 Dave Bouvier
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5ece871d40
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Added option to download pre-built indexes from galaxy servers.
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2012-05-18 09:50:35 -04:00 |
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Jeremy Goecks
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5a0cf3c753
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Fix Trackster bug when fetching more tile data. Pack script.
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2012-05-16 17:27:53 -04:00 |
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Nate Coraor
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0dc1da38b1
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Upgrade pycrypto egg, build Fabric egg.
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2012-05-16 10:30:25 -04:00 |
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Jeremy Goecks
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ee5a7d391b
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Fix bug in Trackster tile management. Pack script.
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2012-05-15 12:09:32 -04:00 |
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Jeremy Goecks
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b261bc7335
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Do not use tabix for GFF/GTF because tabix is woefully naive about these data formats.
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2012-05-15 10:17:44 -04:00 |
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Jeremy Goecks
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7b5f7b25df
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Remove genomes initialization code because it's no longer needed.
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2012-05-15 09:17:36 -04:00 |
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Jeremy Goecks
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db84128c8f
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Refactor genome build status and information out of tracks controllers and into own object.
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2012-05-11 19:27:30 -04:00 |
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Jeremy Goecks
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aacf950854
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Fix bug so that reference track cannot be resized.
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2012-05-11 18:43:51 -04:00 |
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Jeremy Goecks
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9c4d8cf2ea
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Merged in fbacall/galaxy-central-myexp-integration (pull request #45)
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2012-05-10 16:27:33 -04:00 |
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Jeremy Goecks
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b0accee722
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Support UnvalidatedValues when exporting histories.
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2012-05-10 14:08:48 -04:00 |
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Dave Bouvier
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ee9bacb494
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Add admin tool to download and index a reference genome.
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2012-05-10 12:55:29 -04:00 |
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Greg Von Kuster
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a70fc8a440
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Fixes for handling errors when uploading a tarball to a tool shed repository that contains problematic contents. A bit of code cleanup is included as well.
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2012-05-09 20:19:01 -04:00 |
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Daniel Blankenberg
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b4c15c3401
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Fix for clearing implicitly converted dataset association when converted dataset is deleted.
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2012-05-09 15:36:15 -04:00 |
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Dannon Baker
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0245e38f7b
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Fix for history_contents API file display.
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2012-05-09 09:12:42 -04:00 |
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Jeremy Goecks
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80289ec8f8
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Merge
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2012-05-08 20:06:08 -04:00 |
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Jeremy Goecks
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9c9e728a5b
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Fix display bugs associated with c5da9bd8bbfc. Pack script.
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2012-05-08 17:26:14 -04:00 |
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Nate Coraor
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52e8715074
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Fix "TypeError: array item must be char" on tool shed upload.
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2012-05-08 12:32:01 -04:00 |
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Daniel Blankenberg
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89e347625f
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Rewrite HbVar datasource tool.
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2012-05-04 15:35:51 -04:00 |
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Daniel Blankenberg
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14734e345a
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Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths.
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2012-05-04 14:31:22 -04:00 |
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Greg Von Kuster
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dac5a6a728
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Clarify host string value in community_wsgi.ini.
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2012-05-03 14:00:32 -04:00 |
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Greg Von Kuster
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aeaab261b3
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Enhance sample file handling for installed tool shed repositories to handle more than just .loc.sample files in the tool-data directory.
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2012-05-03 13:37:33 -04:00 |
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Daniel Blankenberg
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26e75b3e60
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Allow GenomeSpace importer tool to sniff filetype when GSMetadata object is not available.
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2012-05-03 12:25:06 -04:00 |
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Dannon Baker
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1ace878e28
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Incorporation and slight update to pull request #43. The original contribution allowed access to file_path regardless of admin status and config setting.
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2012-05-03 10:18:38 -04:00 |
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Carlos Borroto
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3de3592ec2
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expose dataset full path through the API
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2012-05-02 19:30:11 -04:00 |
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Daniel Blankenberg
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c44aee110d
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Update WormBase datasource tool to use WormBase 2.
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2012-05-02 17:04:33 -04:00 |
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Daniel Blankenberg
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24e9b5df93
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Fix typo in BAM slice tool.
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2012-05-02 11:47:04 -04:00 |
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Daniel Blankenberg
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e8fe4c4dc1
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Add Slice BAM by regions tool.
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2012-05-02 11:32:19 -04:00 |
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Greg Von Kuster
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ea41f072d6
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Fix popup menu for viewing tool metadata in a tool shed repository to be compatible with new styles.
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2012-05-01 12:17:07 -04:00 |
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Greg Von Kuster
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a164d45c0a
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Eliminate the fabfile/method type from ToolRequirement.
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2012-05-01 09:15:59 -04:00 |
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Greg Von Kuster
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296d954303
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Fix the instructions on the veiw request type page.
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2012-05-01 09:11:07 -04:00 |
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Nate Coraor
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62c9e9af49
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Allow for library deletion from the API (admins only).
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2012-04-30 16:27:55 -04:00 |
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Greg Von Kuster
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634846cd51
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Eliminate resetting all repository metadata on a tool shed repostiory when its not necessary.
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2012-04-30 14:42:39 -04:00 |
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Dannon Baker
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dde79244d8
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Extract workflow - fix nested dataset input mapping.
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2012-04-30 12:16:09 -04:00 |
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Jeremy Goecks
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0cb9ceee2a
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Revert Tophat wrapper version #.
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2012-04-30 11:46:43 -04:00 |
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Jeremy Goecks
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f64f71e7ff
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Revert Tophat wrapper due to parameter incompatibility issues.
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2012-04-30 11:41:04 -04:00 |
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Greg Von Kuster
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007ea825dc
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Fixes for some requests sent from Galaxy to a tool shed.
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2012-04-30 11:00:07 -04:00 |
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Jeremy Goecks
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9c7e7d8635
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Merge
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2012-04-29 20:34:39 -04:00 |
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Jeremy Goecks
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633c3cb9d5
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Update Cuffdiff min-alignment-count default.
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2012-04-28 22:21:30 -04:00 |
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Daniel Blankenberg
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46f0ea7d2d
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Have implicit SAM to BAM converter sort the output BAM file so that indexing will not fail.
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2012-04-27 15:33:10 -04:00 |
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Jeremy Goecks
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80f70cd0de
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More cleaning of Tophat wrapper.
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2012-04-27 15:22:11 -04:00 |
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Jeremy Goecks
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7c40df458e
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Skeleton wrapper for Bowtie2.
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2012-04-26 15:28:17 -04:00 |
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Jeremy Goecks
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78ce10ae5f
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Remove version code from tophat wrappers as this is now handled by <version> tag.
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2012-04-26 14:25:01 -04:00 |
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Jeremy Goecks
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5ad68c65d3
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Fix version references in tophat2 wrapper.
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2012-04-26 13:59:03 -04:00 |
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Jeremy Goecks
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01f80d2844
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Make history export work for optional data inputs.
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2012-04-26 13:32:04 -04:00 |
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Anton Nekrutenko
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8cda02d849
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Fixed number of threads
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2012-04-26 16:49:38 +02:00 |
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Anton Nekrutenko
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a2eb104b31
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Modified metagenomic mapper to use BLAST+ blastn in megablast mode
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2012-04-26 16:44:26 +02:00 |
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Jeremy Goecks
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c0011da861
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Add basic tool execution to the API.
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2012-04-25 18:03:11 -04:00 |
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Jeremy Goecks
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ccb1b9f112
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Revert Tophat wrapper to support versions 1.3.0-1.4.1
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2012-04-25 11:33:05 -04:00 |
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Jeremy Goecks
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64d1faeeb2
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Add explicit Tophat2 wrapper.
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2012-04-25 11:25:17 -04:00 |
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Jeremy Goecks
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c62d567173
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Fix class assignment for links/menus/popups in grids.
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2012-04-24 22:57:56 -04:00 |
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