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galaxy/scripts
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mvdbeek 06b8db47ba Change hardcoded repo location in more place
2024-05-31 11:36:59 +02:00
..
api
Format Python code with black 23.1.0
2023-02-01 23:51:03 +00:00
auth
Apply black formatting.
2022-02-03 07:42:20 -05:00
cleanup_datasets
Wrap session.flush in admin_cleanup_datasets script
2023-06-09 13:05:26 -04:00
grt
Format Python code with black 23.1.0
2023-02-01 23:51:03 +00:00
loc_files
Apply black formatting.
2022-02-03 07:42:20 -05:00
metagenomics
Apply black formatting.
2022-02-03 07:42:20 -05:00
microbes
Fix new B018 errors raised by ruff 0.0.260
2023-04-13 16:53:01 +01:00
objectstore
Apply black formatting.
2022-02-03 07:42:20 -05:00
slideshow
Apply black formatting.
2022-02-03 07:42:20 -05:00
taxonomy
…
tool_shed
Change hardcoded repo location in more place
2024-05-31 11:36:59 +02:00
tools
Apply black formatting.
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
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
Apply black formatting.
2022-02-03 07:42:20 -05:00
common_startup_functions.sh
activate the conda env before the python venv
2023-07-21 00:58:35 +01:00
common_startup.sh
Merge branch 'release_23.0' into release_23.1
2023-07-24 15:16:11 +01:00
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
Apply black formatting.
2022-02-03 07:42:20 -05:00
cwl_conformance_to_test_cases.py
Update lists of non-passing CWL conformance tests
2023-01-17 17:40:11 +00:00
db_dev.py
Add --repair argument to upgrade/downgrade commands on db_dev script
2023-04-26 08:53:35 -04:00
db_dev.sh
Split script into admin and dev
2022-09-28 15:45:00 -04:00
db_shell.py
Drop create_db.sh, create_db.py (see note)
2022-09-28 15:25:43 -04:00
db.py
Edit db wrapper scripts for consistency, add TS script
2023-02-08 00:33:48 -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
Apply black formatting.
2022-02-03 07:42:20 -05:00
dump_openapi_schema.py
Small fixes to YAML export of OpenAPI schema.
2022-12-12 19:44:19 -05:00
edam_mapping.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
external_chown_script.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
extract_dataset_part.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
extract_toolbox_sections.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
fetch_eggs.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
fix_dm_versions.py
Apply black formatting.
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.py
Update inline documentation in scripts
2022-05-31 10:30:30 -04:00
manage_tool_dependencies.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
mypy_config_utils.py
Script for finding unused mypy.ini entries.
2022-09-15 13:20:04 -04:00
pages_identifier_conversion.py
Wrap session.flush in pages_identifier_conversion scripts
2023-06-09 13:05:26 -04:00
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
Write admin announce, add deferred datasets to user announcement
2022-08-19 16:11:41 +02:00
release.sh
Fix release script to be compatible with YY.X dates
2023-04-10 16:51:05 -04:00
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
run_alembic.py
Add shell wrapper for alembic CLI, improve inline docs
2022-09-30 10:34:58 -04:00
run_alembic.sh
Add shell wrapper for alembic CLI, improve inline docs
2022-09-30 10:34:58 -04:00
runtime_stats.py
Fix UP031 errors reported by ruff
2023-03-29 08:55:54 +01:00
secret_decoder_ring.py
Apply black formatting.
2022-02-03 07:42:20 -05:00
set_dataset_sizes.py
Wrap session.flush in set_dataset_sizes script
2023-06-09 13:05:26 -04:00
set_user_disk_usage.py
Implement quota tracking options per ObjectStore.
2023-02-19 10:33:21 -05:00
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
Apply black formatting.
2022-02-03 07:42:20 -05:00
tests_markdown.tpl
Performance metrics for tests.
2021-02-12 20:44:05 -05:00
toolshed_db.py
Edit db wrapper scripts for consistency, add TS script
2023-02-08 00:33:48 -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
Wrap session.flush in update_shed_config_path script
2023-06-09 13:05:26 -04:00
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