Daniel Blankenberg b966989a55 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. ...

2.) Enhance collect_primary_datasets to allow tools to provide extra_files.

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

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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

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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

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microbes

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migrate_tools

Migrate 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -04:00

others

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scramble

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

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

taxonomy

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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

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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

common_startup.sh

Fetch eggs after initializing sample files, per John Chilton's comment.

2014-06-13 17:32:51 -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

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

egg_packager_template.py

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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

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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

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helper.py

Merge

2011-10-07 13:25:19 -07:00

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

Tools now properly migrated into install_database_connection database...

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

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

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

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transfer.py

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yuicompressor.jar

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