 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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Jeremy Goecks
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1747527142
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Include more Tophat2 options.
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2012-04-24 22:30:22 -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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Daniel Blankenberg
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1280d0bf7c
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Add rerun and show info buttons to discarded datasets.
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2012-04-24 13:56:42 -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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Jeremy Goecks
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c976d4d280
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Add support for server-state based jQuery deferreds and use for resetting data URL when running tools in Trackster. Pack script.
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2012-04-24 12:17:01 -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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Jeremy Goecks
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f4350d5712
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Add fusion search parameters to Tophat wrapper.
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2012-04-24 10:35:27 -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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Jeremy Goecks
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e2ea763bcb
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Update Trinity wrapper to support most recent versions.
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2012-04-23 15:29:37 -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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3a19e072c9
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Better message when creating a custom build.
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2012-04-23 11:24:46 -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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68aeff663c
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Fix style conflict between base.css and trackster.css
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2012-04-23 09:28:12 -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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Jeremy Goecks
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82fbebe842
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Refactor and simply tophat wrapper.
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2012-04-22 11:58:24 -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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Jeremy Goecks
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3b0ab79c7b
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Merge
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2012-04-20 17:12:48 -04:00 |
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Jeremy Goecks
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7535ec1326
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Basic support for Tophat2.
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2012-04-20 17:08:55 -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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Jeremy Goecks
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3b2c8731a2
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Merged in hiralv/galaxy-central (pull request #42)
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2012-04-20 12:30:26 -04:00 |
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Dannon Baker
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c7dccc457b
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Pack scripts.
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2012-04-20 11:21:50 -04:00 |
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Dannon Baker
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3ee5a84743
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Fix heavy handed removal of PJAs when not using outputs.
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2012-04-20 11:16:14 -04:00 |
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Hiral Vora
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c0061a75bc
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Merging changes.
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2012-04-20 09:13:41 -04:00 |
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Hiral Vora
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16753d3dbc
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Modifying datatypes_conf.xml.sample to include IGB files.
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2012-04-20 08:59:26 -04:00 |
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Jeremy Goecks
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eff9f81957
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Trackster: better handling of resizing and navigation. Pack script.
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2012-04-19 16:33:29 -04:00 |
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Jeremy Goecks
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3373da10c6
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Trackster: do not subset data with no detail.
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2012-04-19 12:46:31 -04:00 |
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Hiral Vora
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6ebcf10e63
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Adding IGB files.
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2012-04-19 12:35:44 -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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Jeremy Goecks
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47c101e4ce
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Trackster: correctly handle navigation when only chrom name is used and name is the same as chrom currently being viewed.
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2012-04-19 11:49:59 -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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Daniel Blankenberg
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8163333bdb
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Slightly more unique automatically generated filename for GenomeSpace export.
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2012-04-18 19:38:34 -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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