John Chilton 78e0ede829 Fix for running LSF DRMAA jobs as 'real' user. ...

Fix thanks to Chong Chen at IBM - "When invoking the LSF drmma api to submit a job, the API will print the message like 'Job <78> is submitted to default queue <normal>'. So if the Galaxy want to use this API, need modify the drmaa_external_runner.py script to handle this message.  LSF already support a env variable to disable this message print out, "BSUB_QUIET", set this into env can disable this message output."

A second issue was related to subsequent querying of the job state as a user other than the submitter - according to Chong Chen this has been fixed in latest LSF DRMAA changes on github (https://github.com/PlatformLSF/lsf-drmaa/commit/43e62546172b90d9f95e90273d77f4c35a0bb404).

2014-08-18 08:43:37 -04:00

..

api

Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.

2014-05-14 18:13:33 -04:00

cleanup_datasets

Correct usage of "it's" versus "its".

2014-04-17 15:49:32 -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

Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.

2014-02-19 14:27:10 -05:00

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

Migrate tools from the distribution to the tool shed.

2014-07-28 11:58:52 -04:00

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

Correct usage of "it's" versus "its".

2014-04-17 15:49:32 -04:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Add a script to check toolshed dependency files for broken/invalid download URLs.

2014-02-17 12:51:34 -05:00

tools

Migrate 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -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

common_startup.sh

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -04:00

create_db.py

Models: Database migrations for stand-alone tool_shed_install models.

2013-12-05 00:20:54 -06:00

db_shell.py

Add utility for debugging sqlalchemy queries in db_shell.py.

2014-06-10 15:01:38 -05:00

dist-scramble.py

Fix old wiki links.

2014-04-10 20:00:45 +02:00

drmaa_external_killer.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

drmaa_external_runner.py

Fix for running LSF DRMAA jobs as 'real' user.

2014-08-18 08:43:37 -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

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

extract_dataset_part.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

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

Rework test framework testing and tools.

2014-04-28 11:48:51 -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

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

Modles: Clean up stand-alone database scripts.

2013-12-05 00:20:54 -06:00

manage_tools.py

Tools now properly migrated into install_database_connection database...

2013-12-17 11:19:41 -06:00

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

1.) Enhance set_metadata scripts to be able to handle metadata declared by tools for both regular declared outputs and new primary output datasets using JSON.

2014-07-10 12:09:50 -04:00

set_user_disk_usage.py

Fix a few postgres dialect renaming misses.

2013-09-26 09:34:27 -04:00

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