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galaxy/scripts
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Nicola Soranzo 575a1d8358 Merge pull request #14430 from bernt-matthias/unlink-job-template 
Deprecate `cluster_files_directory` and store DRMAA job template and PBS shell, error and out files in job working directory
2022-08-13 01:00:10 +01:00
..
api
Combine "as" imports with other "from" imports
2022-06-20 20:06:30 +01:00
auth
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2022-02-03 07:42:20 -05:00
cleanup_datasets
s/eagerload/joinedload (SQLAlchemy 2.0)
2022-03-16 16:48:33 -04:00
grt
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
loc_files
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2022-02-03 07:42:20 -05:00
metagenomics
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2022-02-03 07:42:20 -05:00
microbes
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2022-02-03 07:42:20 -05:00
objectstore
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2022-02-03 07:42:20 -05:00
slideshow
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2022-02-03 07:42:20 -05:00
taxonomy
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tool_shed
Combine "as" imports with other "from" imports
2022-06-20 20:06:30 +01:00
tools
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2022-02-03 07:42:20 -05:00
__init__.py
…
apply_tags.py
Fix B023 warnings from flake8-bugbear 22.7.1
2022-07-05 12:28:37 +01:00
bootstrap_history.py
Drop uncredit pull requestor list
2022-05-13 12:40:48 +01:00
build_toolbox.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
celery_shell.py
Fix a typo in celery_shell.py
2022-05-25 19:46:47 +02:00
check_eggs.py
Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run
2015-11-06 11:06:11 -05:00
check_model.py
Update db index testing: test both models, gxy and tsi
2022-03-09 18:41:03 -05:00
check_python.py
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2022-02-03 07:42:20 -05:00
common_startup_functions.sh
Fix first startup when only python3 is on PATH
2022-08-08 16:28:26 +02:00
common_startup.sh
Fix first startup when only python3 is on PATH
2022-08-08 16:28:26 +02:00
config_parse.py
Use `load_app_properties()` to load Galaxy config file
2022-04-26 09:48:18 +01:00
config_sample_to_kwalify.py
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2022-02-03 07:42:20 -05:00
create_db.py
Add create/migrate scripts for Alembic dbs (squashed)
2022-03-09 18:41:02 -05:00
create_toolshed_db.py
Apply black, isort (squashed)
2022-03-09 18:41:49 -05:00
cwl_conformance_to_test_cases.py
Update lists of non-passing CWL conformance tests
2022-07-04 14:15:01 +01:00
db_shell.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
drmaa_external_killer.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
drmaa_external_runner.py
remove more leftover references to cluster_files_directory
2022-08-12 16:07:35 +02:00
dump_library_paths.py
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2022-02-03 07:42:20 -05:00
edam_mapping.py
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2022-02-03 07:42:20 -05:00
external_chown_script.py
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2022-02-03 07:42:20 -05:00
extract_dataset_part.py
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2022-02-03 07:42:20 -05:00
extract_toolbox_sections.py
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2022-02-03 07:42:20 -05:00
fetch_eggs.py
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2022-02-03 07:42:20 -05:00
fix_dm_versions.py
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2022-02-03 07:42:20 -05:00
functional_tests.py
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2022-02-03 07:42:20 -05:00
galaxy_main.py
First pass in dropping uwsgi specific things
2022-03-15 21:31:59 +01:00
galaxy_schemadisp.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
galaxy-main
Adjust galaxy-main script so we can import from it for easy app setup
2020-12-22 11:18:00 +01:00
helper.py
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
maintenance.sh
Fix issues reported by ShellCheck
2019-06-13 12:53:26 +01:00
manage_db_adapter.py
Verify db initialization before running upgrade script
2022-07-13 16:38:11 -04:00
manage_db.py
Update inline documentation in scripts
2022-05-31 10:30:30 -04:00
manage_tool_dependencies.py
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2022-02-03 07:42:20 -05:00
migrate_db.py
Adapt manage_db.py for usegalaxy playbook; add tests
2022-03-09 18:41:50 -05:00
migrate_toolshed_db.py
Apply black, isort (squashed)
2022-03-09 18:41:49 -05:00
pages_identifier_conversion.py
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
patch.sh
Add the script I used to create security patches
2016-02-24 16:54:30 -05:00
plugin_staging.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
release-diff.py
First pass in dropping uwsgi specific things
2022-03-15 21:31:59 +01:00
release.sh
Test Galaxy release script
2021-12-08 10:43:09 +00:00
resumable_upload.py
Merge branch 'release_22.01' into release_22.05
2022-07-02 18:07:38 +02:00
rst2html.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
runtime_stats.py
Upgrade syntax to Python 3.7
2022-03-14 14:57:43 +00:00
secret_decoder_ring.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
set_dataset_sizes.py
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
set_user_disk_usage.py
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
summarize_timings.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
tests_markdown_compare.tpl
Performance metrics for tests.
2021-02-12 20:44:05 -05:00
tests_markdown.py
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2022-02-03 07:42:20 -05:00
tests_markdown.tpl
Performance metrics for tests.
2021-02-12 20:44:05 -05:00
update_cwl_conformance_tests.sh
Add CWL conformance API tests
2021-11-23 14:10:21 +00:00
update_shed_config_path.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
validate_tools.sh
Switch to lxml for xml parsing
2020-05-12 15:00:27 +02:00
validate_tours.sh
Tour validation.
2022-06-02 14:53:55 -04:00