| 9e7ed41 | dmorton | 15 February 2014, 17:47:00 UTC | Resolve race condition in make_path | 15 February 2014, 21:45:25 UTC |
| b5fa277 | APipe Tester | 15 February 2014, 13:17:54 UTC | Updated `gmt` tab completion. | 15 February 2014, 13:17:54 UTC |
| d569fdb | APipe Tester | 15 February 2014, 13:17:09 UTC | Updated `genome` tab completion. | 15 February 2014, 13:17:09 UTC |
| 353453b | APipe Tester | 15 February 2014, 13:15:31 UTC | Updated class browser cache. | 15 February 2014, 13:15:31 UTC |
| 9552c2b | Nathaniel Nutter | 07 February 2014, 17:31:51 UTC | use memoize to memoize | 14 February 2014, 21:19:08 UTC |
| 3d19e66 | Nathaniel Nutter | 11 February 2014, 18:52:42 UTC | use Genome::Sys to get username instead of getpwuid | 14 February 2014, 21:18:38 UTC |
| fffe97c | Nathaniel Nutter | 13 February 2014, 19:28:44 UTC | remove commented out sqitch configs | 14 February 2014, 21:18:15 UTC |
| 1d452b6 | Avinash Ramu | 14 February 2014, 20:55:25 UTC | add error checks | 14 February 2014, 20:55:55 UTC |
| df0e23b | Nathaniel Nutter | 14 February 2014, 20:18:01 UTC | fix renamed function in UR | 14 February 2014, 20:18:01 UTC |
| 5ff4272 | Avinash Ramu | 14 February 2014, 19:48:03 UTC | add error checks | 14 February 2014, 19:48:03 UTC |
| edd7ce0 | Avinash Ramu | 14 February 2014, 19:31:25 UTC | add check before writing files | 14 February 2014, 19:31:25 UTC |
| 3b593f9 | Feiyu Du | 14 February 2014, 18:39:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 February 2014, 18:39:02 UTC |
| 383c497 | Chris Miller | 14 February 2014, 17:38:12 UTC | updating params to be more descriptive | 14 February 2014, 17:41:05 UTC |
| 162fb1d | APipe Tester | 14 February 2014, 15:14:15 UTC | updated ur submodule to 1d7fe2b | 14 February 2014, 15:14:15 UTC |
| 82a1d2d | APipe Tester | 14 February 2014, 13:17:58 UTC | Updated `genome` tab completion. | 14 February 2014, 13:17:58 UTC |
| 9e9e34d | Gabriel Sanderson | 13 February 2014, 21:39:55 UTC | added more checking and an error | 13 February 2014, 21:39:55 UTC |
| 5c9be72 | Feiyu Du | 13 February 2014, 21:37:22 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 February 2014, 21:37:22 UTC |
| 8f2913f | Feiyu Du | 13 February 2014, 21:36:42 UTC | Make pindel using proper pindel2vcf based on pindel version | 13 February 2014, 21:36:42 UTC |
| 7beb3f0 | Gabriel Sanderson | 13 February 2014, 21:29:53 UTC | Add a filenames option to tack on the original file basename to the output | 13 February 2014, 21:29:53 UTC |
| a1dbb2e | Gabriel Sanderson | 13 February 2014, 21:04:32 UTC | code duplication refactor: use get_allocation_for_path | 13 February 2014, 21:06:25 UTC |
| c604eb1 | Nathaniel Nutter | 13 February 2014, 20:10:04 UTC | deploy model.model.run_as.sql | 13 February 2014, 20:10:04 UTC |
| 3e5c161 | Nathaniel Nutter | 13 February 2014, 20:00:45 UTC | add run_as column to model.model | 13 February 2014, 20:00:45 UTC |
| eb95cb5 | Nathaniel Nutter | 13 February 2014, 19:25:23 UTC | boostrap Adam's changes for AP and add created_by to Model | 13 February 2014, 19:25:23 UTC |
| 1f36546 | Nathaniel Nutter | 13 February 2014, 19:21:14 UTC | boostrap Adam's changes for AP and add created_by to Model | 13 February 2014, 19:24:02 UTC |
| e761643 | Nathaniel Nutter | 12 February 2014, 23:43:47 UTC | make column adds idempotent | 13 February 2014, 19:24:01 UTC |
| 4a4028a | Nathaniel Nutter | 12 February 2014, 23:01:22 UTC | add .gitignore | 13 February 2014, 19:24:00 UTC |
| d938860 | Nathaniel Nutter | 12 February 2014, 22:10:46 UTC | fix typo, is this safe? | 13 February 2014, 19:23:59 UTC |
| 357d4e3 | Nathaniel Nutter | 12 February 2014, 21:32:19 UTC | add model.model.created_by | 13 February 2014, 19:23:57 UTC |
| a2a8922 | Jim Weible | 13 February 2014, 18:55:06 UTC | make sure files are unique | 13 February 2014, 18:55:36 UTC |
| 3a537b0 | Mark Burnett | 13 February 2014, 17:14:05 UTC | triage: disable slow child allocation query | 13 February 2014, 17:14:05 UTC |
| 66fed2d | APipe Tester | 13 February 2014, 13:18:09 UTC | Updated `gmt` tab completion. | 13 February 2014, 13:18:09 UTC |
| 5e8deba | APipe Tester | 13 February 2014, 13:17:25 UTC | Updated `genome` tab completion. | 13 February 2014, 13:17:25 UTC |
| 9718ee4 | APipe Tester | 13 February 2014, 13:15:40 UTC | Updated class browser cache. | 13 February 2014, 13:15:40 UTC |
| 5e7083b | apregier | 12 February 2014, 19:36:32 UTC | Merge branch 'updated' into gb_master | 12 February 2014, 19:36:32 UTC |
| 18c4052 | apregier | 12 February 2014, 17:04:03 UTC | VerifyBamId wrapper tool | 12 February 2014, 19:35:39 UTC |
| d962521 | Nathaniel Nutter | 10 February 2014, 22:24:55 UTC | switch to Module::Runtime | 12 February 2014, 19:26:11 UTC |
| 5f5b591 | Thomas Mooney | 12 February 2014, 19:08:17 UTC | Explicitly order these dependencies so the correct function is masked. | 12 February 2014, 19:18:52 UTC |
| 4f2e01c | Jim Weible | 12 February 2014, 15:49:44 UTC | add a tool to create analysis menu items from config files | 12 February 2014, 16:32:27 UTC |
| adf292b | Thomas Mooney | 12 February 2014, 14:18:30 UTC | Add explicit disconnects before launching Workflows | 12 February 2014, 14:18:30 UTC |
| 5e65a70 | Thomas Mooney | 12 February 2014, 14:16:53 UTC | Extract disconnect to a method to start calling from elsewhere. | 12 February 2014, 14:16:53 UTC |
| dcf182c | Nathaniel Nutter | 11 February 2014, 21:17:26 UTC | refactor bsub wrapper Add support for more bsub options and make it easier to add more in the future. | 11 February 2014, 21:20:06 UTC |
| 537dbd2 | Nathaniel Nutter | 07 February 2014, 17:58:58 UTC | make sure to lazy load IPC::System::Simple (for LIMS) | 11 February 2014, 21:20:03 UTC |
| 8145cda | Nathaniel Nutter | 03 February 2014, 23:45:07 UTC | test ability to override option building We'll take "advantage" of this when redirecting option handling for starting builds as another user. | 11 February 2014, 21:20:01 UTC |
| 986b1b3 | Nathaniel Nutter | 03 February 2014, 23:32:45 UTC | refactor bsub to couple argument spec with option flags | 11 February 2014, 21:19:57 UTC |
| 4999208 | Nathaniel Nutter | 03 February 2014, 23:08:07 UTC | extract bsub | 11 February 2014, 21:19:55 UTC |
| b99ef13 | Nathaniel Nutter | 03 February 2014, 23:06:09 UTC | rewrite bsub so we can manipulate options | 11 February 2014, 21:19:53 UTC |
| fca465e | Nathaniel Nutter | 07 February 2014, 19:01:29 UTC | re-enable test | 11 February 2014, 21:19:50 UTC |
| c82652c | apregier | 11 February 2014, 21:13:09 UTC | New submodule | 11 February 2014, 21:13:09 UTC |
| 026e6e0 | APipe Tester | 11 February 2014, 13:18:13 UTC | Updated `genome` tab completion. | 11 February 2014, 13:18:13 UTC |
| aa9b409 | APipe Tester | 11 February 2014, 13:16:27 UTC | Updated class browser cache. | 11 February 2014, 13:16:27 UTC |
| 174c523 | Nathaniel Nutter | 11 February 2014, 00:51:58 UTC | Revert "switch to Module::Runtime" This reverts commit a163bf85a690bbd917e240c6e822818b1bfb601e because it breaks /gsc/bin/perl. | 11 February 2014, 00:51:58 UTC |
| 4915d5c | Nathaniel Nutter | 11 February 2014, 00:01:28 UTC | package does not use Genome | 11 February 2014, 00:01:28 UTC |
| a163bf8 | Nathaniel Nutter | 10 February 2014, 22:24:55 UTC | switch to Module::Runtime | 10 February 2014, 23:52:15 UTC |
| b6443bb | Jim Weible | 10 February 2014, 20:14:57 UTC | add lister for analysis menu items | 10 February 2014, 20:14:57 UTC |
| 230c787 | Jason Walker | 10 February 2014, 18:54:12 UTC | Add a method to resolve allocations to consider part of the builds disk usage | 10 February 2014, 18:54:12 UTC |
| 93d6138 | Jason Walker | 10 February 2014, 18:48:57 UTC | Resolve the superset of headers from all inputs. | 10 February 2014, 18:48:57 UTC |
| a35afd5 | apregier | 10 February 2014, 16:39:48 UTC | Merge branch 'updated' into gb_master | 10 February 2014, 16:39:48 UTC |
| e3569df | apregier | 10 February 2014, 16:38:24 UTC | Find the imported annotation model correctly. | 10 February 2014, 16:38:24 UTC |
| 68f11ba | Thomas Mooney | 10 February 2014, 15:56:34 UTC | Close the DB connection by default before running a shell command. | 10 February 2014, 15:56:34 UTC |
| a72321a | Jim Weible | 10 February 2014, 15:23:00 UTC | Stop auto generating convergence models | 10 February 2014, 15:23:00 UTC |
| cf70137 | APipe Tester | 08 February 2014, 13:18:21 UTC | Updated `gmt` tab completion. | 08 February 2014, 13:18:21 UTC |
| 894896c | APipe Tester | 08 February 2014, 13:17:35 UTC | Updated `genome` tab completion. | 08 February 2014, 13:17:35 UTC |
| d057794 | Chris Miller | 07 February 2014, 18:21:23 UTC | adding option to override reference-transcript build | 07 February 2014, 18:23:18 UTC |
| 388ff62 | apregier | 07 February 2014, 18:05:21 UTC | Merge branch 'updated' into gb_master | 07 February 2014, 18:05:21 UTC |
| 157e376 | apregier | 07 February 2014, 18:03:17 UTC | Check that reference sequence matches before re-using a model | 07 February 2014, 18:04:13 UTC |
| 1f3d1c6 | Avinash Ramu | 07 February 2014, 17:56:06 UTC | shell has 2 l s | 07 February 2014, 17:56:06 UTC |
| 7245dea | Nathaniel Nutter | 06 February 2014, 21:51:53 UTC | refactor _launch | 07 February 2014, 16:14:17 UTC |
| 6c85e8a | Nathaniel Nutter | 06 February 2014, 21:51:36 UTC | remove TODOs | 07 February 2014, 16:14:14 UTC |
| bfce2c2 | Nathaniel Nutter | 06 February 2014, 21:46:56 UTC | pass model instead of build into function | 07 February 2014, 16:14:12 UTC |
| dfee689 | Nathaniel Nutter | 03 February 2014, 23:52:43 UTC | extract _job_dispatch | 07 February 2014, 16:14:11 UTC |
| 21b7e19 | Nathaniel Nutter | 03 February 2014, 23:50:55 UTC | extract _server_dispatch | 07 February 2014, 16:14:09 UTC |
| 46e6617 | Nathaniel Nutter | 01 February 2014, 01:09:43 UTC | refactor _job_group_spec for conciseness | 07 February 2014, 16:14:07 UTC |
| 47d6619 | Nathaniel Nutter | 01 February 2014, 01:04:24 UTC | refactor test to use _default_job_group instead of duplicating | 07 February 2014, 16:14:05 UTC |
| fc81306 | Nathaniel Nutter | 01 February 2014, 00:55:06 UTC | extract _default_job_group | 07 February 2014, 16:14:04 UTC |
| c127de4 | Nathaniel Nutter | 01 February 2014, 00:52:59 UTC | extract _job_group_spec | 07 February 2014, 16:14:01 UTC |
| 612aa1e | Susanna Siebert | 07 February 2014, 15:20:03 UTC | test to ensure that the initialization doesn't read in the first line | 07 February 2014, 15:47:46 UTC |
| 4c53df7 | Susanna Siebert | 07 February 2014, 15:18:34 UTC | remove the lsf_resource param after the refactor this module works with the default LSF memory requirements | 07 February 2014, 15:47:45 UTC |
| 2419d71 | Susanna Siebert | 07 February 2014, 15:15:55 UTC | remove the old way of processing the input variants file | 07 February 2014, 15:47:45 UTC |
| ef75183 | Susanna Siebert | 06 February 2014, 21:29:35 UTC | Throw an error if there is an empty line in the file to process | 07 February 2014, 15:47:44 UTC |
| 7285eb4 | Susanna Siebert | 06 February 2014, 21:28:49 UTC | don't parse the first line on initialization | 07 February 2014, 15:47:43 UTC |
| 5efaed7 | Susanna Siebert | 05 February 2014, 20:56:49 UTC | edit test messages for clarity | 07 February 2014, 15:47:43 UTC |
| d6b0a2d | Susanna Siebert | 05 February 2014, 20:56:02 UTC | use OrderedPosition for the variant file | 07 February 2014, 15:47:42 UTC |
| b8d504f | Susanna Siebert | 05 February 2014, 20:54:00 UTC | support string chromosome values | 07 February 2014, 15:47:42 UTC |
| 16bb827 | Susanna Siebert | 05 February 2014, 19:52:35 UTC | minor code cleanup | 07 February 2014, 15:47:41 UTC |
| 7d72af2 | Susanna Siebert | 05 February 2014, 19:50:11 UTC | improved the way the header is retrieved | 07 February 2014, 15:47:40 UTC |
| 1655dbb | Susanna Siebert | 05 February 2014, 16:41:06 UTC | remove templating comments | 07 February 2014, 15:47:40 UTC |
| b63e221 | Susanna Siebert | 05 February 2014, 16:40:02 UTC | use Genome::File::OrderedPosition | 07 February 2014, 15:47:39 UTC |
| b138031 | Susanna Siebert | 05 February 2014, 16:36:53 UTC | new file format for files sorted by chromosome and start position allow retrieval of whole line based on those keys retrieval has to happen in sort order | 07 February 2014, 15:47:38 UTC |
| 6d7bfd0 | Susanna Siebert | 03 February 2014, 18:54:52 UTC | use Genome::Sys->create_directories instead of mkdir | 07 February 2014, 15:47:38 UTC |
| 9afb623 | APipe Tester | 07 February 2014, 13:17:35 UTC | Updated `genome` tab completion. | 07 February 2014, 13:17:35 UTC |
| 72c2343 | Anthony Brummett | 06 February 2014, 19:58:53 UTC | error message now includes to class get_with_lock was called on | 06 February 2014, 19:58:53 UTC |
| e08b0c6 | Feiyu Du | 06 February 2014, 16:33:49 UTC | Fix DV2 filter unit tests to prevent DV2 filter parameter bug in the future | 06 February 2014, 16:36:33 UTC |
| 5d0f466 | Malachi Griffith | 06 February 2014, 15:45:09 UTC | clin-seq add ignore rule for result file containing a build id | 06 February 2014, 15:45:09 UTC |
| 7bae385 | Nathaniel Nutter | 06 February 2014, 15:40:26 UTC | remove build's restart option | 06 February 2014, 15:40:26 UTC |
| 4e240d4 | Nathaniel Nutter | 04 February 2014, 01:01:48 UTC | remove restart | 06 February 2014, 15:38:30 UTC |
| b664dfc | Nathaniel Nutter | 05 February 2014, 20:55:03 UTC | remove restart option | 06 February 2014, 15:38:29 UTC |
| cc285d3 | Nathaniel Nutter | 05 February 2014, 20:54:36 UTC | use build's workflow_name instead of duplicating code | 06 February 2014, 15:38:27 UTC |
| 9c91ed8 | APipe Tester | 06 February 2014, 13:17:13 UTC | Updated `genome` tab completion. | 06 February 2014, 13:17:13 UTC |
| 44759d9 | APipe Tester | 06 February 2014, 13:15:30 UTC | Updated class browser cache. | 06 February 2014, 13:15:30 UTC |
| 7b08bf1 | Malachi Griffith | 06 February 2014, 05:51:26 UTC | clin-seq add snv-indel-report to clinseq workflow | 06 February 2014, 05:51:26 UTC |
