| 33f5b3b | Eddie Belter | 07 January 2013, 22:58:08 UTC | Sync: mv misc update library to library summary | 09 January 2013, 18:42:11 UTC |
| 6a204f5 | Eddie Belter | 07 January 2013, 22:57:17 UTC | Sync: misc updat subject test use_ok all subclasses | 09 January 2013, 18:42:10 UTC |
| fc7f341 | Eddie Belter | 07 January 2013, 22:55:25 UTC | Sync: misc update now subclasses based on subject class name | 09 January 2013, 18:42:10 UTC |
| 70fac8a | Eddie Belter | 07 January 2013, 22:29:57 UTC | Sync: rename misc update test | 09 January 2013, 18:42:10 UTC |
| c26dfa3 | Eddie Belter | 07 January 2013, 22:29:30 UTC | Sync: dir for misc updates | 09 January 2013, 18:42:09 UTC |
| a4a056e | Eddie Belter | 07 January 2013, 19:31:47 UTC | Sync: add lib summary to misc update reconciling | 09 January 2013, 18:42:09 UTC |
| 0c68530 | Eddie Belter | 07 January 2013, 19:31:16 UTC | Sync: add is UR::Object to lib summary | 09 January 2013, 18:42:09 UTC |
| d1738e2 | Eddie Belter | 03 January 2013, 23:10:54 UTC | Sync: Add library summary | 09 January 2013, 18:42:08 UTC |
| d1a7a21 | Eddie Belter | 03 January 2013, 23:02:57 UTC | Library: remove fragment_size_range, it is really called library_insert_size | 09 January 2013, 18:42:08 UTC |
| f5cb938 | Eddie Belter | 03 January 2013, 22:24:46 UTC | Library: rm protocol_name; add protocol, original and library insert size - all in table | 09 January 2013, 18:42:07 UTC |
| 7040c71 | Scott Smith | 09 January 2013, 18:37:24 UTC | updated test cases to produce more helpful debug output | 09 January 2013, 18:37:24 UTC |
| 5d77a26 | Scott Smith | 09 January 2013, 18:28:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 January 2013, 18:28:48 UTC |
| 43a2b43 | APipe Tester | 09 January 2013, 18:25:54 UTC | updated ur submodule to a10c039 | 09 January 2013, 18:25:54 UTC |
| f4b7767 | Malachi Griffith | 09 January 2013, 17:22:06 UTC | ClinSeq - update snv summary and convergence | 09 January 2013, 17:22:06 UTC |
| 0365a5f | Scott Smith | 09 January 2013, 16:08:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 January 2013, 16:08:54 UTC |
| b679cb5 | Scott Smith | 09 January 2013, 16:08:19 UTC | ensure Genome::Model::Define::BaseMinimal avoids adding an input to a define command when anything in its inheritance implements it (instead of just checking direct properties) | 09 January 2013, 16:08:19 UTC |
| a6ff6cd | apregier | 09 January 2013, 16:04:40 UTC | Merge branch 'fireteam2' into gb_master | 09 January 2013, 16:04:40 UTC |
| c77ab80 | Scott Smith | 09 January 2013, 16:02:51 UTC | update the log4perl observer to dump a call stack if it gets inappropriate parameters | 09 January 2013, 16:02:51 UTC |
| 204070c | Scott Smith | 09 January 2013, 16:02:18 UTC | complete replacement of hard-coded "/gsc/scripts/lib/java" with $ENV{GENOME_SW_LEGACY_JAVA} | 09 January 2013, 16:02:18 UTC |
| ced4aa2 | apregier | 08 January 2013, 23:38:02 UTC | Make diffs more specific | 09 January 2013, 16:01:36 UTC |
| c5d83c5 | Travis Abbott | 09 January 2013, 04:02:34 UTC | fix failing gmdefine gene-prediction tests recent changes made it so that the processing profile and model name were not passed along to the core bit of model definition code. this is an intermediate fix to make sure those attributes make their way to the right place. | 09 January 2013, 04:02:34 UTC |
| 1a946eb | Feiyu Du | 08 January 2013, 22:28:02 UTC | increase mem limit to 25g | 08 January 2013, 22:28:02 UTC |
| 7ae592c | Scott Smith | 08 January 2013, 21:44:54 UTC | updated convergence docs for latest synopsis generation | 08 January 2013, 21:44:54 UTC |
| d278dfc | Scott Smith | 08 January 2013, 21:40:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 January 2013, 21:40:32 UTC |
| 7d7744b | Nathan Nutter | 08 January 2013, 21:02:58 UTC | Revert "supress logging when self is not defined" This reverts commit cc1ec522adf9400618584666d014d5c71df0bf91. Upstream issue in UR is corrected, this observer should now receive the class name instead of undef. | 08 January 2013, 21:02:58 UTC |
| 04c90b4 | Scott Smith | 08 January 2013, 21:02:22 UTC | Updated synopsis definition results in new output for the define-docs test case. | 08 January 2013, 21:02:22 UTC |
| a052e8f | Scott Smith | 08 January 2013, 21:01:24 UTC | update test case to use --add-to-projects instead of --projects | 08 January 2013, 21:01:24 UTC |
| 397ec37 | Scott Smith | 08 January 2013, 21:00:22 UTC | Handle --add-to-projects correctly. Resolve the command name for the synopsis from command_name() instead of composing in manually, preventing an error on some models which override the processing profile subclass. | 08 January 2013, 21:00:22 UTC |
| 6d032be | Scott Smith | 08 January 2013, 20:58:20 UTC | if model create gets nothing at SUPER::create fail immediately instead of attempting to use an undefined $self | 08 January 2013, 20:58:20 UTC |
| 310d2a8 | Travis Abbott | 08 January 2013, 20:09:43 UTC | don't try to add processing_profile{,_id} to Define/Convergence | 08 January 2013, 20:09:43 UTC |
| d3b0755 | Eddie Belter | 08 January 2013, 19:47:26 UTC | Inst data import: add new basic importer w/ improved functionality | 08 January 2013, 19:47:26 UTC |
| df14db2 | Thomas Mooney | 08 January 2013, 16:30:01 UTC | Go for the target class directly when creating models. This fixes some old model definers that expect this behaviour (e.g. Somatic). | 08 January 2013, 16:30:01 UTC |
| 8bab1bb | apregier | 08 January 2013, 15:42:28 UTC | Merge branch 'fix' into gb_master | 08 January 2013, 15:42:28 UTC |
| 4fb6009 | apregier | 08 January 2013, 15:41:41 UTC | Update tests for new reference sequence import process | 08 January 2013, 15:42:04 UTC |
| 4312ce8 | Thomas Mooney | 08 January 2013, 15:17:40 UTC | Remove redundant processing-profile property. Quiets warnings. | 08 January 2013, 15:17:40 UTC |
| 448f61a | Thomas Mooney | 08 January 2013, 14:57:11 UTC | Remove tests of abstract parent class. Every concrete subclass has doc-generation tests, and the docs depend on the subclass, so these don't test a useful case. | 08 January 2013, 14:57:11 UTC |
| 3d06320 | Thomas Mooney | 08 January 2013, 14:56:17 UTC | Move the eval to the part that might fail. | 08 January 2013, 14:56:17 UTC |
| a0caf79 | Nathan Nutter | 08 January 2013, 02:50:41 UTC | diff was ~150 MB and causing email notification problems in Jenkins | 08 January 2013, 02:50:41 UTC |
| cc1ec52 | Nathan Nutter | 08 January 2013, 01:51:01 UTC | supress logging when self is not defined | 08 January 2013, 01:51:11 UTC |
| be64ca5 | Nathan Nutter | 08 January 2013, 01:49:35 UTC | update .test-tracker.conf | 08 January 2013, 01:51:11 UTC |
| 804093d | APipe Tester | 08 January 2013, 01:39:02 UTC | updated jenkins submodule to 55c6103 | 08 January 2013, 01:39:02 UTC |
| 775915f | APipe Tester | 08 January 2013, 01:37:17 UTC | updated jenkins submodule to 836bb89 | 08 January 2013, 01:37:17 UTC |
| 504b132 | APipe Tester | 07 January 2013, 23:37:58 UTC | updated ur submodule to b9a6490 | 07 January 2013, 23:37:58 UTC |
| abca3e8 | apregier | 07 January 2013, 21:22:21 UTC | Add strelka | 07 January 2013, 21:22:36 UTC |
| fe9d860 | Gabriel Sanderson | 07 January 2013, 21:20:02 UTC | Fixed a typo | 07 January 2013, 21:20:02 UTC |
| 4ed11d6 | Gabriel Sanderson | 07 January 2013, 21:16:31 UTC | Merge branch 'qchack' into gb_master | 07 January 2013, 21:16:31 UTC |
| 47657f9 | Gabriel Sanderson | 07 January 2013, 21:00:47 UTC | The build will now continue even if QC failed. QC Failure will still be marked in the build notes. | 07 January 2013, 21:00:47 UTC |
| fafa52f | apregier | 07 January 2013, 19:20:46 UTC | Merge branch 'fix' into gb_master | 07 January 2013, 19:20:46 UTC |
| 03e387c | apregier | 07 January 2013, 19:19:53 UTC | Reformat the fasta file when importing a reference sequence | 07 January 2013, 19:19:53 UTC |
| 0c5d2bc | APipe Tester | 05 January 2013, 02:19:45 UTC | updated ur submodule to a8964a5 | 05 January 2013, 02:19:45 UTC |
| 42e78bf | Scott Smith | 05 January 2013, 01:04:16 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 January 2013, 01:04:16 UTC |
| 94a6817 | Scott Smith | 05 January 2013, 01:03:46 UTC | moved disk_usage_for_path into the main Genome::Sys since it is used in pipelines | 05 January 2013, 01:03:46 UTC |
| 312a675 | Scott Smith | 05 January 2013, 00:08:25 UTC | updated instdata solexa constructor to set subset_name from lane and index_sequnece | 05 January 2013, 00:08:25 UTC |
| 95e79d9 | Scott Smith | 04 January 2013, 23:17:57 UTC | Updated "genome model define" significantly. Added a new base class called ::BaseMinimal. ::Helper now inherits from that. The Genome::Model::Command::Define tree now no longer explicitly adds inputs to the modules it generates, but makes new subclasses of the above which add these. Hand written subclasses of ::BaseMinimal automatically get inputs and params based on the model definition also. | 04 January 2013, 23:17:57 UTC |
| a1770e8 | Thomas Mooney | 04 January 2013, 18:38:15 UTC | Correct the input name. | 04 January 2013, 18:38:15 UTC |
| 4608229 | Eddie Belter | 03 January 2013, 22:16:43 UTC | Revert "Library: rm protocol_name; add protocol, original and library insert size - all in table" This reverts commit 2e5ab16f5f580f29985ebc8186a3e6270ed9e852. | 03 January 2013, 22:16:43 UTC |
| 2e5ab16 | Eddie Belter | 03 January 2013, 00:56:13 UTC | Library: rm protocol_name; add protocol, original and library insert size - all in table | 03 January 2013, 22:05:28 UTC |
| 481faf8 | APipe Tester | 03 January 2013, 21:14:09 UTC | updated graphite submodule to f552b86 | 03 January 2013, 21:14:09 UTC |
| 13ae467 | APipe Tester | 03 January 2013, 20:48:34 UTC | updated graphite submodule to a448b6a | 03 January 2013, 20:48:34 UTC |
| f05f27c | APipe Tester | 03 January 2013, 20:48:27 UTC | updated ur submodule to e544805 | 03 January 2013, 20:48:27 UTC |
| a9279fb | Eddie Belter | 03 January 2013, 20:08:54 UTC | MetaShot: update status to give more detailed output | 03 January 2013, 20:09:06 UTC |
| 3e0c796 | Eddie Belter | 03 January 2013, 19:59:58 UTC | MetaShot: clean up create | 03 January 2013, 20:09:06 UTC |
| f4487d1 | Anthony Brummett | 03 January 2013, 19:59:59 UTC | Merge branch 'syslog' error_message()s are now sent to syslog via Log4Perl | 03 January 2013, 19:59:59 UTC |
| fc94617 | Anthony Brummett | 03 January 2013, 19:57:27 UTC | Clean up Log4Perl output Don't print to the screen Print the class name of the thing the error is being called on | 03 January 2013, 19:57:27 UTC |
| ae0a503 | Anthony Brummett | 03 January 2013, 19:41:46 UTC | Add observer for error_message to send errors to syslog via Log4Perl | 03 January 2013, 19:41:46 UTC |
| e86acd0 | Thomas Mooney | 03 January 2013, 19:26:11 UTC | Use Picard to convert the merged BAM into two FASTQs directly. Additionally, this re-reverses negative-strand reads back to their original version and doesn't print duplicate reads for multiple alignments. | 03 January 2013, 19:26:11 UTC |
| 26d36db | Thomas Mooney | 03 January 2013, 19:02:04 UTC | Add a command wrapper for the unmodified picard "SamToFastq" command. | 03 January 2013, 19:02:04 UTC |
| 3008364 | Thomas Mooney | 03 January 2013, 19:01:28 UTC | Edit the help to reflect that this isn't the real Picard SamToFastq command. | 03 January 2013, 19:01:28 UTC |
| 77cfa9c | Thomas Mooney | 03 January 2013, 16:12:55 UTC | fix typo same => sam | 03 January 2013, 16:12:55 UTC |
| 7ae48a3 | Thomas Mooney | 03 January 2013, 16:12:34 UTC | Remove some redundant information from docs. | 03 January 2013, 16:12:34 UTC |
| 3e4a358 | Scott Smith | 03 January 2013, 16:03:30 UTC | moved druggable gene logic from the module body into the execute() method | 03 January 2013, 16:03:30 UTC |
| 42d24f9 | Nathan Nutter | 03 January 2013, 00:59:19 UTC | add test_regex to .test-tracker.conf | 03 January 2013, 01:00:34 UTC |
| bb84433 | Eddie Belter | 03 January 2013, 00:50:47 UTC | Stie TGI Org Sample: typo in props to copy | 03 January 2013, 00:51:00 UTC |
| 47e32bf | Obi Griffith | 03 January 2013, 00:49:57 UTC | added option to upper case or not for alternate gene names to all importers | 03 January 2013, 00:49:57 UTC |
| 4225996 | Eddie Belter | 02 January 2013, 20:55:19 UTC | Build: uniq allocations from all_allocations | 02 January 2013, 20:55:19 UTC |
| 4ef1d0a | Eddie Belter | 02 January 2013, 20:41:30 UTC | Build Unarchive: unarchives and relinks symlinked alloations | 02 January 2013, 20:41:45 UTC |
| e444ff0 | Eddie Belter | 02 January 2013, 20:40:45 UTC | Build: add getting symlinked allocations in all_allocations and add method to attempt to relink broken ones | 02 January 2013, 20:41:44 UTC |
| 2510af8 | Chris Miller | 02 January 2013, 15:50:03 UTC | updating bam-window path | 02 January 2013, 15:50:03 UTC |
| 73248cf | Thomas Mooney | 31 December 2012, 22:27:25 UTC | Match large indel BAM diffs by regex. | 31 December 2012, 22:27:25 UTC |
| 723d858 | Chris Miller | 31 December 2012, 20:57:17 UTC | adding a DV2 module for bam-window - windowed readcounts | 31 December 2012, 20:57:34 UTC |
| c60dd04 | Thomas Mooney | 31 December 2012, 20:23:00 UTC | Reduce CPU request since can only use 2 CPUs at present. | 31 December 2012, 20:23:00 UTC |
| dcdbc61 | Thomas Mooney | 31 December 2012, 18:51:11 UTC | Cleanup error handling: $self not self, die not exit. | 31 December 2012, 18:51:11 UTC |
| 7a89af9 | APipe Tester | 31 December 2012, 18:09:11 UTC | updated ur submodule to 1a27ed4 | 31 December 2012, 18:09:11 UTC |
| f29bdeb | Thomas Mooney | 31 December 2012, 16:59:19 UTC | Skip tests if license has expired. | 31 December 2012, 16:59:19 UTC |
| a19e439 | Thomas Mooney | 31 December 2012, 15:07:15 UTC | More hard-coded paths... add the PATH to the executables this pipeline uses. | 31 December 2012, 15:07:15 UTC |
| 6d5f2ef | Jim Weible | 31 December 2012, 14:16:12 UTC | allow somatic validation commands to pass and do nothing if tier variants has no tiering version | 31 December 2012, 14:16:19 UTC |
| 6bb8a91 | Gabriel Sanderson | 29 December 2012, 05:45:55 UTC | Merge branch 'validation' into gb_master | 29 December 2012, 05:45:55 UTC |
| 9750742 | Gabriel Sanderson | 29 December 2012, 02:13:46 UTC | Refactor ValidateSmallIndels to implement a workflow to parallelize things. | 29 December 2012, 05:44:18 UTC |
| 1415144 | Chris Miller | 28 December 2012, 17:24:29 UTC | fixing broken test | 28 December 2012, 17:24:36 UTC |
| d3308cb | Beifang Niu | 28 December 2012, 16:44:04 UTC | add mutation spectrum tool | 28 December 2012, 16:44:04 UTC |
| 05c0cf1 | Chris Miller | 27 December 2012, 22:14:50 UTC | adding test for BamWindow | 27 December 2012, 22:14:50 UTC |
| 5b8890c | apregier | 27 December 2012, 21:53:30 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 21:53:30 UTC |
| 0606ef1 | apregier | 27 December 2012, 21:53:16 UTC | Ignore files with bam paths for large indel validation | 27 December 2012, 21:53:16 UTC |
| 3fea7ec | apregier | 27 December 2012, 21:49:25 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 21:49:25 UTC |
| f76770a | apregier | 27 December 2012, 21:49:09 UTC | Fix build diffs for somatic validation lage indels | 27 December 2012, 21:49:09 UTC |
| 4addc89 | apregier | 27 December 2012, 20:39:14 UTC | Merge branch 'fix' into gb_master | 27 December 2012, 20:39:14 UTC |
| 2d40da8 | apregier | 27 December 2012, 20:30:03 UTC | Make inputs optional so that skip option is functional | 27 December 2012, 20:38:54 UTC |
| bb57624 | Chris Miller | 27 December 2012, 20:21:02 UTC | namefix | 27 December 2012, 20:21:02 UTC |
| 384945e | Chris Miller | 27 December 2012, 19:56:44 UTC | blew away a bunch of legacy code and modified this to be a simple wrapper around the new bam-window c program. Will update the absolute path to the executable after it is installed system-wide | 27 December 2012, 19:56:44 UTC |
| 181d90e | Chris Miller | 27 December 2012, 18:36:59 UTC | initial commit of CopyCat for paired tumor/normal samples | 27 December 2012, 18:37:07 UTC |
