galaxy

api

Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it.

2011-03-15 15:39:35 -04:00

cleanup_datasets

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

Fix minor typo in 5233:b5f4df8c3956

2011-03-18 13:40:58 -04:00

check_eggs.py

Sync hashbangs

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

check_galaxy.py

Update the check_galaxy script for the recent changes to the User controller

2011-03-24 14:33:05 -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

Fix some scramble problems

2011-04-12 22:08:09 -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

Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.

2011-03-23 12:18:57 -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

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