galaxy

api

Add the ability to export a specified repository revision from the tool shed to a gzip compressed archive saved locally. The ability to import this archive to the same or another tool shed is not yet implemented, but coming soon. All of the repository's repository dependencies can optionally be exported into the same archive. The archive includes a manifest.xml file that contains the order in whcih the repositories in the archive must be imported.

2013-08-02 19:30:03 -04:00

cleanup_datasets

Fix unicode issue when printing history names in cleanup_datasets.py script

2013-07-22 14:24:13 -04:00

data_libraries

Brad Chapman's patch for fixing an issue where the current user roles were not passed to a template.

2011-02-01 13:11:24 -05:00

galaxy_messaging

Fix the data transfer script to work with new API library content ids.

2012-03-30 09:51:04 -04:00

loc_files

Fix create_all_fasta_loc to work when inspect_dir is not set.

2012-09-18 20:49:29 -04:00

metagenomics

Sync hashbangs

2010-04-01 20:36:31 -04:00

microbes

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

migrate_tools

Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.

2013-02-26 15:52:51 -05:00

others

Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week.

2008-12-22 13:35:01 -05:00

scramble

Testing Python 2.7.

2011-06-08 23:50:07 -04:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.

2013-03-18 10:24:03 -04:00

tools

Fix minor typo in 5233:b5f4df8c3956

2011-03-18 13:40:58 -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

build_toolbox.py

* Remove Todo's that have been done

2011-04-14 14:07:36 +02:00

build_universe_config.py

Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.

2012-09-21 22:04:15 -05:00

check_eggs.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

check_galaxy.py

Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.

2012-04-16 14:56:24 -04:00

check_python.py

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

create_db.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

db_shell.py

galaxy.model.orm is a more sensible location than mapping for dialect_to_egg

2013-06-20 10:58:52 -04:00

dist-scramble.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_killer.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_runner.py

Fix passing of job name when running jobs as a system user.

2012-10-03 11:51:07 -04:00

egg_packager_template.py

Fix the platform argument to fetch_eggs.py and create an egg packager for easing the installation/updating of Galaxy on systems without a direct connection to the internet.

2010-08-30 11:31:58 -04:00

external_chown_script.py

Some fixes to actual user code to negate the need for world-writable directories and write external metadata and job stdout/stderr to the job working directory.

2011-10-31 16:15:00 -04:00

extract_dataset_part.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -04:00

extract_toolbox_sections.py

introduction of toolboxposition elements

2011-04-14 15:09:00 +02:00

fetch_eggs.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

functional_tests.py

GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."

2013-06-30 10:04:58 -04:00

get_platforms.py

Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES

2010-03-01 15:41:30 -05:00

helper.py

Merge

2011-10-07 13:25:19 -07:00

make_egg_packager.py

Bugfix for the offline egg packaging script.

2011-08-03 10:13:01 -04:00

manage_db.py

galaxy.model.orm is a more sensible location than mapping for dialect_to_egg

2013-06-20 10:58:52 -04:00

manage_tools.py

galaxy.model.orm is a more sensible location than mapping for dialect_to_egg

2013-06-20 10:58:52 -04:00

nosetests.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

paster.py

core: add PasteDeploy dependency back, used inside Paste#httpserver

2013-02-01 17:30:58 -05:00

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

scramble.py

Typo in scramble.py.

2011-09-02 14:37:09 -04:00

set_dataset_sizes.py

Merge

2011-10-07 13:25:19 -07:00

set_metadata.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -04:00

set_user_disk_usage.py

Fix for Postgres versions < 9 (see https://trello.com/c/Z0EynAV2 )

2012-12-10 16:23:11 -05:00

sync_reports_config.py

Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.

2012-09-21 22:04:15 -05:00

test_dist_egg.py

Add numpy egg, update bx_python egg (now with 100% more numpy) and include code that allows scrambling to depend on other eggs existing and being importable.

2010-03-15 14:35:35 -04:00

transfer.py

1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set.

2011-04-13 13:52:05 -04:00

yuicompressor.jar

Updating the packed versions of all javascripts.

2009-02-25 14:24:46 -05:00