John Chilton c3e99bc384 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. ...

Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.

Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh

Added usage documentation to run_reports.sh.

Added extension points to tweak pid and log location for reports application via environment variables.

2012-09-21 22:04:15 -05:00

..

api

Cleaned up codebase for attempting adding api additions to the galaxy main branch

2012-08-03 02:09:05 -04:00

cleanup_datasets

More pgcleanup.py fixes and addition of cleanup event tables for library items.

2012-09-17 12:51:17 -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

Fix the data transfer script to work with new API library content ids.

2012-03-30 09:51:04 -04:00

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 NCBI Blast+ (and blastxml) to the toolshed.

2012-08-17 11:35:31 -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

Testing Python 2.7.

2011-06-08 23:50:07 -04:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Commit versions of tools from the last_gen tool shed in order of oldest -> newest in the next-gen tool shed. Fixes issue # 578.

2011-06-07 11:32:11 -04:00

tools

Fix minor typo in 5233:b5f4df8c3956

2011-03-18 13:40:58 -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

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

create_db.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

db_shell.py

Actually we don't want to set that environment variable, that make

2012-03-05 15:23:28 -06:00

dist-scramble.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_killer.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -04:00

drmaa_external_runner.py

minor docstring adds in /scripts

2012-08-03 13:31:48 -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

Some fixes to actual user code to negate the need for world-writable directories and write external metadata and job stdout/stderr to the job working directory.

2011-10-31 16:15:00 -04:00

extract_dataset_part.py

Not all datatype splitters write a JSON file

2012-02-16 16:22:58 +00:00

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

Add a running_functional_tests config setting.

2012-04-18 16:20:17 -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

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

Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).

2011-06-08 12:10:51 -04:00

manage_tools.py

The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.

2012-02-28 11:38:08 -05:00

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

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

Pass the config file name to set_metadata.py rather than relying on a hardcoded value.

2012-02-08 11:12:10 -05:00

set_user_disk_usage.py

Make set_user_disk_usage.py object store-aware.

2012-02-09 13:26:14 -05:00

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