| 3e0af21 | Chris Mungall | 31 May 2013, 17:50:52 UTC | add amelias scripts | 31 May 2013, 17:50:52 UTC |
| 8b91216 | Chris Mungall | 07 April 2013, 15:14:51 UTC | new | 07 April 2013, 15:14:51 UTC |
| dcd2f29 | Chris Mungall | 07 April 2013, 08:13:33 UTC | new | 07 April 2013, 08:13:33 UTC |
| e202ff5 | Chris Mungall | 07 April 2013, 07:34:49 UTC | new | 07 April 2013, 07:34:49 UTC |
| 106457c | Chris Mungall | 05 April 2013, 23:19:57 UTC | map2slim | 05 April 2013, 23:19:57 UTC |
| 201b473 | Chris Mungall | 05 April 2013, 23:07:18 UTC | new | 05 April 2013, 23:07:18 UTC |
| 213dc67 | Chris Mungall | 05 April 2013, 21:53:05 UTC | new | 05 April 2013, 21:53:05 UTC |
| e8c8e13 | Chris Mungall | 05 April 2013, 18:33:10 UTC | galaxy | 05 April 2013, 18:33:10 UTC |
| fd1a9a6 | Chris Mungall | 05 April 2013, 18:32:40 UTC | galaxy | 05 April 2013, 18:32:40 UTC |
| d915725 | Chris Mungall | 05 April 2013, 04:53:50 UTC | adv | 05 April 2013, 04:53:50 UTC |
| 225785f | Chris Mungall | 05 April 2013, 02:39:26 UTC | enrichment | 05 April 2013, 02:39:26 UTC |
| c16032f | Chris Mungall | 05 April 2013, 00:44:45 UTC | tf wrap | 05 April 2013, 00:44:45 UTC |
| 00b193c | Chris Mungall | 05 April 2013, 00:39:41 UTC | mv | 05 April 2013, 00:39:41 UTC |
| e43bab7 | Chris Mungall | 05 April 2013, 00:37:07 UTC | tf | 05 April 2013, 00:37:07 UTC |
| eae5b46 | Chris Mungall | 04 April 2013, 23:23:39 UTC | ontologizer | 04 April 2013, 23:23:39 UTC |
| 06cdd12 | Chris Mungall | 04 April 2013, 20:55:19 UTC | ontology-cache | 04 April 2013, 20:55:19 UTC |
| 28db373 | Chris Mungall | 04 April 2013, 01:20:12 UTC | new | 04 April 2013, 01:20:12 UTC |
| d927c20 | Chris Mungall | 04 April 2013, 01:18:14 UTC | new | 04 April 2013, 01:18:14 UTC |
| 5ee49ec | Chris Mungall | 03 April 2013, 23:17:18 UTC | use bash for errwrap | 03 April 2013, 23:17:18 UTC |
| 6a4cd0e | Chris Mungall | 03 April 2013, 23:07:15 UTC | new | 03 April 2013, 23:07:15 UTC |
| fc7abf0 | Chris Mungall | 03 April 2013, 22:55:54 UTC | new | 03 April 2013, 22:55:54 UTC |
| af2126b | Chris Mungall | 03 April 2013, 22:41:34 UTC | new | 03 April 2013, 22:41:34 UTC |
| 5ebdc48 | Chris Mungall | 03 April 2013, 22:26:35 UTC | jars in hg not a good idea | 03 April 2013, 22:26:35 UTC |
| aed68dc | Chris Mungall | 03 April 2013, 22:17:57 UTC | new | 03 April 2013, 22:17:57 UTC |
| 2ffeac7 | Chris Mungall | 03 April 2013, 21:34:24 UTC | new | 03 April 2013, 21:34:24 UTC |
| 1e09bdb | Chris Mungall | 03 April 2013, 21:31:23 UTC | new | 03 April 2013, 21:31:23 UTC |
| eb8b4bf | Chris Mungall | 03 April 2013, 21:15:31 UTC | latest | 03 April 2013, 21:15:31 UTC |
| e4be61e | Chris Mungall | 01 February 2013, 20:48:28 UTC | docs | 01 February 2013, 20:48:28 UTC |
| 528c8a9 | Chris Mungall | 01 February 2013, 20:48:21 UTC | docs | 01 February 2013, 20:48:21 UTC |
| 0d2be72 | Chris Mungall | 20 November 2012, 01:27:41 UTC | new | 20 November 2012, 01:27:41 UTC |
| 7a358f6 | Chris Mungall | 06 October 2012, 21:04:41 UTC | new | 06 October 2012, 21:04:41 UTC |
| 2390012 | Chris Mungall | 06 October 2012, 00:03:57 UTC | new | 06 October 2012, 00:03:57 UTC |
| 655c4f1 | Chris Mungall | 03 April 2012, 21:33:34 UTC | merged | 03 April 2012, 21:33:34 UTC |
| 16d85b5 | Chris Mungall | 03 April 2012, 21:29:47 UTC | merged in latest galaxy-dist | 03 April 2012, 21:29:47 UTC |
| 8220bf1 | Chris Mungall | 03 April 2012, 21:14:08 UTC | new | 03 April 2012, 21:14:08 UTC |
| 03dbd4b | Greg Von Kuster | 07 March 2012, 18:35:34 UTC | Fix for populating the tool panel and generating the integrated_tool_panel.xml file. | 07 March 2012, 18:35:34 UTC |
| 1ef10a5 | Dannon Baker | 07 March 2012, 18:13:58 UTC | Workflows: Multiple run workflows now copy input datasets to newly created histories when used. | 07 March 2012, 18:13:58 UTC |
| 38884bf | Greg Von Kuster | 06 March 2012, 22:15:38 UTC | Fix for generating ToolSectionLabels in the integrated_tool_panel.xml file. | 06 March 2012, 22:15:38 UTC |
| c56222a | jeremy goecks | 06 March 2012, 21:30:03 UTC | Editable text support: (a) use jQuery function style and (b) add support for tipsy. Trackster: add help/tipsy text when setting line track/histogram max/min. Pack scripts. | 06 March 2012, 21:30:03 UTC |
| 896392a | Daniel Blankenberg | 06 March 2012, 20:43:32 UTC | Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) when downloading exported histories. | 06 March 2012, 20:43:32 UTC |
| 6ea6177 | Daniel Blankenberg | 06 March 2012, 20:32:46 UTC | Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) on downloads from a library. | 06 March 2012, 20:32:46 UTC |
| 4f0c98d | Daniel Blankenberg | 06 March 2012, 20:23:56 UTC | Fix for 'Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION): Multiple Content-Disposition headers received.' error occuring when downloading certain datasets using Chrome browser. | 06 March 2012, 20:23:56 UTC |
| 160c01b | Greg Von Kuster | 06 March 2012, 19:50:55 UTC | Introduce a new integrated_tool_panle.xml file which is initially created by parsing all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc). After the file is created, the order of the items displayed in the tool panel is defined by integrated_tool_panel.xml. Galaxy admins can easily edit the file to change the order of items in the tool panel. After it is generated, all tool panel config files (e.g., tool_conf.xml, shed_tool_conf.xml, migrated_tools.xml, etc) will be used to load tools, workflows, etc, while integrated tool_panel.xml will define where they are displayed. | 06 March 2012, 19:50:55 UTC |
| 6a6aa14 | jeremy goecks | 06 March 2012, 16:43:53 UTC | Trackster: manually track view redraw requests so that only one redraw is done. | 06 March 2012, 16:43:53 UTC |
| 540d2ba | Dannon Baker | 05 March 2012, 20:17:41 UTC | Run workflow: Update and clarify label selector. | 05 March 2012, 20:17:41 UTC |
| bc151b6 | jeremy goecks | 05 March 2012, 20:10:31 UTC | Trackster: dynamic filtering of read tracks. | 05 March 2012, 20:10:31 UTC |
| 9aeef3b | Dannon Baker | 05 March 2012, 19:44:19 UTC | Workflow Running - Properly select only Input Dataset steps for multi-input configuration. | 05 March 2012, 19:44:19 UTC |
| 1678d62 | Daniel Blankenberg | 05 March 2012, 18:25:14 UTC | In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history. | 05 March 2012, 18:25:14 UTC |
| f6378eb | Dannon Baker | 05 March 2012, 17:00:53 UTC | Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization. | 05 March 2012, 17:00:53 UTC |
| 2223304 | Greg Von Kuster | 02 March 2012, 20:37:35 UTC | Keep empty sections in the tool panel when deactivating / uninstalling a repository with tools. | 02 March 2012, 20:37:35 UTC |
| 2ed53de | jeremy goecks | 02 March 2012, 19:35:57 UTC | Merge | 02 March 2012, 19:35:57 UTC |
| dcea617 | Greg Von Kuster | 02 March 2012, 19:30:41 UTC | Fixes for deactivating / uninstalling a repository containing tools. | 02 March 2012, 19:30:41 UTC |
| 1cb1eca | jeremy goecks | 02 March 2012, 19:29:21 UTC | Fix custom-build UI bugs. | 02 March 2012, 19:29:21 UTC |
| 6f9c915 | jeremy goecks | 02 March 2012, 18:40:46 UTC | Decode visualization dataset ids before saving them. | 02 March 2012, 18:40:46 UTC |
| ada9c27 | Greg Von Kuster | 02 March 2012, 18:33:58 UTC | Fixes for managing installed repositories. | 02 March 2012, 18:33:58 UTC |
| e84657c | Greg Von Kuster | 01 March 2012, 20:04:51 UTC | Allow installed tools to have more than 1 entry in the tool panel, and several fixes for deactivating / activating / uninstalling / reinstalling repositories. | 01 March 2012, 20:04:51 UTC |
| d42f05b | jeremy goecks | 01 March 2012, 19:19:17 UTC | Fix CSS bugs in displaying feature popups in embedded visualizations. | 01 March 2012, 19:19:17 UTC |
| 6847554 | jeremy goecks | 01 March 2012, 17:19:28 UTC | Fix bug in embedded visualization drag-zoom. | 01 March 2012, 17:19:28 UTC |
| 12aae7a | Daniel Blankenberg | 01 March 2012, 15:11:55 UTC | Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined. | 01 March 2012, 15:11:55 UTC |
| 5a5bf80 | Dannon Baker | 01 March 2012, 14:31:18 UTC | Quick fix for ftp upload unicode normalization failure. TODO: Refactor, shouldn't happen this way. | 01 March 2012, 14:31:18 UTC |
| 22da07a | jeremy goecks | 29 February 2012, 21:54:13 UTC | Merge | 29 February 2012, 21:54:13 UTC |
| 1ac1485 | jeremy goecks | 29 February 2012, 21:53:53 UTC | Pack trackster script. | 29 February 2012, 21:53:53 UTC |
| e25d96a | Greg Von Kuster | 29 February 2012, 21:27:46 UTC | Potential fix for the buildbot. | 29 February 2012, 21:27:46 UTC |
| 5495ad3 | jeremy goecks | 29 February 2012, 17:53:48 UTC | Style updates for embedded items to reduce visual footprint. | 29 February 2012, 17:53:48 UTC |
| 0857caf | Dannon Baker | 29 February 2012, 16:58:22 UTC | Cloud launch basics. TODO: Tons of help text, shift instance dns wait to page level. pkey direct download. | 29 February 2012, 16:58:22 UTC |
| bb4f3dc | Greg Von Kuster | 29 February 2012, 16:34:10 UTC | Fixes for installing tool shed repositories that contain tools when done by the InstallManager, and loading the tool panel with tools in an installed repository. | 29 February 2012, 16:34:10 UTC |
| 94bcc03 | jeremy goecks | 29 February 2012, 15:42:40 UTC | Fix incorrect sniffing for encodepeak datatype. | 29 February 2012, 15:42:40 UTC |
| 4d0272d | jeremy goecks | 29 February 2012, 15:35:49 UTC | Fix background for embedded visualizations. | 29 February 2012, 15:35:49 UTC |
| b3c2c1e | Daniel Blankenberg | 29 February 2012, 15:27:49 UTC | Fix missing gatk_report datatype in datatypes_conf.xml.sample. | 29 February 2012, 15:27:49 UTC |
| cb04eb2 | jeremy goecks | 29 February 2012, 14:53:56 UTC | Enable Pages and Trackster by default in universe. | 29 February 2012, 14:53:56 UTC |
| c45c8fc | Daniel Blankenberg | 29 February 2012, 14:36:03 UTC | Headers, which are important, are kept. Original ordering, which may be specifically needed by tools or external display applications is also maintained. | 29 February 2012, 14:36:03 UTC |
| 16986d7 | jeremy goecks | 28 February 2012, 22:50:26 UTC | Parameterize per-tool job runners so that parameter name/value pairs can be used to define multiple runners per tool. Documentation is in sample universe file. Add 'params' column to jobs table to store job parameters, and add source parameter for all jobs initiated in Trackster. | 28 February 2012, 22:50:26 UTC |
| 7c2a089 | Greg Von Kuster | 28 February 2012, 20:52:03 UTC | Fix for installing a tool shed repository that includes tools. | 28 February 2012, 20:52:03 UTC |
| 6fa41e6 | Daniel Blankenberg | 28 February 2012, 19:51:22 UTC | Fix for vcf_bgzip_to_tabix converter that was broken in changeset ac77414506d4 | 28 February 2012, 19:51:22 UTC |
| 166f5b4 | Greg Von Kuster | 28 February 2012, 19:07:20 UTC | File missed in the change set for the re-engineered InstallManager. | 28 February 2012, 19:07:20 UTC |
| a1200a3 | Greg Von Kuster | 28 February 2012, 18:41:01 UTC | Fix for generating metadata in a tool shed repository for a change set that contains data types but is not the repository tip. | 28 February 2012, 18:41:01 UTC |
| 97a3220 | Dannon Baker | 28 February 2012, 17:26:29 UTC | Merged in peterjc/galaxy-central/split_blast (pull request #37) | 28 February 2012, 17:26:29 UTC |
| 737e48e | Greg Von Kuster | 28 February 2012, 16:38:08 UTC | The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed. | 28 February 2012, 16:38:08 UTC |
| 7916bae | Dannon Baker | 28 February 2012, 16:00:16 UTC | Workflows: Additional rename options available to Rename Datasets action -- from Dave Walton. Syntax: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case Example: #{input1 | basename | upper} | 28 February 2012, 16:00:16 UTC |
| 8df04e7 | jeremy goecks | 27 February 2012, 18:47:41 UTC | Trackster bug fixes: (a) prevent dragging tracks above reference track and (b) fix tile's low location when showing tile. | 27 February 2012, 18:47:41 UTC |
| 5d81353 | Daniel Blankenberg | 27 February 2012, 17:49:30 UTC | Remove bam index metadata validator from GATK tools. The GATK wrapper will now build missing bam indexes on the fly as needed. | 27 February 2012, 17:49:30 UTC |
| a8ccc6f | Dannon Baker | 24 February 2012, 22:47:47 UTC | Preliminary autopacking for javascript. Disabled by default (pack_scripts in universe_wsgi.ini) and the packed scripts are still in the distribution, to be removed at some point. | 24 February 2012, 22:47:47 UTC |
| 80ce005 | Ross Lazarus | 24 February 2012, 21:48:03 UTC | remove validator from input genome - as Jeremy pointed out it will prevent the use of an unspecified build local genome. | 24 February 2012, 21:48:03 UTC |
| 9cc6b68 | Nate Coraor | 24 February 2012, 20:49:54 UTC | Include the job id in the error message when a job operation raises an exception in the PBS runner. | 24 February 2012, 20:49:54 UTC |
| 917e810 | Dannon Baker | 24 February 2012, 18:58:01 UTC | boto 2.2.2 - update eggs.ini | 24 February 2012, 18:58:01 UTC |
| 5e9c166 | Dannon Baker | 24 February 2012, 18:37:57 UTC | FTP Upload - Normalize filesystem and input filename encodings prior to comparison. Umlauts, etc will now behave properly in FTP upload dialog and will no longer default to "No data was entered in the upload form...". | 24 February 2012, 18:37:57 UTC |
| 968357e | Ross Lazarus | 24 February 2012, 07:27:34 UTC | Add a validator type="unspecified_build" to extract genomic dna tool | 24 February 2012, 07:27:34 UTC |
| aa77274 | jeremy goecks | 23 February 2012, 19:47:08 UTC | Put Trackster stylesheets in display base so that they are available for embedded visualizations. | 23 February 2012, 19:47:08 UTC |
| 24e9604 | Daniel Blankenberg | 23 February 2012, 18:48:09 UTC | Correct typo in GATK EvalVariant tool. | 23 February 2012, 18:48:09 UTC |
| b7e853d | Guru Ananda | 23 February 2012, 18:38:01 UTC | Added apiMel3 to manual builds. | 23 February 2012, 18:38:01 UTC |
| 862d536 | jeremy goecks | 23 February 2012, 17:24:49 UTC | Pack trackster script. | 23 February 2012, 17:24:49 UTC |
| ead3f2c | jeremy goecks | 23 February 2012, 17:23:36 UTC | Enable visualization of ENCODE peak tracks. Create 'encodepeak' datatype and add data providers for new datatype. | 23 February 2012, 17:23:36 UTC |
| 926217b | jeremy goecks | 22 February 2012, 21:04:12 UTC | Bug fixes for ac77414506d4 | 22 February 2012, 21:04:12 UTC |
| d42b072 | jeremy goecks | 22 February 2012, 20:23:44 UTC | Enable interval files to be converted to tabix. | 22 February 2012, 20:23:44 UTC |
| e592eb5 | jeremy goecks | 22 February 2012, 18:57:17 UTC | Enable interval files to be converted to interval_index and summary_tree datatypes. | 22 February 2012, 18:57:17 UTC |
| ef62813 | peterjc | 22 February 2012, 18:43:23 UTC | Basic BLAST XML merge implementation | 22 February 2012, 18:43:23 UTC |
| 6d0f59d | jeremy goecks | 22 February 2012, 16:05:31 UTC | Trackster: fix display of shared/embedded visualizations. | 22 February 2012, 16:05:31 UTC |
| a5deac9 | jeremy goecks | 22 February 2012, 15:53:53 UTC | Trackster bug fix: initialize name in track preferences. | 22 February 2012, 15:53:53 UTC |
| f2181e1 | jeremy goecks | 21 February 2012, 21:32:09 UTC | Trackster bug fix for running tool outside of a group. | 21 February 2012, 21:32:09 UTC |
| 9e113b9 | jeremy goecks | 21 February 2012, 19:14:48 UTC | Trackster bug fixes: hide 'more rows' icons by default and fix adding dataset from a history. | 21 February 2012, 19:14:48 UTC |
