 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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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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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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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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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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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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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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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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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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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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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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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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Greg Von Kuster
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fc41d8a5f5
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Fix for installing from a list of tool shed repositories that matched a search criteria.
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2012-04-24 14:25:23 -04:00 |
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Jeremy Goecks
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98e5c9522a
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Fix bug in packaging GFF features for visualization.
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2012-04-24 12:31:51 -04:00 |
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Dannon Baker
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7b926ee58a
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Workflow editor fix for the case where RenameActions had null action arguments vs being unspecified or {} as expected. This situation exists in very few rename actions and hasn't been reproduced, may be legacy workflow steps.
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2012-04-24 11:53:35 -04:00 |
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Jeremy Goecks
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624b4b7f68
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Minor curation of data providers: (a) rename gff data provider to match similar providers and (b) add note about how to extend GTF tabix to support GFF/GFF3 as well.
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2012-04-24 11:05:47 -04:00 |
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Greg Von Kuster
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7e2ba8c8ea
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Enhance the "find workflows" feature in the tool shed and installe dtool shed repositories to allow for finding all workflows if the search criteria is blank.
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2012-04-23 15:59:04 -04:00 |
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Greg Von Kuster
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854a488e8f
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More fixes for retrieving updates for an installed tool shed repository.
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2012-04-23 14:50:27 -04:00 |
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Greg Von Kuster
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8e300dd9c6
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Fix for getting updates to an installed tool shed repository where no updates are available.
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2012-04-23 14:19:42 -04:00 |
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Nate Coraor
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e736047c9f
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Fix the tasks runner that I broke when I split job management into multiple processes.
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2012-04-23 14:04:45 -04:00 |
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Nate Coraor
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cbbfb1c78c
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Provide mercurial as an egg for tool shed operations.
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2012-04-23 13:20:29 -04:00 |
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Jeremy Goecks
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6c0061e0e7
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Create GTF features directly rather than parsing from lines. This is much faster than parsing.
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2012-04-23 11:14:27 -04:00 |
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Jeremy Goecks
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50791f5802
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Use tabix for indexing and getting data from GTF files. This is faster and more flexible than using interval index.
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2012-04-23 09:08:29 -04:00 |
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Daniel Blankenberg
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1bdf8b2cb7
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Partial revert for c32b71dcfc84.
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2012-04-23 06:42:19 -04:00 |
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Greg Von Kuster
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7142248e04
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More fixes for setting tool shed repsoitory metadata.
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2012-04-20 21:45:30 -04:00 |
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Greg Von Kuster
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c30aae2342
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Fixes for setting repository metadata on older change sets in a tool shed repository.
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2012-04-20 21:27:34 -04:00 |
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Greg Von Kuster
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05df3a3683
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Use the mercurial api for all tool shed hg actions.
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2012-04-20 14:27:16 -04:00 |
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Daniel Blankenberg
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9090faffda
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Fix for clearing implicitly converted dataset association when converted dataset is deleted.
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2012-04-19 12:07:31 -04:00 |
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Daniel Blankenberg
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0362b2cc57
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Tweak for 7079:7ca527380818.
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2012-04-19 11:05:10 -04:00 |
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Daniel Blankenberg
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28f625dbc5
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Add a transform_publicname method that coerces a provided string into a valid username. This is now used during user creation.
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2012-04-19 10:16:30 -04:00 |
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Dannon Baker
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cd94acd3c2
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Fix zipfile failure for composite datatypes. Rename variables in data.display method to be consistent with 'data' for hda naming convention. Remove duplicated comment from tabular_chunked.mako.
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2012-04-18 18:49:31 -04:00 |
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Jeremy Goecks
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9bcf3e2416
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Enable interval datasets to be visualized in trackster.
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2012-04-18 16:59:14 -04:00 |
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Dannon Baker
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5a6b43f46f
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Fix missing sanitize_html import.
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2012-04-18 16:30:11 -04:00 |
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Greg Von Kuster
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2632e05024
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Add a running_functional_tests config setting.
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2012-04-18 16:20:17 -04:00 |
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Jeremy Goecks
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182bb66d5c
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Fix decode issues with library datasets in Trackster.
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2012-04-18 15:09:36 -04:00 |
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Greg Von Kuster
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cd8c4f6d93
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Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ.
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2012-04-18 14:29:01 -04:00 |
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Nate Coraor
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6f71fd9c04
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Handle errors in the job handler caused by idata.hid being None.
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2012-04-18 14:15:52 -04:00 |
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Daniel Blankenberg
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b83d6e0a5d
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Fix for LibraryDatasetDatasetAssociation.templates_dict when a content value is not set.
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2012-04-18 12:54:01 -04:00 |
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Greg Von Kuster
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500cea1b24
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Fixes for setting tool shed repository metadata, and enhance the hg command line handler to reset all metadata on a repository to which a push is occurring.
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2012-04-18 10:56:57 -04:00 |
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Dannon Baker
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ecf83a5be5
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Merged in peterjc/galaxy-central/split_blast2 (pull request #41)
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2012-04-18 07:56:05 -04:00 |
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