Ramkrishna Chakrabarty c925dc1f2c lims: ...

- added a new table 'sample_dataset' to store sample datasets & their info when they are transfered from the sequencer
- the datasets transfer page now uses a grid to facilitate bulk renaming
- bulk renaming possible to fix the problem with the way SOLiD generates datasets
- the remote file browser is now independent of a specific sample, the user may select any sample when transferring datasets from the sequencer

2010-07-29 10:55:08 -04:00

..

api

API: Add library creation functionality. Note that no roles can be associated with libraries via the API at this time.

2010-06-23 14:44:37 -04:00

cleanup_datasets

Fix for cleanup_datasets.py - add app param to the _purge_dataset method signature.

2009-11-14 20:32:41 -05:00

galaxy_messaging

lims:

2010-07-29 10:55:08 -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

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

Upgrade pbs_python to 4.1.0 and use PBS exit_status (if keep_completed is set) so we can detect PBS failures. This is a reapplication of 3786:48432330228e, which was backed out in a subsequent revision due to crashes experienced in pbs_python 2.9.8.

2010-07-19 12:29:53 -04:00

taxonomy

Finalizing taxonomy. Removed taxonomy processing from scripts. This does not require sqlite anymore. Script for fetching taxonomy now uses flat files directly and is much faster

2008-03-20 19:38:31 +00:00

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

fetch_eggs.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

functional_tests.py

Fix for set metadata tests when setting metadata externally

2010-02-24 15:54:52 -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

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

yuicompressor.jar

Updating the packed versions of all javascripts.

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