| ca6ebca | Nathan Nutter | 14 August 2013, 16:56:55 UTC | can't use this lib since it is not installed for Perl 5.8 | 14 August 2013, 17:01:47 UTC |
| c8ad53c | APipe Tester | 14 August 2013, 15:37:32 UTC | Updated `gmt` tab completion. | 14 August 2013, 15:37:32 UTC |
| 9d32896 | APipe Tester | 14 August 2013, 15:36:26 UTC | Updated `genome` tab completion. | 14 August 2013, 15:36:26 UTC |
| 9b2f2e2 | APipe Tester | 14 August 2013, 15:34:13 UTC | Updated class browser cache. | 14 August 2013, 15:34:13 UTC |
| 482c6e5 | Dan Koboldt | 14 August 2013, 15:23:46 UTC | Pushing updates to Merge branch 'master' of git+ssh://git/srv/git/genome | 14 August 2013, 15:23:46 UTC |
| fc559cc | Dan Koboldt | 14 August 2013, 15:23:31 UTC | Updates to Mendelian analysis tools | 14 August 2013, 15:23:31 UTC |
| 8d74bd3 | Dan Koboldt | 14 August 2013, 15:23:10 UTC | New tools for Mendelian analysis | 14 August 2013, 15:23:10 UTC |
| 8506270 | Nathan Nutter | 14 August 2013, 15:15:15 UTC | all arguments must be array elements to pass an array to system | 14 August 2013, 15:15:15 UTC |
| 3551b91 | APipe Tester | 14 August 2013, 14:05:30 UTC | Updated `genome` tab completion. | 14 August 2013, 14:05:30 UTC |
| 2f35f4d | APipe Tester | 14 August 2013, 14:03:11 UTC | Updated class browser cache. | 14 August 2013, 14:03:11 UTC |
| 5b7e28e | dmorton | 14 August 2013, 13:19:23 UTC | Added UR_DBI_NO_COMMIT to Notable.t It seems someone added the entities it creates to the database by mistake somehow. | 14 August 2013, 13:19:23 UTC |
| ae6707b | dmorton | 10 August 2013, 00:03:34 UTC | Make _execute_system_command avoid invoking the shell That way arguments don't have to be escaped carefully. Escaping strings for the shell is difficult and almost everyone gets it wrong in some subtle way. IPC::System::Simple never invokes the shell and so avoids the issue entirely. | 14 August 2013, 12:53:17 UTC |
| 30f95ba | dmorton | 09 August 2013, 22:59:14 UTC | Ensure strings are properly formatted | 14 August 2013, 12:53:17 UTC |
| be7a6f4 | APipe Tester | 14 August 2013, 07:07:53 UTC | updated workflow submodule to c0449f9 | 14 August 2013, 07:07:53 UTC |
| d2af94f | Nathan Nutter | 14 August 2013, 06:38:43 UTC | bypass until expected data is updated | 14 August 2013, 06:38:43 UTC |
| 5a3080f | Nathan Nutter | 14 August 2013, 06:31:09 UTC | add ORA-03135 to retriable operations | 14 August 2013, 06:31:09 UTC |
| beea803 | Nathan Nutter | 14 August 2013, 02:46:44 UTC | should inherit from parent | 14 August 2013, 02:46:44 UTC |
| dadd613 | Thomas Mooney | 13 August 2013, 20:48:02 UTC | Update refalign build diffs to account for UUIDs. | 14 August 2013, 02:34:52 UTC |
| 43eafb7 | Thomas Mooney | 13 August 2013, 20:21:22 UTC | Update somval build diffs to account for UUIDs. | 14 August 2013, 02:34:40 UTC |
| ce29425 | Ben Oberkfell | 29 July 2013, 20:23:28 UTC | numeric comparison fails w/ uuids | 14 August 2013, 02:31:52 UTC |
| cdcd41e | Nathan Nutter | 26 July 2013, 22:04:56 UTC | deal with sort differences caused by UUIDs | 14 August 2013, 02:31:51 UTC |
| 7b01c61 | Nathan Nutter | 14 August 2013, 02:26:27 UTC | fix test counts after cherry-pick | 14 August 2013, 02:26:27 UTC |
| 86b8382 | Nathan Nutter | 26 July 2013, 21:42:41 UTC | put old test into a subtest | 14 August 2013, 02:22:22 UTC |
| d81ef62 | Nathan Nutter | 18 July 2013, 20:27:51 UTC | temporarily remove `genome disk allocation archive-expired` Due to PostgreSQL migration and poor date handling in UR::BoolExpr we are temporarily removing this command. We created AR-89 and AR-90 to address these issues at a later time. | 14 August 2013, 02:22:08 UTC |
| 21989b9 | Nathan Nutter | 23 July 2013, 19:18:42 UTC | sort order cannot be predetermined with UUIDs | 14 August 2013, 02:20:48 UTC |
| f072b80 | Nathan Nutter | 23 July 2013, 20:05:04 UTC | use appropriate sorter | 14 August 2013, 02:17:42 UTC |
| 586078c | Nathan Nutter | 25 July 2013, 15:48:26 UTC | extract method | 14 August 2013, 02:17:20 UTC |
| 1455741 | Nathan Nutter | 25 July 2013, 15:45:50 UTC | whitespace | 14 August 2013, 02:17:07 UTC |
| 76d73fc | Ben Oberkfell | 30 July 2013, 18:55:37 UTC | remove sorting assumption | 14 August 2013, 02:13:29 UTC |
| dbb772d | Nathan Nutter | 07 August 2013, 22:26:05 UTC | remove numeric comparison to ID | 14 August 2013, 02:03:26 UTC |
| 625b5ce | Nathan Nutter | 26 July 2013, 21:39:28 UTC | use is_equal_set instead of is_deeply and deal with sort difference | 14 August 2013, 01:45:24 UTC |
| a961c0d | Nathan Nutter | 26 July 2013, 21:39:11 UTC | add is_equal_set | 14 August 2013, 01:45:01 UTC |
| 2dbeefb | Nathan Nutter | 10 August 2013, 21:55:12 UTC | remove deprecated lock code This is follow up to 659c1fb. The deprecated lock code used subdirectories which leaves behind empty directories when the lock is removed. Since it is safe to assume all the old-lock-only code is no longer running we can now remove that. | 14 August 2013, 01:44:25 UTC |
| a98addf | Nathan Nutter | 09 August 2013, 21:09:48 UTC | add a SIGPIPE handler to BQM | 14 August 2013, 01:44:24 UTC |
| 9997bac | APipe Tester | 13 August 2013, 21:55:31 UTC | Updated `gmt` tab completion. | 13 August 2013, 21:55:31 UTC |
| d6968b6 | APipe Tester | 13 August 2013, 21:54:16 UTC | Updated `genome` tab completion. | 13 August 2013, 21:54:16 UTC |
| 6e4d0b9 | APipe Tester | 13 August 2013, 21:51:49 UTC | Updated class browser cache. | 13 August 2013, 21:51:49 UTC |
| 2f7e813 | Chris Miller | 13 August 2013, 21:37:43 UTC | adding test | 13 August 2013, 21:42:13 UTC |
| 71f6bb8 | Chris Miller | 13 August 2013, 21:17:47 UTC | first working version | 13 August 2013, 21:42:11 UTC |
| f996ad9 | Chris Miller | 13 August 2013, 17:33:58 UTC | removing testing code, reverting to older better version | 13 August 2013, 21:42:10 UTC |
| dfcc458 | Chris Miller | 13 August 2013, 17:33:01 UTC | updates - still nonfunctional | 13 August 2013, 21:42:10 UTC |
| ad7284a | Chris Miller | 12 August 2013, 20:46:47 UTC | initial commit of filter vcf info | 13 August 2013, 21:42:05 UTC |
| e1c70d4 | Chris Miller | 07 August 2013, 19:47:18 UTC | parsing info field by default | 13 August 2013, 21:42:05 UTC |
| 5e46f02 | Adam Coffman | 13 August 2013, 20:52:55 UTC | update approved docs for somatic validation define command | 13 August 2013, 20:52:55 UTC |
| f5cd3da | APipe Tester | 13 August 2013, 17:44:54 UTC | Updated `genome` tab completion. | 13 August 2013, 17:46:26 UTC |
| 64b1a2c | APipe Tester | 13 August 2013, 17:41:45 UTC | Updated class browser cache. | 13 August 2013, 17:46:26 UTC |
| 4edb203 | Eddie Belter | 13 August 2013, 17:42:35 UTC | InstData GATK: use sr user to get base recal in base recal bam result | 13 August 2013, 17:45:40 UTC |
| ee8f7d1 | Chris Miller | 09 August 2013, 17:15:52 UTC | adding --force option to somval to handle samples that don't match | 13 August 2013, 17:34:35 UTC |
| 4ef7050 | Eddie Belter | 13 August 2013, 17:29:27 UTC | Refine Reads GATK: rm setting user of indel realign; add tests for setting users of all gatk result generated | 13 August 2013, 17:29:27 UTC |
| 8e69a81 | Eddie Belter | 13 August 2013, 16:59:05 UTC | InstData GATK: add user to bam source; update tests; move status msgs to base class | 13 August 2013, 16:59:05 UTC |
| a78fccf | Eddie Belter | 13 August 2013, 16:58:24 UTC | InstData GATK: move known sites display to base class | 13 August 2013, 16:58:24 UTC |
| 38e0d19 | Eddie Belter | 13 August 2013, 16:45:39 UTC | InstData GATK: update var name in base recal bam result test | 13 August 2013, 16:45:39 UTC |
| 5804552 | Mark Burnett | 13 August 2013, 14:32:16 UTC | SomVal: add build_id to outputproperties for inner model | 13 August 2013, 14:33:29 UTC |
| 373ada8 | APipe Tester | 13 August 2013, 03:02:14 UTC | Updated `gmt` tab completion. | 13 August 2013, 03:02:14 UTC |
| aa1f308 | APipe Tester | 13 August 2013, 03:01:22 UTC | Updated `genome` tab completion. | 13 August 2013, 03:01:22 UTC |
| 0df30d8 | APipe Tester | 13 August 2013, 02:59:28 UTC | Updated class browser cache. | 13 August 2013, 02:59:28 UTC |
| 8b33473 | Eddie Belter | 13 August 2013, 00:51:10 UTC | InstData GATK Best Practices: add base recal bam result as user to indel realigner result | 13 August 2013, 00:51:23 UTC |
| a726f6a | Eddie Belter | 13 August 2013, 00:50:37 UTC | InstData GATK: add base recal bam result as user to base recal result | 13 August 2013, 00:51:23 UTC |
| 5789da6 | APipe Tester | 13 August 2013, 00:41:36 UTC | updated workflow submodule to 83abf49 | 13 August 2013, 00:41:36 UTC |
| 091075c | Nathan Nutter | 12 August 2013, 23:41:24 UTC | diag the log for debugging this intermittent failure | 12 August 2013, 23:44:15 UTC |
| cf6d088 | Anthony Brummett | 12 August 2013, 23:35:47 UTC | Use UR's RDBMS retry code instead of Genome's | 12 August 2013, 23:36:29 UTC |
| a236022 | APipe Tester | 12 August 2013, 23:15:06 UTC | updated ur submodule to 7ed4a34 | 12 August 2013, 23:15:06 UTC |
| 2b20708 | APipe Tester | 12 August 2013, 22:56:31 UTC | updated ur submodule to 466d3eb | 12 August 2013, 22:56:31 UTC |
| 8fa5fd5 | Anthony Brummett | 12 August 2013, 22:38:58 UTC | Use parent method to set the date format besides using common code, it will also benefit from being able to use the retry code | 12 August 2013, 22:38:58 UTC |
| d0ca72d | Nathan Nutter | 12 August 2013, 22:24:27 UTC | make runtime dependency This gets loaded early on so, specifically, when /gsc/bin/perl is used which means any compile time dependencies must be satisfied by /gsc/bin/perl; IPC::System::Simple was not. | 12 August 2013, 22:27:30 UTC |
| 76adaa2 | Eddie Belter | 12 August 2013, 21:49:53 UTC | InstData GATK: delete result on error | 12 August 2013, 21:49:53 UTC |
| 96454d9 | APipe Tester | 12 August 2013, 21:03:05 UTC | Updated `genome` tab completion. | 12 August 2013, 21:03:05 UTC |
| 46614f8 | APipe Tester | 12 August 2013, 21:00:44 UTC | Updated class browser cache. | 12 August 2013, 21:00:44 UTC |
| 154d1a5 | Dave Larson | 12 August 2013, 18:01:24 UTC | Start on SubmissionSummary command for SomaticValidation models. Since these models do not produce md5 checksums currently, this tool dies with an appropriate message. | 12 August 2013, 20:51:12 UTC |
| 69230ec | Mark Burnett | 12 August 2013, 20:28:30 UTC | SomVal: pass build_id along in Validate Large Indels | 12 August 2013, 20:29:16 UTC |
| 251f115 | Mark Burnett | 12 August 2013, 20:22:40 UTC | ClinSeq: stop treating singular builds as arrays in workflow | 12 August 2013, 20:29:15 UTC |
| f5e95ef | APipe Tester | 12 August 2013, 19:46:19 UTC | Updated `gmt` tab completion. | 12 August 2013, 19:46:19 UTC |
| a32e0a5 | APipe Tester | 12 August 2013, 19:45:19 UTC | Updated `genome` tab completion. | 12 August 2013, 19:45:19 UTC |
| 9bed82c | APipe Tester | 12 August 2013, 19:42:56 UTC | Updated class browser cache. | 12 August 2013, 19:42:56 UTC |
| 709c037 | Feiyu Du | 09 August 2013, 20:37:41 UTC | turn on BamQc for bwamem/sw bam, but skip samstat for bwamem/sw bam | 12 August 2013, 18:58:16 UTC |
| d9f6b42 | Feiyu Du | 07 August 2013, 18:19:21 UTC | update error rate C tool to version 0.9 | 12 August 2013, 18:58:15 UTC |
| de02754 | Feiyu Du | 02 August 2013, 18:14:38 UTC | 1.update ref-aling bamqc related codes and bamqc software results with new gmt bio-samtools error-rate 2. use instrument data id (per lane) for bamqc output file name | 12 August 2013, 18:58:15 UTC |
| cd2d816 | Feiyu Du | 25 July 2013, 15:25:09 UTC | refactor G::M::T::BioSamtools::ErrorRate | 12 August 2013, 18:58:14 UTC |
| 7a2d78a | Mark Burnett | 09 August 2013, 21:17:04 UTC | bugfix: omitted modifications from mc16s change | 09 August 2013, 21:17:04 UTC |
| 0630127 | APipe Tester | 09 August 2013, 15:51:00 UTC | Updated `gmt` tab completion. | 09 August 2013, 15:51:00 UTC |
| 0e63c56 | APipe Tester | 09 August 2013, 15:49:57 UTC | Updated `genome` tab completion. | 09 August 2013, 15:49:57 UTC |
| 2acbcc5 | APipe Tester | 09 August 2013, 15:47:38 UTC | Updated class browser cache. | 09 August 2013, 15:47:38 UTC |
| 6c0d26e | Jasreet Hundal | 09 August 2013, 15:36:22 UTC | Removing RunNetmhc.t | 09 August 2013, 15:36:22 UTC |
| 97bccf9 | Jasreet Hundal | 09 August 2013, 15:11:53 UTC | New version of NetMHC added | 09 August 2013, 15:11:53 UTC |
| 1c7187e | APipe Tester | 09 August 2013, 14:32:53 UTC | Updated `gmt` tab completion. | 09 August 2013, 14:32:53 UTC |
| adf7dc2 | APipe Tester | 09 August 2013, 14:31:37 UTC | Updated `genome` tab completion. | 09 August 2013, 14:31:37 UTC |
| 9563ceb | APipe Tester | 09 August 2013, 14:29:09 UTC | Updated class browser cache. | 09 August 2013, 14:29:09 UTC |
| 62536a0 | APipe Tester | 09 August 2013, 14:22:51 UTC | Updated `genome` tab completion. | 09 August 2013, 14:24:38 UTC |
| 0a4de14 | APipe Tester | 09 August 2013, 14:20:31 UTC | Updated class browser cache. | 09 August 2013, 14:24:38 UTC |
| 2b7a85a | Jasreet Hundal | 09 August 2013, 14:22:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 August 2013, 14:22:13 UTC |
| 6e1f325 | Nathan Nutter | 09 August 2013, 14:19:51 UTC | fix scoping bug preventing commit from working | 09 August 2013, 14:20:30 UTC |
| 0924f0c | Jasreet Hundal | 09 August 2013, 14:19:42 UTC | changes to handle new annotation format | 09 August 2013, 14:19:42 UTC |
| c5823eb | Travis Abbott | 08 August 2013, 22:21:49 UTC | add documentation to File/Vcf/Entry.pm | 08 August 2013, 22:22:39 UTC |
| 37f0e94 | dmorton | 08 August 2013, 16:28:30 UTC | Merge branch 'remove-ben' | 08 August 2013, 22:13:21 UTC |
| 5af4a55 | dmorton | 08 August 2013, 14:48:39 UTC | Replace Ben with Jim in Task.t | 08 August 2013, 22:13:21 UTC |
| 9ff6faf | dmorton | 08 August 2013, 14:45:42 UTC | Replace Ben with Jim in Task/Command/Run.t Jim is the least likely user to change :) | 08 August 2013, 22:13:20 UTC |
| 8e7bcf7 | dmorton | 08 August 2013, 14:44:11 UTC | Remove Ben's email from Site/TGI/LegacyConfig | 08 August 2013, 22:13:20 UTC |
| c617167 | dmorton | 08 August 2013, 14:42:27 UTC | Remove Ben's email from gmt sam merge | 08 August 2013, 22:13:19 UTC |
| c33b9f9 | dmorton | 08 August 2013, 16:27:35 UTC | Merge branch 'add-lab-requestor-unarchive' | 08 August 2013, 22:13:18 UTC |
| 2faf0ac | dmorton | 08 August 2013, 16:21:31 UTC | Fix test related to --lab being required | 08 August 2013, 22:13:18 UTC |
