Ramkrishna Chakrabarty cea3324bbb Sequencer data acquisition for LIMS ...

- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer

Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine

2010-02-04 11:01:45 -05:00

..

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

Sequencer data acquisition for LIMS

2010-02-04 11:01:45 -05:00

metagenomics

add scripts for preparing nt and wgs databases.

2008-03-27 17:41:40 +00:00

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

Fix libdrmaa runtime link path on OS X

2009-12-09 10:15:15 -05:00

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

check_eggs.py

Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building

2009-11-16 14:42:09 -05:00

check_galaxy.py

Fix history deletion method in Galaxy check script

2009-05-05 13:03:23 -04:00

check_python.py

Fix another exception error (only in 2.4) with check_python.py

2010-01-28 13:37:53 -05:00

dist-scramble.py

Don't unpack dist-eggs

2009-10-21 15:03:09 -04:00

fetch_eggs.py

Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code.

2009-11-04 12:58:48 -05:00

functional_tests.py

require pysqlite in functional_tests to work around a bug in nose

2010-01-28 14:52:02 -05:00

get_platforms.py

Add fetch_eggs option to pull for other platforms (e.g. cluster nodes)

2009-01-30 11:37:18 -05:00

manage_db.py

Add database versioning support

2009-04-15 15:43:26 -04:00

nosetests.py

Separate framework and tool environments.

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

paster.py

Fix run.sh --reload by requiring Paste before PasteScript

2009-11-23 17:20:01 -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 the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code.

2009-11-04 12:58:48 -05:00

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

yuicompressor.jar

Updating the packed versions of all javascripts.

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