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galaxy/scripts
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Nate Coraor c9cf15576c Move gunicorn to regular requirements (not just dev) and add uvloop. 
Swap circusd for gravity to start dev-mode/run.sh Galaxy.
2022-01-21 13:29:14 -05:00
..
api
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
auth
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
cleanup_datasets
Drop old sqlalchemy patterns
2021-12-16 12:30:49 +01:00
grt
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
interactivetools
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
loc_files
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
metagenomics
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
microbes
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
objectstore
Remove unnecessary list creations
2021-11-29 16:33:05 +00:00
slideshow
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
taxonomy
Tweaks to taxonomy tools
2010-11-15 15:04:59 -05:00
tool_shed
Drop old sqlalchemy patterns
2021-12-16 12:30:49 +01:00
tools
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
__init__.py
Adding db_shell.py that can be used to simplify writing command line
2012-03-05 12:11:53 -06:00
apply_tags.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
bootstrap_history.py
Adjust check_blocking_issues to PyGithub usage
2021-11-01 13:01:02 +01:00
build_toolbox.py
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
celery_shell.py
Add interactive shell for celery tasks
2021-11-29 10:34:01 +01:00
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
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
check_python.py
Drop support for Python 3.6, add Python 3.10
2021-12-08 08:14:10 +00:00
common_startup_functions.sh
Move gunicorn to regular requirements (not just dev) and add uvloop.
2022-01-21 13:29:14 -05:00
common_startup.sh
If creating venv, modify activate to set $GRAVITY_STATE_DIR so that
2022-01-21 09:51:34 -05:00
config_sample_to_kwalify.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
create_db.py
Create install database with create_db.sh
2021-03-30 13:44:36 +02:00
cwl_conformance_to_test_cases.py
Remove unnecessary list creations
2021-11-29 16:33:05 +00:00
db_shell.py
Add interactive shell for celery tasks
2021-11-29 10:34:01 +01:00
docker_swarm_manager.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
drmaa_external_killer.py
Fix all E201 and E202 style errors
2017-08-17 11:35:39 +01:00
drmaa_external_runner.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
dump_library_paths.py
Add a script for dumping library file paths for backup
2018-02-01 13:05:16 -05:00
edam_mapping.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
external_chown_script.py
Fix all E201 and E202 style errors
2017-08-17 11:35:39 +01:00
extract_dataset_part.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
extract_toolbox_sections.py
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
fetch_eggs.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
fix_dm_versions.py
add script for fixing shed_data_manager_conf.xml
2021-07-14 17:13:26 +02:00
functional_tests.py
Cleanup galaxy_test.base.api_util.
2021-01-16 20:11:39 -05:00
galaxy
Make Galaxy installable the Pythonic way via setup.py. Incomplete, but
2016-07-07 13:49:27 -04:00
galaxy_main.py
First pass fstring conversion
2021-05-11 13:47:00 -04:00
galaxy_schemadisp.py
Lint fixes, prompt for sqlalchemy_schemadisplay install
2021-01-12 08:23:10 -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
get_platforms.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
get_uwsgi_args.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
helper.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
maintenance.sh
Fix issues reported by ShellCheck
2019-06-13 12:53:26 +01:00
manage_db.py
Enable on-screen logging for create_db.py and manage_db.py
2019-08-18 11:17:34 +01:00
manage_tool_dependencies.py
Rework config locating logic (it was reading the sample again).
2019-07-08 11:28:31 +02:00
nosetests.py
Fix all E201 and E202 style errors
2017-08-17 11:35:39 +01:00
pages_identifier_conversion.py
clean-fix-page-api - move page revision creation to manager.
2019-05-29 13:43:49 -04:00
paster.py
Restore pastescript, make new stack depend on APP_WEBSERVER=dev
2021-04-07 14:39:06 +02:00
patch.sh
Add the script I used to create security patches
2016-02-24 16:54:30 -05:00
plugin_staging.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
release-diff.py
Adjust release-diff.py
2022-01-19 18:20:19 +00:00
release.sh
Test Galaxy release script
2021-12-08 10:43:09 +00:00
resumable_upload.py
Adapt scripts/resumable_upload.py to fetch API
2021-10-13 18:05:42 +02:00
rst2html.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
runtime_stats.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
secret_decoder_ring.py
Refactor galaxy.web.security into galaxy.security.idencoding.
2019-03-19 14:28:31 -04:00
set_dataset_sizes.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
set_user_disk_usage.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
summarize_timings.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
tests_markdown_compare.tpl
Performance metrics for tests.
2021-02-12 20:44:05 -05:00
tests_markdown.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
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
Don't use triple-quoted strings as comments
2021-11-29 23:02:34 +00:00
validate_tools.sh
Switch to lxml for xml parsing
2020-05-12 15:00:27 +02:00