galaxy

api

Enhance the Tool Shed and Galaxy APIs to support resetting metadata on repositories in the Tool Shed or installed into Galaxy respectively. When resetting repository metadata in the Tool Shed, if the API key is associated with an admin user, then setting the my_writable param value to True will restrict resetting metadata to only repositories that are writable by the user in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. Also, when resetting metadata in the Tool Shed, repositories of type tool_dependency_definition are reset before repositories of type unrestricted. When setting metadata for installed repositories in Galaxy, neither repository types nor order are considered since these concepts are irrelevant in that environment.

2013-10-16 14:19:26 -04:00

cleanup_datasets

Merged in lance_parsons/galaxy-central-pull-requests/dataset-cleanup (pull request #158 )

2013-09-10 13:14:10 -04:00

data_libraries

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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

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microbes

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migrate_tools

Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.

2013-10-01 15:49:08 -04:00

others

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scramble

Experimental/alpha/in-development/incomplete object store plugin for iRODS. This plugin will probably set your iRODS instance on fire: do not use except in development/testing.

2013-08-28 16:20:19 -04:00

taxonomy

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tool_shed

Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.

2013-03-18 10:24:03 -04:00

tools

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__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

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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

create_db.py

Models: Database migrations for stand-alone tool_shed_install models.

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

db_shell.py

Models: Introduce real class for app.model (ModelMapping).

2013-12-05 00:20:54 -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

Fix passing of job name when running jobs as a system user.

2012-10-03 11:51:07 -04:00

egg_packager_template.py

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external_chown_script.py

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extract_dataset_part.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -04:00

extract_toolbox_sections.py

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fetch_eggs.py

minor docstring adds in /scripts

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

functional_tests.py

Use walltime configured in job_conf.xml instead of maxseconds for determining whether a test tool run is stuck.

2013-12-05 13:52:22 -05:00

get_platforms.py

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helper.py

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make_egg_packager.py

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manage_db.py

Modles: Clean up stand-alone database scripts.

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

manage_tools.py

galaxy.model.orm is a more sensible location than mapping for dialect_to_egg

2013-06-20 10:58:52 -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

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scramble.py

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set_dataset_sizes.py

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set_metadata.py

Metadata setting: Always set externally.

2013-05-06 12:50:06 -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

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transfer.py

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yuicompressor.jar

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