galaxy

Set workflow scripts ugo+x, like the others in scripts/api.

2011-03-05 12:44:32 -05:00

Add a purged column to the LibraryDataset table - a LibraryDataset is marked purged when all associated LibraryDatasetDatasetAssociations are marked deleted. Fix the cleanup_datasets.py script to more correclty handle the lifecycle of LibraryDatasets.

2011-02-09 15:42:09 -05:00

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

Moving sample state and dataset transfer status update api methods to the samples api controller.

2010-12-20 16:05:08 -05:00

loc_files

Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.

2010-11-08 00:43:02 -05:00

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

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

Fixes for scrambling python-daemon and pysam.

2011-02-09 16:29:50 -05:00

taxonomy

Tweaks to taxonomy tools

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

tools

Updates for 'Profile Annotations for a set of genomic intervals' tool. This tool will now report a 'data version'. Add a script that creates the indexes and table description xml from a UCSC database dump.

2010-04-23 11:14:26 -04:00

check_eggs.py

Sync hashbangs

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

check_galaxy.py

Have check_galaxy.py script get twill from galaxy.eggs instead of directly from the (defunct) eggs/py-(version) directory

2010-07-28 12:57:16 -04:00

check_python.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

dist-scramble.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

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

fetch_eggs.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

functional_tests.py

Bugfix for the last commit when running functional tests with sqlite.

2011-02-28 09:52:17 -05:00

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

make_egg_packager.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

manage_db.py

Fix for sqlalchemy-migrate scripts so they will function across webapps - galaxy is the default, so no command line changes necessary when migrating the db.

2010-07-20 09:27:14 -04:00

nosetests.py

Separate framework and tool environments.

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

paster.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

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

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

set_metadata.py

When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.

2009-11-30 14:55:30 -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

Do away with the daemonized transfer manager and have the deferred job runner start off individual daemonized transfer workers. The workers update their own major states and can be queries for in-transfer progress via a socket, and an interface to that socket in app.transfer_manager. All socket communication is now JSON-RPC.

2011-01-19 10:06:44 -05:00

yuicompressor.jar

Updating the packed versions of all javascripts.

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