galaxy

api

Use `yaml.safe_load() instead of load()`

2019-04-23 16:50:55 +01:00

auth

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

cleanup_datasets

Fix use of pgcleanup's purge_deleted_users when there are no users to

2019-05-17 16:37:19 -04:00

communication

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

grt

swap to exception

2019-04-26 13:29:12 +02:00

loc_files

Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()

2018-09-18 10:06:13 +01:00

metagenomics

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

microbes

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

migrate_tools

Fix typos

2018-03-05 09:44:26 +00:00

slideshow

Fix many links

2018-09-03 14:34:13 +01:00

taxonomy

Tweaks to taxonomy tools

2010-11-15 15:04:59 -05:00

tool_shed

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

tools

Python3: fix remaining print statements

2017-10-12 18:34:29 +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

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

bootstrap_history.py

Merge remote-tracking branch 'upstream/release_19.01' into dev

2019-03-22 10:49:37 -04:00

build_toolbox.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

build_universe_config.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

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_galaxy.py

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

check_python.py

Drop support for Python 3.4. Officially support Python >=3.5

2019-01-31 23:31:44 +00:00

common_startup_functions.sh

Fix activation of `_galaxy_` conda env

2018-12-14 00:22:12 +00:00

common_startup.sh

Fix comments

2019-04-14 18:02:42 +01:00

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

2017-08-10 13:14:55 -04:00

create_db.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

db_shell.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

docker_swarm_manager.py

Make the swarm manager recover on uncaught exceptions. It should do a

2018-04-13 12:34:55 -04:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

drmaa_external_runner.py

external_runner: load json template first

2018-11-09 17:48:36 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

2018-02-01 13:05:16 -05:00

dump_tour.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

edam_mapping.py

Backport of hardening fixes to 17.09

2017-10-18 13:03:49 -04:00

external_chown_script.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_dataset_part.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_toolbox_sections.py

Fix deprecated `getchildren()`

2019-04-23 12:51:13 +01:00

fetch_eggs.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

functional_tests.py

Rework and simplify data manager testing

2018-08-13 17:19:25 +02:00

galaxy-main

Make processes and mules report heartbeat in database

2019-03-29 21:46:18 +01:00

get_platforms.py

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

get_uwsgi_args.py

Drop static-safe navigation to plugin dirs. These are no longer symlinks, they are staged files.

2019-03-14 13:23:45 -04:00

helper.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

maintenance.sh

Use consistent preference order for config files

2018-06-02 03:28:54 +01:00

manage_db.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

manage_tool_dependencies.py

To avoid duplication, move common utilities used by external scripts to

2017-11-13 12:18:09 -05:00

nosetests.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

pages_identifier_conversion.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

paster.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

patch.sh

Add the script I used to create security patches

2016-02-24 16:54:30 -05:00

plugin_staging.py

Update plugin_staging to actually stage instead of symlink, since it no longer needs to be quite as fast (on startup). This will allow us to drop unnecessary trust rules from uwsgi static.

2019-03-14 13:18:43 -04:00

rst2html.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

runtime_stats.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +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

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

set_user_disk_usage.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

summarize_timings.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

sync_reports_config.py

Mark scripts/* that don't work with YAML configuraiton options as deprecated.

2018-03-23 16:14:49 -04:00

transfer.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

update_shed_config_path.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

validate_tools.sh

Refactor most of tool validation for CI into a standalone script.

2016-09-16 15:07:42 -04:00