 James Taylor
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2a2003c606
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circster: Allow data_standalone types to work; phyloviz: add tree datatypes to sample conf
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2012-09-10 17:09:09 -04:00 |
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James Taylor
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218e32119b
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Datatype conversion exceptions no imported but used in base controller.
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2012-09-10 14:05:56 -04:00 |
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Dannon Baker
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13abf22d96
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Merged in nuwan_ag/galaxy-central (pull request #63)
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2012-09-10 12:33:01 -04:00 |
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Nate Coraor
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e19092e9c5
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Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
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2012-09-10 12:03:23 -04:00 |
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Greg Von Kuster
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495669bbd1
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Enhancements to tool dependency installation when installing with a tool shed repository: multiple environment variables can now be set and a new "make_directory" tag is supported.
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2012-09-07 14:49:46 -04:00 |
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Dave Bouvier
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bf636a7e67
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Added an error message to the repository clone error handling.
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2012-09-07 11:54:02 -04:00 |
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Dave Bouvier
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bf744b4c9c
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Handle errors when cloning a tool shed repository.
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2012-09-07 11:22:09 -04:00 |
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Greg Von Kuster
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702ab05095
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Fix bug introduced 2 commits ago.
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2012-09-06 16:27:35 -04:00 |
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Greg Von Kuster
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7520bcdf8a
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Fix a mis-named variable.
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2012-09-06 16:22:57 -04:00 |
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Greg Von Kuster
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80ffd0ddee
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Fixes for displaying error messages when displaying invalid tools in tool shed repository changeset revisions.
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2012-09-06 16:17:15 -04:00 |
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Greg Von Kuster
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f99bf6c981
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Enhance the way that multiple versions of the same tool simultaneously loaded into a Galaxy instance are displayed in the tool panel. Only one link will now be displayed in the tool panel for the tool versions, but the tool page will inlcude a select list allowing the user to select a specific version of the tool. Re-running a job for a specific version of a tool (from the history item) works the same as it did before this change set.
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2012-09-06 14:33:11 -04:00 |
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Jeremy Goecks
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0d2a7cf7ea
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Add feature search to Trackster; typing in location box will search tracks in visualization for features that start with entered text. Works with both GFF/GTF and BED datasets. Fixes #611
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2012-09-05 17:26:43 -04:00 |
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Dave Bouvier
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233378619c
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Added API integration for genome downloader. Improved detection of existing liftover files.
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2012-09-05 08:24:29 -04:00 |
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Carl Eberhard
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4f83877e81
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Fix sniff.py blastxml doc/unittest, removal of func.test_get_data.py 0140 (megablast xml upload), increased lines_diff in cuffmerge_wrapper.xml to handle inconsistent oId assignment (cuffmerge.test_tool_000000)
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2012-09-04 13:28:25 -04:00 |
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Nate Coraor
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9b7b994ce8
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Merged in jmchilton/galaxy-central-binary-type-enhancements (pull request #59)
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2012-09-04 11:07:45 -04:00 |
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Dave Bouvier
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3c67587880
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Improve display of job status, migration script to accomodate same
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2012-09-04 09:42:54 -04:00 |
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John Chilton
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3ef2cb0a7c
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I messed up the previous merge, this fixes that commit.
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2012-09-03 22:25:42 -05:00 |
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John Chilton
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886a5c61b9
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Merge.
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2012-09-03 22:14:36 -05:00 |
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Greg Von Kuster
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587fbae3ac
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Fix for resetting all metadata on a tool shed repository.
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2012-08-31 16:04:46 -04:00 |
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Greg Von Kuster
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c0b7ea3f56
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Display error message when unable to set metadata on a tool shed repository because of invalid tool configs. Also correct the way metadata is set on a tool shed repository when all repository files are deleted in a changeset.
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2012-08-31 15:25:48 -04:00 |
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Jeremy Goecks
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5a650ed653
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Set attribute metadata for GFF and GFF3 in addition to GTF.
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2012-08-31 15:24:25 -04:00 |
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Greg Von Kuster
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6cda697f85
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Add new repository tip column to tool shed repository grids, and differentiate between the repository tip revision and the repository's metadata revisions and installable revisions in various grids.
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2012-08-31 14:03:40 -04:00 |
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Carl Eberhard
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f1c09ee6cf
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merge; add temporary template to commit
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2012-08-31 12:12:28 -04:00 |
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Carl Eberhard
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ac67dc378e
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(WIP) history panel, backbone.js conversion (includes alternate_history.mako as a temporary transition template)
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2012-08-31 11:53:46 -04:00 |
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Greg Von Kuster
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2d589bd376
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Change the implementation for importing proprietary datatype class modules that are included in installed tool shed repositories. This approach will correctly import proprietary datatype classes whose file names conflict with a Python standard library module name (e.g., if a proprietary datatype class file is named xml.py, it will conflict with the Python standard library's xml module when attempting to import it).
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2012-08-30 14:40:28 -04:00 |
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Greg Von Kuster
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d018ca4734
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Fix for loading a tool from a tool config located in a temporary working directory.
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2012-08-30 10:54:12 -04:00 |
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Greg Von Kuster
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4823c62333
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Enhancements, fixes and code cleanup related to setting metadata and loading and displaying tools in the tool shed.
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2012-08-30 10:42:55 -04:00 |
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Daniel Blankenberg
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ae893c4b3e
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Have form_builder class's get_html methods return unicode.
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2012-08-29 13:50:31 -04:00 |
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Nate Coraor
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dc7ebc62ba
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When creating the temp directory for library zip downloads, use the Galaxy user's umask and group on the directory.
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2012-08-29 12:36:21 -04:00 |
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Dannon Baker
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45c8339f3c
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Merge.
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2012-08-29 11:41:13 -04:00 |
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Dannon Baker
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b676ddd99c
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Merge.
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2012-08-29 10:18:23 -04:00 |
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Dannon Baker
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4dccf1227e
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Merge of rpark's workflow API changes to support parameter execution and workflow creation.
TODO: Refactor copied workflow methods back out.
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2012-08-29 10:17:53 -04:00 |
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Dave Bouvier
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01e92b00e1
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Made download status page more informative, fixed intermittent indexing error.
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2012-08-29 10:16:11 -04:00 |
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Daniel Blankenberg
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77cc560eef
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Unicode fixes for annotations
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2012-08-29 10:03:42 -04:00 |
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Daniel Blankenberg
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4c06d073d4
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Handle non-ascii unicode in dataset error report emails.
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2012-08-28 19:23:40 -04:00 |
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Daniel Blankenberg
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d84ab3226e
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Handle non-ascii unicode in data source tools. Add util.is_binary() method that returns true when provided string contains a null byte.
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2012-08-28 19:23:39 -04:00 |
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Greg Von Kuster
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131fb1e226
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Fix handling of ToolSectionLabel objects in the tool panel.
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2012-08-28 14:32:04 -04:00 |
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Nate Coraor
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acb8767200
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Don't attempt to run util.umask_fix_perms() on data that is being linked to. Fixes #801.
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2012-08-28 13:50:54 -04:00 |
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Greg Von Kuster
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c68066fac2
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Apply the improvements for generation of tool shed URLs to the repository controller.
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2012-08-28 11:49:43 -04:00 |
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Dave Bouvier
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112d13e066
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Improved generation of tool shed URLs
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2012-08-28 11:32:17 -04:00 |
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Greg Von Kuster
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f047aa99e8
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Add the ability to browse writable repositories in a tool shed.
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2012-08-28 11:01:07 -04:00 |
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Jeremy Goecks
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e9c26d05d3
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Fixes for phyloviz parser and a4c7aeb61c7b.
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2012-08-28 09:05:31 -04:00 |
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Clare Sloggett
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d0a0276c42
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In workflows api, when show workflow request is made, now displaying info on steps and connectors.
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2012-08-28 17:54:15 +10:00 |
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Jeremy Goecks
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ce86cf2715
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Comment out phyloviz XML parser until native Python XML parsing is used.
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2012-08-27 15:44:01 -04:00 |
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Jeremy Goecks
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d2a96e66bd
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Merged in Tomithy/galaxy-central-phyloviz-2 (pull request #65)
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2012-08-27 14:08:55 -04:00 |
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Dave Bouvier
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cb0614f0fa
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Fixed truncation of downloaded fasta files.
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2012-08-27 12:52:43 -04:00 |
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Tomithy Too
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516d727229
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re-integrated phyloviz to a new fork of galaxy-central with a tat of minor touch up; save and edit now works
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2012-08-26 18:22:23 +08:00 |
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Jeremy Goecks
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37c07fa1eb
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Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization.
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2012-08-24 18:15:29 -04:00 |
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Dave Bouvier
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334983c4df
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Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.
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2012-08-23 16:36:58 -04:00 |
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Dannon Baker
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61059cc61d
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Merged in jmchilton/galaxy-central-roles-api-fixes (pull request #62)
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2012-08-23 09:34:43 -04:00 |
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