galaxy

api

Strip newlines

2015-10-14 14:43:08 -05:00

auth

Clean up pam auth helper.

2015-07-17 08:06:04 -04:00

cleanup_datasets

Update other quota manipulations to use the new user.adjust_quota_usage function.

2015-10-13 13:53:15 -04:00

data_libraries

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

loc_files

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -05:00

metagenomics

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

microbes

Fix all E712 errors. Standardize sqlalchemy imports.

2015-07-14 20:49:34 +01:00

migrate_tools

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

others

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

scramble

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

fix overriding the name variable

2015-08-06 10:38:12 -04:00

tools

Migrate 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -04:00

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

bootstrap_history_announce_template.rst

Fixup end of release items for release notes.

2015-08-27 13:04:17 +01:00

bootstrap_history.py

Fix flake8 broken when merging 041c94bf78 from release_15.07 .

2015-09-02 16:30:50 +01:00

build_toolbox.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

build_universe_config.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

check_eggs.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

check_galaxy.py

Print to stderr when calling sys.exit(1)

2015-09-11 19:05:37 +01:00

check_python.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

common_startup.sh

Move manual_builds.txt to manual_builds.txt.sample to allow for customization

2015-08-18 14:00:30 -04:00

create_db.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

db_shell.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

dist-scramble.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

drmaa_external_killer.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

drmaa_external_runner.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

edam_mapping.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

egg_packager_template.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

external_chown_script.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

extract_dataset_part.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

extract_toolbox_sections.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

fetch_eggs.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

functional_tests.py

Add testing environment variable GALAXY_TEST_LOGGING_CONFIG.

2015-09-16 16:24:53 +01:00

get_platforms.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

helper.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

make_egg_packager.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

manage_db.py

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

manage_tools.py

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

nosetests.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

paster.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

rst2html.py

Cleaning up modules. Still a few stragglers that can't be easily eggified.

2006-11-15 18:27:21 +00:00

run_selenium_tests.sh

Adding workflow tests using Selenium. These actually drive the web browser to test the Javascript UI effectively. Currently can't run under buildbot.

2009-03-27 18:55:00 -04:00

runtime_stats.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

scramble.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

set_dataset_sizes.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

set_metadata.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

set_user_disk_usage.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

summarize_timings.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

sync_reports_config.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

test_dist_egg.py

Use os.pardir everywhere instead of '..' .

2015-07-14 16:20:29 +01:00

transfer.py

Do not explicitly require pexpect. If anyone wants to use the old and

2015-09-17 13:56:44 -04:00

update_shed_config_path.py

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00