------------- 1 | %(body)s 2 | -------------------------------------------------------------------------------- /galaxy/util/expressions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/expressions.py -------------------------------------------------------------------------------- /galaxy/util/facts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/facts.py -------------------------------------------------------------------------------- /galaxy/util/filelock.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/filelock.py -------------------------------------------------------------------------------- /galaxy/util/hash_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/hash_util.py -------------------------------------------------------------------------------- /galaxy/util/heartbeat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/heartbeat.py -------------------------------------------------------------------------------- /galaxy/util/image_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/image_util.py -------------------------------------------------------------------------------- /galaxy/util/inflection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/inflection.py -------------------------------------------------------------------------------- /galaxy/util/json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/json.py -------------------------------------------------------------------------------- /galaxy/util/lazy_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/lazy_process.py -------------------------------------------------------------------------------- /galaxy/util/logging/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/logging/__init__.py -------------------------------------------------------------------------------- /galaxy/util/logging/fluent_log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/logging/fluent_log.py -------------------------------------------------------------------------------- /galaxy/util/object_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/object_wrapper.py -------------------------------------------------------------------------------- /galaxy/util/odict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/odict.py -------------------------------------------------------------------------------- /galaxy/util/oset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/oset.py -------------------------------------------------------------------------------- /galaxy/util/path/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/path/__init__.py -------------------------------------------------------------------------------- /galaxy/util/path/ntpath.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/path/ntpath.py -------------------------------------------------------------------------------- /galaxy/util/path/posixpath.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/path/posixpath.py -------------------------------------------------------------------------------- /galaxy/util/plugin_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/plugin_config.py -------------------------------------------------------------------------------- /galaxy/util/properties.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/properties.py -------------------------------------------------------------------------------- /galaxy/util/simplegraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/simplegraph.py -------------------------------------------------------------------------------- /galaxy/util/sleeper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/sleeper.py -------------------------------------------------------------------------------- /galaxy/util/sockets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/sockets.py -------------------------------------------------------------------------------- /galaxy/util/specs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/specs.py -------------------------------------------------------------------------------- /galaxy/util/sqlite.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/sqlite.py -------------------------------------------------------------------------------- /galaxy/util/submodules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/submodules.py -------------------------------------------------------------------------------- /galaxy/util/tool_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/tool_version.py -------------------------------------------------------------------------------- /galaxy/util/topsort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/topsort.py -------------------------------------------------------------------------------- /galaxy/util/xml_macros.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/galaxy/util/xml_macros.py -------------------------------------------------------------------------------- /galaxy/web/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | boltons 2 | six>=1.9.0 3 | docutils 4 | pyyaml 5 | packaging 6 | markupsafe 7 | -------------------------------------------------------------------------------- /scripts/commit_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/commit_version.py -------------------------------------------------------------------------------- /scripts/new_version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/new_version.py -------------------------------------------------------------------------------- /scripts/pre-commit-lint: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | make lint 4 | -------------------------------------------------------------------------------- /scripts/pre-commit-lint-and-test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/pre-commit-lint-and-test -------------------------------------------------------------------------------- /scripts/print_version_for_release.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/print_version_for_release.py -------------------------------------------------------------------------------- /scripts/test_wheel.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/test_wheel.bash -------------------------------------------------------------------------------- /scripts/update_bioconda.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/scripts/update_bioconda.bash -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/setup.py -------------------------------------------------------------------------------- /tests/test_lazy_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_lazy_process.py -------------------------------------------------------------------------------- /tests/test_objectstore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_objectstore.py -------------------------------------------------------------------------------- /tests/test_sockets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_sockets.py -------------------------------------------------------------------------------- /tests/test_sqlite_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_sqlite_utils.py -------------------------------------------------------------------------------- /tests/test_topsort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_topsort.py -------------------------------------------------------------------------------- /tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/test_utils.py -------------------------------------------------------------------------------- /tests/tools/test_cwl_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_cwl_util.py -------------------------------------------------------------------------------- /tests/tools/test_parsing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_parsing.py -------------------------------------------------------------------------------- /tests/tools/test_tool_deps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_tool_deps.py -------------------------------------------------------------------------------- /tests/tools/test_tool_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_tool_loader.py -------------------------------------------------------------------------------- /tests/tools/test_toolbox_filters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_toolbox_filters.py -------------------------------------------------------------------------------- /tests/tools/test_watcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tests/tools/test_watcher.py -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/tox.ini -------------------------------------------------------------------------------- /update_galaxy_utils.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/galaxy-lib/HEAD/update_galaxy_utils.sh --------------------------------------------------------------------------------