Nate Coraor 150c17b9e8 Do not explicitly require pexpect. If anyone wants to use the old and ...

mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.

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

..

api

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

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

auth

Clean up pam auth helper.

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

cleanup_datasets

Merge branch 'release_15.07' into dev

2015-08-20 14:12:27 +01:00

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

Ensure the correct default Galaxy config file is found in common_startup.sh, it

2015-02-12 11:47:58 -05:00

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