HISTORY.rst
LICENSE
MANIFEST.in
README.rst
dev-requirements.txt
pyproject.toml
setup.cfg
test-requirements.txt
galaxy/__init__.py
galaxy/app.py
galaxy/config_watchers.py
galaxy/di.py
galaxy/main.py
galaxy/main_config.py
galaxy/py.typed
galaxy/queue_worker.py
galaxy/queues.py
galaxy/structured_app.py
galaxy/actions/__init__.py
galaxy/actions/library.py
galaxy/app_unittest_utils/__init__.py
galaxy/app_unittest_utils/galaxy_mock.py
galaxy/app_unittest_utils/toolbox_support.py
galaxy/app_unittest_utils/tools_support.py
galaxy/authnz/__init__.py
galaxy/authnz/custos_authnz.py
galaxy/authnz/managers.py
galaxy/authnz/psa_authnz.py
galaxy/authnz/tapis.py
galaxy/authnz/util.py
galaxy/carbon_emissions/__init__.py
galaxy/carbon_emissions/carbon_intensity.csv
galaxy/celery/__init__.py
galaxy/celery/_serialization.py
galaxy/celery/base_task.py
galaxy/celery/tasks.py
galaxy/dependencies/__init__.py
galaxy/dependencies/conditional-requirements.txt
galaxy/dependencies/dev-requirements.txt
galaxy/dependencies/lint-requirements.txt
galaxy/dependencies/pinned-lint-requirements.txt
galaxy/dependencies/pinned-requirements.txt
galaxy/dependencies/pinned-typecheck-requirements.txt
galaxy/dependencies/script.py
galaxy/dependencies/update.sh
galaxy/dependencies/update_lint_requirements.sh
galaxy/forms/__init__.py
galaxy/forms/forms.py
galaxy/jobs/__init__.py
galaxy/jobs/command_factory.py
galaxy/jobs/dynamic_tool_destination.py
galaxy/jobs/handler.py
galaxy/jobs/manager.py
galaxy/jobs/mapper.py
galaxy/jobs/rule_helper.py
galaxy/jobs/stock_rules.py
galaxy/jobs/rules/__init__.py
galaxy/jobs/runners/__init__.py
galaxy/jobs/runners/aws.py
galaxy/jobs/runners/chronos.py
galaxy/jobs/runners/cli.py
galaxy/jobs/runners/condor.py
galaxy/jobs/runners/drmaa.py
galaxy/jobs/runners/godocker.py
galaxy/jobs/runners/kubernetes.py
galaxy/jobs/runners/local.py
galaxy/jobs/runners/pbs.py
galaxy/jobs/runners/pulsar.py
galaxy/jobs/runners/slurm.py
galaxy/jobs/runners/state_handler_factory.py
galaxy/jobs/runners/tasks.py
galaxy/jobs/runners/univa.py
galaxy/jobs/runners/state_handlers/__init__.py
galaxy/jobs/runners/state_handlers/_safe_eval.py
galaxy/jobs/runners/state_handlers/resubmit.py
galaxy/jobs/runners/util/__init__.py
galaxy/jobs/runners/util/env.py
galaxy/jobs/runners/util/external.py
galaxy/jobs/runners/util/fork_safe_write.py
galaxy/jobs/runners/util/kill.py
galaxy/jobs/runners/util/process_groups.py
galaxy/jobs/runners/util/pykube_util.py
galaxy/jobs/runners/util/sudo.py
galaxy/jobs/runners/util/cli/__init__.py
galaxy/jobs/runners/util/cli/factory.py
galaxy/jobs/runners/util/cli/job/__init__.py
galaxy/jobs/runners/util/cli/job/lsf.py
galaxy/jobs/runners/util/cli/job/pbs.py
galaxy/jobs/runners/util/cli/job/slurm.py
galaxy/jobs/runners/util/cli/job/slurm_torque.py
galaxy/jobs/runners/util/cli/job/torque.py
galaxy/jobs/runners/util/cli/shell/__init__.py
galaxy/jobs/runners/util/cli/shell/local.py
galaxy/jobs/runners/util/cli/shell/rsh.py
galaxy/jobs/runners/util/condor/__init__.py
galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT_TEMPLATE.sh
galaxy/jobs/runners/util/job_script/__init__.py
galaxy/jobs/splitters/__init__.py
galaxy/jobs/splitters/basic.py
galaxy/jobs/splitters/multi.py
galaxy/managers/__init__.py
galaxy/managers/_config_templates.py
galaxy/managers/annotatable.py
galaxy/managers/api_keys.py
galaxy/managers/base.py
galaxy/managers/chat.py
galaxy/managers/citations.py
galaxy/managers/collections.py
galaxy/managers/collections_util.py
galaxy/managers/configuration.py
galaxy/managers/context.py
galaxy/managers/datasets.py
galaxy/managers/datatypes.py
galaxy/managers/dbkeys.py
galaxy/managers/deletable.py
galaxy/managers/display_applications.py
galaxy/managers/executables.py
galaxy/managers/export_tracker.py
galaxy/managers/file_source_instances.py
galaxy/managers/folders.py
galaxy/managers/forms.py
galaxy/managers/genomes.py
galaxy/managers/group_roles.py
galaxy/managers/group_users.py
galaxy/managers/groups.py
galaxy/managers/hdas.py
galaxy/managers/hdcas.py
galaxy/managers/histories.py
galaxy/managers/history_contents.py
galaxy/managers/interactivetool.py
galaxy/managers/item_tags.py
galaxy/managers/job_connections.py
galaxy/managers/jobs.py
galaxy/managers/landing.py
galaxy/managers/lddas.py
galaxy/managers/libraries.py
galaxy/managers/library_datasets.py
galaxy/managers/licenses.json
galaxy/managers/licenses.py
galaxy/managers/markdown_export_base.css
galaxy/managers/markdown_parse.py
galaxy/managers/markdown_util.py
galaxy/managers/metrics.py
galaxy/managers/model_stores.py
galaxy/managers/notification.py
galaxy/managers/object_store_instances.py
galaxy/managers/pages.py
galaxy/managers/quotas.py
galaxy/managers/ratable.py
galaxy/managers/rbac_secured.py
galaxy/managers/remote_files.py
galaxy/managers/roles.py
galaxy/managers/secured.py
galaxy/managers/session.py
galaxy/managers/sharable.py
galaxy/managers/taggable.py
galaxy/managers/tags.py
galaxy/managers/tasks.py
galaxy/managers/tool_data.py
galaxy/managers/tools.py
galaxy/managers/users.py
galaxy/managers/visualizations.py
galaxy/managers/workflows.py
galaxy/short_term_storage/__init__.py
galaxy/tool_shed/__init__.py
galaxy/tool_shed/cache.py
galaxy/tool_shed/repository_type.py
galaxy/tool_shed/galaxy_install/__init__.py
galaxy/tool_shed/galaxy_install/client.py
galaxy/tool_shed/galaxy_install/install_manager.py
galaxy/tool_shed/galaxy_install/installed_repository_manager.py
galaxy/tool_shed/galaxy_install/update_repository_manager.py
galaxy/tool_shed/galaxy_install/metadata/__init__.py
galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
galaxy/tool_shed/galaxy_install/repository_dependencies/__init__.py
galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
galaxy/tool_shed/galaxy_install/tools/__init__.py
galaxy/tool_shed/galaxy_install/tools/data_manager.py
galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
galaxy/tool_shed/metadata/__init__.py
galaxy/tool_shed/metadata/metadata_generator.py
galaxy/tool_shed/tools/__init__.py
galaxy/tool_shed/tools/data_table_manager.py
galaxy/tool_shed/tools/tool_validator.py
galaxy/tool_shed/unittest_utils/__init__.py
galaxy/tool_shed/util/__init__.py
galaxy/tool_shed/util/basic_util.py
galaxy/tool_shed/util/container_util.py
galaxy/tool_shed/util/dependency_display.py
galaxy/tool_shed/util/hg_util.py
galaxy/tool_shed/util/metadata_util.py
galaxy/tool_shed/util/repository_util.py
galaxy/tool_shed/util/shed_util_common.py
galaxy/tool_shed/util/tool_dependency_util.py
galaxy/tool_shed/util/tool_util.py
galaxy/tool_shed/util/utility_container_manager.py
galaxy/tools/__init__.py
galaxy/tools/_types.py
galaxy/tools/apply_rules.xml
galaxy/tools/biotools.py
galaxy/tools/build_list.xml
galaxy/tools/build_list_1.2.0.xml
galaxy/tools/cache.py
galaxy/tools/cross_product_flat.xml
galaxy/tools/cross_product_nested.xml
galaxy/tools/data_fetch.py
galaxy/tools/data_fetch.xml
galaxy/tools/duplicate_file_to_collection.xml
galaxy/tools/errors.py
galaxy/tools/evaluation.py
galaxy/tools/exception_handling.py
galaxy/tools/execute.py
galaxy/tools/execution_helpers.py
galaxy/tools/extract_dataset.xml
galaxy/tools/filter_empty_collection.xml
galaxy/tools/filter_empty_collection_1.1.0.xml
galaxy/tools/filter_failed_collection.xml
galaxy/tools/filter_from_file.xml
galaxy/tools/filter_from_file_1.1.0.xml
galaxy/tools/filter_null.xml
galaxy/tools/filter_null_1.1.0.xml
galaxy/tools/flatten_collection.xml
galaxy/tools/harmonize_two_collections_list.xml
galaxy/tools/keep_success_collection.xml
galaxy/tools/keep_success_collection_1.1.0.xml
galaxy/tools/merge_collection.xml
galaxy/tools/model_operation_macros.xml
galaxy/tools/recommendations.py
galaxy/tools/relabel_from_file.xml
galaxy/tools/remote_tool_eval.py
galaxy/tools/repositories.py
galaxy/tools/sort_collection_list.xml
galaxy/tools/special_tools.py
galaxy/tools/split_paired_and_unpaired.xml
galaxy/tools/stock.py
galaxy/tools/tag_collection_from_file.xml
galaxy/tools/unzip_collection.xml
galaxy/tools/wrappers.py
galaxy/tools/zip_collection.xml
galaxy/tools/actions/__init__.py
galaxy/tools/actions/data_manager.py
galaxy/tools/actions/data_source.py
galaxy/tools/actions/history_imp_exp.py
galaxy/tools/actions/metadata.py
galaxy/tools/actions/model_operations.py
galaxy/tools/actions/upload.py
galaxy/tools/actions/upload_common.py
galaxy/tools/bundled/__init__.py
galaxy/tools/bundled/data_export/export_remote.py
galaxy/tools/bundled/data_export/export_remote.xml
galaxy/tools/bundled/data_source/__init__.py
galaxy/tools/bundled/data_source/access_libraries.xml
galaxy/tools/bundled/data_source/biomart.xml
galaxy/tools/bundled/data_source/biomart_test.xml
galaxy/tools/bundled/data_source/cbi_rice_mart.xml
galaxy/tools/bundled/data_source/data_source.py
galaxy/tools/bundled/data_source/diced.xml
galaxy/tools/bundled/data_source/ebi_sra.xml
galaxy/tools/bundled/data_source/eupathdb.xml
galaxy/tools/bundled/data_source/fly_modencode.xml
galaxy/tools/bundled/data_source/flymine.xml
galaxy/tools/bundled/data_source/flymine_test.xml
galaxy/tools/bundled/data_source/genbank.py
galaxy/tools/bundled/data_source/genbank.xml
galaxy/tools/bundled/data_source/gramene_mart.xml
galaxy/tools/bundled/data_source/hapmapmart.xml
galaxy/tools/bundled/data_source/hbvar.xml
galaxy/tools/bundled/data_source/import.py
galaxy/tools/bundled/data_source/import.xml
galaxy/tools/bundled/data_source/intermine.xml
galaxy/tools/bundled/data_source/metabolicmine.xml
galaxy/tools/bundled/data_source/microbial_import.py
galaxy/tools/bundled/data_source/microbial_import.xml
galaxy/tools/bundled/data_source/microbial_import_code.py
galaxy/tools/bundled/data_source/modmine.xml
galaxy/tools/bundled/data_source/mousemine.xml
galaxy/tools/bundled/data_source/ncbi_datasets.xml
galaxy/tools/bundled/data_source/ratmine.xml
galaxy/tools/bundled/data_source/sra.xml
galaxy/tools/bundled/data_source/ucsc_tablebrowser.xml
galaxy/tools/bundled/data_source/ucsc_tablebrowser_archaea.xml
galaxy/tools/bundled/data_source/ucsc_tablebrowser_test.xml
galaxy/tools/bundled/data_source/upload.py
galaxy/tools/bundled/data_source/upload.xml
galaxy/tools/bundled/data_source/worm_modencode.xml
galaxy/tools/bundled/data_source/wormbase.xml
galaxy/tools/bundled/data_source/wormbase_test.xml
galaxy/tools/bundled/data_source/yeastmine.xml
galaxy/tools/bundled/data_source/zebrafishmine.xml
galaxy/tools/bundled/expression_tools/expression_macros.xml
galaxy/tools/bundled/expression_tools/parse_values_from_file.xml
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galaxy/tools/bundled/extract/extract_genomic_dna.py
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galaxy/tools/bundled/extract/liftOver_wrapper.py
galaxy/tools/bundled/extract/liftOver_wrapper.xml
galaxy/tools/bundled/filters/CreateInterval.pl
galaxy/tools/bundled/filters/CreateInterval.xml
galaxy/tools/bundled/filters/__init__.py
galaxy/tools/bundled/filters/axt_to_concat_fasta.py
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galaxy/tools/bundled/filters/joiner2.xml
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galaxy/tools/bundled/filters/gff/__init__.py
galaxy/tools/bundled/filters/gff/extract_GFF_Features.py
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galaxy/tools/bundled/filters/gff/gff_filter_by_attribute.py
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