├── .coveragerc ├── .editorconfig ├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── .isort.cfg ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── dev-requirements.txt ├── docs ├── Makefile ├── _static │ └── .gitkeep ├── commands.rst ├── commands │ ├── galaxy-wait.rst │ ├── get-tool-list.rst │ ├── install-tool-deps.rst │ ├── run-data-managers.rst │ ├── setup-data-libraries.rst │ ├── shed-tools.rst │ ├── workflow-install.rst │ └── workflow-to-tools.rst ├── conduct.rst ├── conf.py ├── contributing.rst ├── developing.rst ├── ephemeris.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── organization.rst ├── readme.rst └── requirements.txt ├── pyproject.toml ├── requirements.txt ├── scripts ├── bootstrap_history.py ├── commit_version.py ├── new_version.py ├── pre-commit-lint ├── pre-commit-lint-and-test ├── print_version_for_release.py └── test_wheel.bash ├── setup.cfg ├── setup.py ├── src └── ephemeris │ ├── __init__.py │ ├── _config_models.py │ ├── _idc_data_managers_to_tools.py │ ├── _idc_lint.py │ ├── _idc_split_data_manager_genomes.py │ ├── common_parser.py │ ├── ephemeris_log.py │ ├── generate_tool_list_from_ga_workflow_files.py │ ├── get_tool_list_from_galaxy.py │ ├── install_tool_deps.py │ ├── run_data_managers.py │ ├── set_library_permissions.py │ ├── setup_data_libraries.py │ ├── shed_tools.py │ ├── shed_tools_args.py │ ├── shed_tools_methods.py │ ├── sleep.py │ └── workflow_install.py ├── tests ├── .gitkeep ├── __init__.py ├── conftest.py ├── data_manager_list.yaml ├── library_data_example.yaml ├── library_data_example_legacy.yaml ├── run_data_managers.yaml.sample ├── run_data_managers.yaml.sample.advanced ├── run_data_managers.yaml.test ├── test_idc_data_managers_to_tools.py ├── test_idc_lint.py ├── test_run_data_managers.py ├── test_setup_data_libraries_cli.py ├── test_shed_tools.py ├── test_shed_tools_cli.py ├── test_shed_tools_methods.py ├── test_split_genomes.py ├── test_workflow.ga ├── test_workflow_2.ga ├── test_workflow_install_cli.py └── tool_list.yaml.sample └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/ephemeris/HEAD/.coveragerc -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/ephemeris/HEAD/.editorconfig -------------------------------------------------------------------------------- /.github/workflows/ci.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/ephemeris/HEAD/.github/workflows/ci.yaml -------------------------------------------------------------------------------- /.gitignore: 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