 Jeremy Goecks
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6acc73cf5c
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Trackster: multi-track dynamic filtering, multiple filtering bug fixes, and packed script.
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2012-01-25 11:08:23 -05:00 |
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Daniel Blankenberg
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bb8309e4d4
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Add sort tag to Print Reads test output element.
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2012-01-25 08:54:16 -05:00 |
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Nate Coraor
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b6d94f9fb8
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Merge.
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2012-01-24 21:33:21 -05:00 |
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Nate Coraor
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06d6b7918f
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Minor change to user creation via API
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2012-01-24 21:33:02 -05:00 |
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Daniel Blankenberg
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718782e103
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Add GATK Print Reads walker tool.
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2012-01-24 16:29:28 -05:00 |
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Daniel Blankenberg
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c74f916ec0
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Enhance Picard SamToFastq to allow read group aware processing.
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2012-01-24 15:03:35 -05:00 |
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Nate Coraor
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b9e84afbec
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Merged in jdlogicman/galaxy-central-eland-datatype (pull request #29)
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2012-01-24 14:06:05 -05:00 |
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Nate Coraor
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0354480bd2
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Merge jdlogicman/galaxy-central-startup-integration-apis
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2012-01-24 12:18:21 -05:00 |
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Jeremy Goecks
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997a00b766
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Trackster: refactoring in preparation for multi-track filtering.
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2012-01-24 12:13:00 -05:00 |
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Nate Coraor
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c28cb963d3
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Object store fixes for Python 2.5. S3 not currently supported on 2.5, although it can most likely be worked around.
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2012-01-24 10:32:18 -05:00 |
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Jeremy Goecks
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5e9fc86553
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Trackster: fix drawing bug when clear_after is true.
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2012-01-23 18:37:39 -05:00 |
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Jeremy Goecks
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59ef1a4510
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Merge.
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2012-01-23 18:06:03 -05:00 |
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Jeremy Goecks
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aac19f189e
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Tweak Trackster filter display.
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2012-01-23 18:05:46 -05:00 |
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Daniel Blankenberg
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314fa69f71
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Update GATK to version 1.4.
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2012-01-23 18:03:15 -05:00 |
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Jeremy Goecks
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4f9546ce2a
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Do not use math.isnan because it is not compatible with python 2.5
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2012-01-23 17:56:37 -05:00 |
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Jeremy Goecks
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89128ebaa4
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Better error reporting in Cufflinks.
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2012-01-23 17:40:36 -05:00 |
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Nate Coraor
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4f32b4aced
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In the local job runner, use NamedTemporaryFiles rather than subprocess.PIPEs to prevent Popen from hanging when a lot of data is written to STDOUT/STDERR. Fixes #662.
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2012-01-23 16:17:29 -05:00 |
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Nate Coraor
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c764913a37
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Allow whitespace between addresses in admin_users in the Galaxy config file. Fixes #609.
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2012-01-23 15:04:45 -05:00 |
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Nate Coraor
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06dda3a4ad
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Merge closed branch
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2012-01-23 14:47:16 -05:00 |
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Nate Coraor
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765799ac1a
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Closed branch set-picard-java-tmpdir
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2012-01-23 14:46:20 -05:00 |
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Nate Coraor
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40e980ab1d
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Merged in jmchilton/umn-galaxy-central (pull request #28)
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2012-01-23 14:44:50 -05:00 |
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Nate Coraor
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6dc2ef8d2a
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Bugfix for the DrmCommunicationException change this morning (Thanks aswarren and Shantanu Pavgi).
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2012-01-23 14:38:55 -05:00 |
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Nate Coraor
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943ce1de96
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Merged in jdlogicman/galaxy-central-add-xml-mimetype (pull request #16)
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2012-01-23 14:34:38 -05:00 |
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Jeremy Goecks
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306678aa45
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Merge.
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2012-01-23 14:24:23 -05:00 |
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Jeremy Goecks
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090a2b9c2c
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Trackster: provide icon to randomly set color in drawable config. Pack script.
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2012-01-23 14:24:03 -05:00 |
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Nate Coraor
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e51f4e7286
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Merge closed branch
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2012-01-23 14:23:22 -05:00 |
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Nate Coraor
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4ccf8e4486
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Closed branch sam_merge_patch
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2012-01-23 14:22:50 -05:00 |
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Nate Coraor
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c4a6c157b6
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Merged in lance_parsons/galaxy-central-princeton (pull request #7)
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2012-01-23 14:20:37 -05:00 |
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Nate Coraor
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302b1600a5
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Add tool_dependency_dir to the sample config.
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2012-01-23 12:29:00 -05:00 |
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Daniel Blankenberg
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a7c62d8159
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GATK Updates.
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2012-01-23 11:37:49 -05:00 |
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Nate Coraor
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2bc58de701
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Ignore DrmCommunicationException when checking job state. Thanks Ed Kirton.
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2012-01-23 11:04:04 -05:00 |
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Greg Von Kuster
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efc25ffaab
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Fix for loading tools from tool config(s).
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2012-01-23 09:44:22 -05:00 |
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Jeremy Goecks
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44c5e2dc15
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Do not find valid chroms because this is computationally expensive and not currently used.
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2012-01-22 19:48:05 -05:00 |
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Jeremy Goecks
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65294ae543
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Trackster: fix bugs in summary tree display & pack script.
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2012-01-22 16:21:59 -05:00 |
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Jeremy Goecks
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816cbd7bf4
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Remove unneeded ftype attribute.
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2012-01-22 14:39:19 -05:00 |
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Jeremy Goecks
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7f94c0af21
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Update cuffdiff test data for v1.3.0
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2012-01-22 14:35:13 -05:00 |
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Jeremy Goecks
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087bfbdb50
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Update test-data for cuffcompare v1.3.0
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2012-01-22 14:19:46 -05:00 |
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Jeremy Goecks
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39fea42347
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Update test data for cufflinks v1.3.0
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2012-01-22 14:06:18 -05:00 |
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Daniel Blankenberg
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dd9c71de9a
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Fix for setting up column assignments for dynamic options wrt tool data tables when the index file is missing.
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2012-01-20 16:40:34 -05:00 |
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Nate Coraor
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e65a2e5d79
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Fix for the object store doctest.
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2012-01-20 16:20:13 -05:00 |
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Greg Von Kuster
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9d37afcef3
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Keep an in-memory version of each tool shed related tool conf xml file which will evolve as tool shed repositories are installed / deactivated / uninstalled / activated. Whenever new entries are added to any of these tool shed related tool conf xml files, use this in-memory version for persistence.
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2012-01-20 15:47:56 -05:00 |
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Greg Von Kuster
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7e7cf3edbe
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When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store.
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2012-01-20 10:26:54 -05:00 |
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Daniel Blankenberg
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a29eb66d87
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Add mpileup to tool_conf.xml.main.
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2012-01-20 10:06:24 -05:00 |
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Daniel Blankenberg
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ac5744c4d4
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Add GATK VariantSelect tool.
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2012-01-19 16:16:31 -05:00 |
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Greg Von Kuster
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a70c300af7
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Add more flexibility in generating a workflow image in the tool shed.
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2012-01-19 14:58:48 -05:00 |
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Greg Von Kuster
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3272ec4174
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Fix for comparing workflows in repository metadata when resetting all metadata on a tool shed repository.
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2012-01-19 14:23:41 -05:00 |
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Greg Von Kuster
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190423a517
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Add the drmaa_external_runjob_script attribute to the tool shed's config so that setting repositroy metadata works.
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2012-01-19 14:21:32 -05:00 |
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Greg Von Kuster
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7b2e96b5e0
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Add columns for datatypes and workflows in the tool shed repository metadata grid.
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2012-01-19 13:44:00 -05:00 |
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Jeremy Goecks
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a87b0a6476
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Trackster: (a) simplify nav bar width control; (b) fix embedded visualizations; (c) pack script.
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2012-01-19 11:48:56 -05:00 |
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Greg Von Kuster
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dd51806a83
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Fix for setting tool shed repository metadata.
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2012-01-19 11:03:30 -05:00 |
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