| a99b4cf | Feiyu Du | 27 October 2015, 21:56:17 UTC | Merge pull request #1075 from dufeiyu/sdrf Add reagent info of new target_region_set_name to TCGA Sdrf.pm | 27 October 2015, 21:56:17 UTC |
| 0597880 | Feiyu Du | 27 October 2015, 20:50:43 UTC | add info for new reagent | 27 October 2015, 20:50:43 UTC |
| c653d1c | APipe Tester | 27 October 2015, 18:33:33 UTC | updated jenkins submodule to c4d38e7 | 27 October 2015, 20:10:16 UTC |
| 03ef329 | Eddie Belter | 27 October 2015, 20:09:50 UTC | Merge pull request #1068 from ebelter/site-command Add Genome Site Command | 27 October 2015, 20:09:50 UTC |
| 669522d | APipe Tester | 26 October 2015, 22:30:48 UTC | updated sqitch/genome submodule to 6ea7fdc | 26 October 2015, 22:30:48 UTC |
| 98abcb8 | APipe Tester | 26 October 2015, 18:30:45 UTC | updated jenkins submodule to 34e51e1 | 26 October 2015, 18:30:45 UTC |
| 51730a4 | Eddie Belter | 26 October 2015, 18:27:44 UTC | Site Cmd: add verb sync to lims and genome | 26 October 2015, 18:27:44 UTC |
| 540a5ae | Eddie Belter | 26 October 2015, 18:26:26 UTC | Site Cmd: remove unused sync capture sets | 26 October 2015, 18:26:26 UTC |
| 4810d97 | Thomas B. Mooney | 26 October 2015, 13:28:11 UTC | Merge pull request #1045 from tmooney/build_launching_supports_workflowbuilder Changes to handle either a Workflow::Model or a G::WorkflowBuilder::DAG. | 26 October 2015, 13:28:11 UTC |
| aa0685c | APipe Tester | 23 October 2015, 22:58:08 UTC | updated jenkins submodule to d3b251d | 23 October 2015, 22:58:08 UTC |
| 2e4e147 | Anthony Brummett | 23 October 2015, 20:56:17 UTC | Merge pull request #1067 from brummett/remove-postgres-logging Remove obsolete postgres logging | 23 October 2015, 20:56:17 UTC |
| ea348b4 | Anthony Brummett | 23 October 2015, 15:32:15 UTC | Use Perl's built-in version checking for DBD::Pg LIMS is using a new enough version of DBD::Pg, so this special check isn't necessary anymore | 23 October 2015, 15:32:15 UTC |
| 41c52c9 | APipe Tester | 23 October 2015, 12:18:29 UTC | Updated `genome` tab completion. | 23 October 2015, 12:18:29 UTC |
| 9860fd8 | APipe Tester | 23 October 2015, 12:16:38 UTC | Updated class browser cache. | 23 October 2015, 12:16:38 UTC |
| 1ae96d4 | Eddie Belter | 22 October 2015, 23:24:40 UTC | Site Command: move sync capture sets | 22 October 2015, 23:24:40 UTC |
| 5180ff9 | Eddie Belter | 22 October 2015, 23:13:15 UTC | Site Command: remove synchronize tree command | 22 October 2015, 23:13:15 UTC |
| 828a033 | Eddie Belter | 22 October 2015, 23:12:18 UTC | Site COmmand: add/update command help doc | 22 October 2015, 23:12:18 UTC |
| a6aef4e | Eddie Belter | 22 October 2015, 23:06:04 UTC | Rename sys user with ldap | 22 October 2015, 23:06:04 UTC |
| 76662cd | Eddie Belter | 21 October 2015, 22:20:11 UTC | Site TGI Command: remove the sync directory | 22 October 2015, 22:56:39 UTC |
| 31e9b5a | Eddie Belter | 21 October 2015, 21:10:42 UTC | Site TGI: update sync command class names | 22 October 2015, 22:56:38 UTC |
| 16f5258 | Eddie Belter | 21 October 2015, 21:05:27 UTC | Site TGI: move commands from synchronize into command/sync | 22 October 2015, 22:56:38 UTC |
| dfd4bc8 | Eddie Belter | 21 October 2015, 20:59:18 UTC | Remove CompareSyncTime | 22 October 2015, 22:56:37 UTC |
| 69d778c | Eddie Belter | 21 October 2015, 20:44:38 UTC | Site Commands: update class names | 22 October 2015, 22:56:36 UTC |
| beeadba | Eddie Belter | 24 September 2015, 21:25:03 UTC | Site TGI: renmae sync sys users with ldap | 22 October 2015, 22:56:36 UTC |
| dface6a | Eddie Belter | 24 September 2015, 21:18:29 UTC | Stie TGI: add sync command tree | 22 October 2015, 22:56:35 UTC |
| e06d267 | Eddie Belter | 24 September 2015, 19:34:58 UTC | Site TGI: add command tree | 22 October 2015, 22:56:35 UTC |
| 324c02b | Eddie Belter | 22 October 2015, 22:49:32 UTC | Merge pull request #1063 from ebelter/disk-under-allocated Disk Volume Under Allocated | 22 October 2015, 22:49:32 UTC |
| ab89354 | Eddie Belter | 22 October 2015, 22:49:26 UTC | Merge pull request #1058 from ebelter/disk-move Disk Alloc Move: do not allow specifying target group and volume | 22 October 2015, 22:49:26 UTC |
| 0f41088 | Eddie Belter | 22 October 2015, 22:49:07 UTC | Merge pull request #1059 from ebelter/validate-disk-groups Disk Group Validate: add info_archive and update test | 22 October 2015, 22:49:07 UTC |
| 86182c7 | Eddie Belter | 22 October 2015, 22:47:53 UTC | Merge pull request #1064 from ebelter/build-event-view Build View Status XML: remove unused load jobs from lsf file methods | 22 October 2015, 22:47:53 UTC |
| 2857c8c | Anthony Brummett | 22 October 2015, 20:42:14 UTC | Remove the code that generates the logs for CompareSyncTime These logs were used during the transition from Oracle to Postgres, to compare commit times, and to find errors in out implementation of Postgres. | 22 October 2015, 20:42:14 UTC |
| bf4bf61 | Anthony Brummett | 22 October 2015, 20:39:37 UTC | Remove obsolete CompareSyncTime command Used during our transition from Oracle to Postgres to compare the time it took to commit to the two databases. | 22 October 2015, 20:41:49 UTC |
| 8c45471 | Anthony Brummett | 22 October 2015, 18:17:16 UTC | Merge pull request #1040 from brummett/unarchive-wait-for-lsf-jobs More efficient unarchive wait for lsf jobs | 22 October 2015, 18:17:16 UTC |
| 8c90a41 | Thomas B. Mooney | 22 October 2015, 16:20:13 UTC | Merge pull request #1044 from tmooney/reference_sequence_buckets New SR to create "buckets" of chromosomes for a reference. | 22 October 2015, 16:20:13 UTC |
| 864e219 | Thomas B. Mooney | 22 October 2015, 13:14:03 UTC | Merge pull request #924 from tmooney/alignment_dispatcher_uses_workflowbuilder Alignment Dispatcher uses WorkflowBuilder | 22 October 2015, 13:14:03 UTC |
| 9a89476 | APipe Tester | 22 October 2015, 12:19:12 UTC | Updated `gmt` tab completion. | 22 October 2015, 12:19:12 UTC |
| ad63289 | APipe Tester | 22 October 2015, 12:18:17 UTC | Updated `genome` tab completion. | 22 October 2015, 12:18:17 UTC |
| d964157 | APipe Tester | 22 October 2015, 12:16:32 UTC | Updated class browser cache. | 22 October 2015, 12:16:32 UTC |
| c4c82e2 | Thomas Mooney | 11 August 2015, 20:29:19 UTC | Update workflow unit test to use WorkflowBuilder. | 21 October 2015, 22:44:50 UTC |
| 72aa6bb | Thomas Mooney | 11 August 2015, 14:57:03 UTC | Cleanup: Removed unused variables. | 21 October 2015, 22:44:50 UTC |
| 85840d5 | Thomas Mooney | 11 August 2015, 14:49:58 UTC | Couple refinement to merge. Callers expect not to see the "Merged" results if refined results are available, so we'll skip adding the merge to the outputs if refiners are being run. | 21 October 2015, 22:44:50 UTC |
| b5dd26f | Thomas Mooney | 11 August 2015, 14:41:16 UTC | Fixup: output_properties is not an arrayref. | 21 October 2015, 22:44:50 UTC |
| 422e012 | Thomas Mooney | 10 August 2015, 22:57:44 UTC | Convert decorators to WorkflowBuilder. | 21 October 2015, 22:44:50 UTC |
| 8c52413 | Thomas Mooney | 10 August 2015, 22:42:58 UTC | Stop using _add_link_to_workflow helper. | 21 October 2015, 22:44:50 UTC |
| 458ef74 | Thomas Mooney | 10 August 2015, 22:42:27 UTC | Add ability to specify an input is optional. | 21 October 2015, 22:44:50 UTC |
| 28f49ed | Thomas Mooney | 10 August 2015, 21:23:51 UTC | Use the DAG directly when running the workflow. | 21 October 2015, 22:44:50 UTC |
| b6ff0a8 | Thomas Mooney | 10 August 2015, 21:02:58 UTC | Remove UR optimization--it cloned objects with WorkflowBuilder links. | 21 October 2015, 22:44:49 UTC |
| 1d12e4f | Thomas Mooney | 10 August 2015, 20:42:23 UTC | WorkflowBuilder requires that inputs/outputs be declared implicitly. | 21 October 2015, 22:44:49 UTC |
| e4998b3 | Thomas Mooney | 10 August 2015, 20:25:12 UTC | Remove disused property lists. | 21 October 2015, 22:44:49 UTC |
| ff2b278 | Thomas Mooney | 10 August 2015, 20:17:22 UTC | Move linking between steps to occur within each group. *The old master workflow generation is now completely parted out. | 21 October 2015, 22:44:49 UTC |
| aaa7537 | Thomas Mooney | 10 August 2015, 19:35:59 UTC | WIP: Convert Refine step to WorkflowBuilder | 21 October 2015, 22:44:49 UTC |
| 9a54edd | Thomas Mooney | 10 August 2015, 18:51:44 UTC | Don't need to compute inputs and outputs any more. | 21 October 2015, 22:44:49 UTC |
| 0c998e7 | Thomas Mooney | 10 August 2015, 18:45:36 UTC | WIP: Convert Merge step to WorkflowBuilder. | 21 October 2015, 22:44:49 UTC |
| 232b556 | Thomas Mooney | 10 August 2015, 14:03:57 UTC | WIP: Convert "object" workflows to WorkflowBuilder (Align(AndMerge)) | 21 October 2015, 22:44:49 UTC |
| dbc8c02 | Thomas Mooney | 06 August 2015, 22:46:15 UTC | WIP: Convert first step of workflow generation (AlignerIndex) * Create master workflow in advance. * Create Block for aligner indices inside aligner index step. * Use constants to avoid needing to keep track of inputs. | 21 October 2015, 22:43:49 UTC |
| 1342dc5 | Thomas Mooney | 06 August 2015, 21:59:08 UTC | Intermediate step: Convert object creation to WorkflowBuilder This is broken since WorkflowBuilder expects to learn of its inputs and outputs by the creation of links, but Workflow expects to be informed in advance of link creation so it can validate the links as they are added. | 21 October 2015, 22:43:49 UTC |
| da090db | Thomas Mooney | 06 August 2015, 20:36:57 UTC | Use _add_link_to_workflow helper. It uses the precomputed UR templates for efficiency. | 21 October 2015, 22:37:57 UTC |
| e0789b8 | Chris Miller | 21 October 2015, 21:45:46 UTC | Merge pull request #1038 from chrisamiller/concordance Addition of an option, cleanup of edge cases and tests | 21 October 2015, 21:45:46 UTC |
| e2022dd | Chris Miller | 21 October 2015, 21:35:18 UTC | adds another example SNP file for easy reference | 21 October 2015, 21:35:18 UTC |
| 47c8483 | Susanna Kiwala | 21 October 2015, 20:55:20 UTC | Merge pull request #1031 from susannasiebert/epitope_prediction Move variant sequence fasta generation into variant reporting framework and handle frameshifte and in frame indels | 21 October 2015, 20:55:20 UTC |
| 165cca8 | Eddie Belter | 21 October 2015, 20:10:58 UTC | Model Event View: rm commented out code | 21 October 2015, 20:10:58 UTC |
| 213fd73 | Eddie Belter | 21 October 2015, 18:33:23 UTC | Build View Status XML: remove unused load jobs from lsf file methods adn properties | 21 October 2015, 18:33:23 UTC |
| f251710 | Eddie Belter | 21 October 2015, 17:48:10 UTC | Disk Alloc Move: do not specify the target group to the mover if we have a target volume | 21 October 2015, 17:48:10 UTC |
| 6dcd201 | Eddie Belter | 21 October 2015, 17:38:55 UTC | Disk Volume UderAlloc: test cleanup | 21 October 2015, 17:38:55 UTC |
| ff47bbd | Eddie Belter | 21 October 2015, 17:35:34 UTC | Disk Volume UnderAlloc: use fake group, rename volume | 21 October 2015, 17:35:34 UTC |
| 7821697 | Eddie Belter | 21 October 2015, 17:34:20 UTC | Disk Volume UnderAlloc: return undef if under allocd volumes found | 21 October 2015, 17:34:20 UTC |
| 3618e9d | Thomas B. Mooney | 21 October 2015, 14:24:50 UTC | Merge pull request #1056 from tmooney/refseq_df Use Filesys::Df to get available KB | 21 October 2015, 14:24:50 UTC |
| 8a7edd8 | Thomas B. Mooney | 21 October 2015, 13:14:20 UTC | Merge pull request #1060 from tmooney/stop_testing_58 Stop testing that Genome classes work under older Perl. | 21 October 2015, 13:14:20 UTC |
| cc8b659 | Eddie Belter | 21 October 2015, 01:01:23 UTC | Disk Alloc Move: check if target volume is in group is both are specified | 21 October 2015, 01:01:23 UTC |
| 2b6be0f | Eddie Belter | 21 October 2015, 00:59:18 UTC | Disk Alloc Move: fix idempotent move test | 21 October 2015, 00:59:18 UTC |
| 4a18780 | APipe Tester | 20 October 2015, 19:36:45 UTC | updated ur submodule to 45bb80e | 20 October 2015, 20:56:27 UTC |
| b186521 | Eddie Belter | 20 October 2015, 20:27:36 UTC | Disk Alloc: do not allow allcoations to be created in disk_group_archive | 20 October 2015, 20:27:36 UTC |
| a697924 | Eddie Belter | 20 October 2015, 20:03:54 UTC | Disk Group: add is_archive method | 20 October 2015, 20:26:50 UTC |
| c65add8 | Thomas B. Mooney | 20 October 2015, 20:11:24 UTC | Merge pull request #1057 from tmooney/java7_in_gatk Make Java 1.7 the default for running GATK tools. | 20 October 2015, 20:11:24 UTC |
| e6aa190 | Eddie Belter | 20 October 2015, 19:39:46 UTC | Disk Group Validate: use lives_ok in test | 20 October 2015, 19:39:46 UTC |
| 58c4230 | Thomas B. Mooney | 20 October 2015, 19:12:49 UTC | Merge pull request #1055 from tmooney/remove_db_skip_postgres Remove old db_skip_postgres configuration variable. | 20 October 2015, 19:12:49 UTC |
| eb5ccad | Eddie Belter | 20 October 2015, 00:18:01 UTC | Disk Under Allocated: use volume mock object | 20 October 2015, 00:22:03 UTC |
| 140f10a | Eddie Belter | 19 October 2015, 23:59:57 UTC | Disk Uder Allocated: convert to subtests | 19 October 2015, 23:59:57 UTC |
| d3728fa | Eddie Belter | 19 October 2015, 23:57:25 UTC | Disk Uder Allocated: use is many for disk group names instead of splitting by commas | 19 October 2015, 23:57:25 UTC |
| 3fb96bb | Eddie Belter | 19 October 2015, 23:45:37 UTC | Disk Under Allocated: remove send alert feature | 19 October 2015, 23:45:37 UTC |
| a983750 | Eddie Belter | 19 October 2015, 23:39:49 UTC | Disk Group Validate: use test::exception instead of test::fatal | 19 October 2015, 23:39:49 UTC |
| 49ba430 | Eddie Belter | 19 October 2015, 23:37:06 UTC | Disk Group Validate: remove db singles | 19 October 2015, 23:37:06 UTC |
| 71e9b38 | Eddie Belter | 19 October 2015, 23:36:07 UTC | Disk Group Validate: convert to subtests | 19 October 2015, 23:36:07 UTC |
| e4b0b72 | Eddie Belter | 19 October 2015, 23:35:10 UTC | Disk Group Validate: add disk_group_archive to valid group names | 19 October 2015, 23:35:21 UTC |
| 3ee0181 | Eddie Belter | 19 October 2015, 23:24:04 UTC | Disk Alloc Move: only add existing alloc group if no target group and volume | 19 October 2015, 23:24:12 UTC |
| a568448 | Eddie Belter | 19 October 2015, 23:20:46 UTC | Disk Alloc Move: function to get move params | 19 October 2015, 23:20:46 UTC |
| ed0e639 | Eddie Belter | 19 October 2015, 23:07:13 UTC | Disk Alloc Mover: cannot specify target group and volume | 19 October 2015, 23:07:13 UTC |
| 0b13da1 | Thomas Mooney | 19 October 2015, 20:56:36 UTC | Stop testing that Genome classes work under older Perl. | 19 October 2015, 20:56:36 UTC |
| 2f15f25 | Thomas Mooney | 19 October 2015, 19:34:49 UTC | Make Java 1.7 the default for GATK. | 19 October 2015, 19:39:51 UTC |
| 07b6775 | Thomas Mooney | 19 October 2015, 17:34:00 UTC | Use Filesys::Df instead of piping df output. | 19 October 2015, 17:41:02 UTC |
| bcede52 | Thomas Mooney | 19 October 2015, 16:13:08 UTC | Use -P to avoid wrapping lines. | 19 October 2015, 16:13:08 UTC |
| 6c94eb7 | Thomas B. Mooney | 19 October 2015, 14:03:13 UTC | Merge pull request #1054 from tmooney/use_array_form_in_import_helper_shellcmd Use array form of shellcmd. | 19 October 2015, 14:03:13 UTC |
| 9bb4577 | Eddie Belter | 15 October 2015, 22:20:56 UTC | Disk Alloc Move: convert to subtests | 15 October 2015, 22:20:56 UTC |
| 9942417 | APipe Tester | 15 October 2015, 20:45:11 UTC | updated workflow submodule to c0f1230 | 15 October 2015, 20:45:11 UTC |
| e88eb33 | Thomas Mooney | 15 October 2015, 20:31:10 UTC | Remove comment. If preserving order is important, we'll already be handcrafting the bucket result instead of running this. It was confusing, anyway, since it didn't really apply to the code that was present. | 15 October 2015, 20:31:10 UTC |
| dfe51e3 | Thomas Mooney | 15 October 2015, 20:24:32 UTC | Remove old db_skip_postgres configuration variable. | 15 October 2015, 20:24:32 UTC |
| d75430d | Thomas Mooney | 15 October 2015, 20:08:42 UTC | Workflow::Model has been updated to have get_xml(), so always call that. | 15 October 2015, 20:08:42 UTC |
| 13e2f3d | Thomas Mooney | 15 October 2015, 19:15:31 UTC | Use array form of shellcmd. | 15 October 2015, 19:15:31 UTC |
| f4e03af | Thomas B. Mooney | 15 October 2015, 16:49:11 UTC | Merge pull request #1053 from tmooney/add_run_as_to_mc16s_test_factory_model Add run_as to test factory model. | 15 October 2015, 16:49:11 UTC |
| c10972d | Dan Koboldt | 15 October 2015, 16:34:36 UTC | Added LSF log output files | 15 October 2015, 16:34:36 UTC |
