galaxy

api

API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories.

2011-08-26 13:55:08 -04:00

cleanup_datasets

Decrease user disk usage when files are removed from disk by the cleanup_datasets.py.

2011-08-22 16:19:49 -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

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

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

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

build_toolbox.py

* Remove Todo's that have been done

2011-04-14 14:07:36 +02:00

check_eggs.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

check_galaxy.py

Bugfix for check_galaxy (monitor script) since dataset deletion moved to the dataset controller.

2011-08-04 11:01:22 -04:00

check_python.py

Testing Python 2.7.

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

dist-scramble.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

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

extract_toolbox_sections.py

introduction of toolboxposition elements

2011-04-14 15:09:00 +02:00

fetch_eggs.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

functional_tests.py

Changes to allow all test outputs generated by twill to be saved to a folder pointed to by

2011-04-14 08:09:48 -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

Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.

2011-08-22 10:45:22 -04:00

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

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

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

set_dataset_sizes.py

Disk space usage accounting: Users can see how much disk a history is consuming. Disk used is also a column on the history grid. Users can also forcibly purge a dataset from their history. Included is a script (scripts/set_dataset_sizes.py) which will set the value of the new total_size column on the dataset table (includes the contents of the extra_files_path and metadata files).

2011-06-14 12:43:42 -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

set_user_disk_usage.py

Move a number of dataset-related methods from the root controller to the dataset controller and encode their ids. Also add user disk usage accounting.

2011-07-26 13:30:07 -04:00

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