John Chilton 8c7c1b64be Fix run_tests.sh --with_framework_test_tools for 9a05d1e. ...

Now appends test tools to sample tools instead of to default tools Galaxy would other wise load (config/tool_conf.xml or tool_conf.xml if these exist instead of sample) - so this is different behavior but I am unsure if it is worse. --with_framework_test_tools was added for API tests and these should probably target the distribution and not random tools someone might have configured so perhaps this new behavior is superior.

2014-09-23 13:38:25 -04:00

..

api

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

cleanup_datasets

merge.

2014-09-15 16:57:28 -04:00

data_libraries

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -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

Switch to_json_string/from_json_string in galaxy/scripts.

2014-09-09 10:04:28 -04:00

microbes

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migrate_tools

Migrate tools from the distribution to the tool shed.

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

others

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

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

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

check_eggs.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -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

Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found.

2014-09-15 22:12:18 -04:00

create_db.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

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

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

functional_tests.py

Fix run_tests.sh --with_framework_test_tools for 9a05d1e.

2014-09-23 13:38:25 -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

Bug fixes to scripts for config subdir.

2014-09-15 16:52:50 -04:00

make_egg_packager.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

manage_db.py

Modles: Clean up stand-alone database scripts.

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

manage_tools.py

Fix scripts that use galaxy.model.orm.scripts' get_config method to find either config/galaxy.ini or universe_wsgi.ini. For the tool_shed database it'll find either config/tool_shed.ini or tool_shed_wsgi.ini. Also re-fix the unit test.

2014-09-17 01:33:17 -04:00

nosetests.py

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paster.py

core: add PasteDeploy dependency back, used inside Paste#httpserver

2013-02-01 17:30:58 -05:00

rst2html.py

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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

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

set_dataset_sizes.py

Bug fixes to scripts for config subdir.

2014-09-15 16:52:50 -04:00

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

Bug fixes to scripts for config subdir.

2014-09-15 16:52:50 -04:00

sync_reports_config.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -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

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

yuicompressor.jar

Updating the packed versions of all javascripts.

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