| 87cd404 | APipe Tester | 28 May 2013, 23:30:40 UTC | updated workflow submodule to c68e0fa | 28 May 2013, 23:30:40 UTC |
| 494f787 | APipe Tester | 28 May 2013, 23:23:02 UTC | updated ur submodule to 9a5d195 | 28 May 2013, 23:23:02 UTC |
| e671c51 | APipe Tester | 28 May 2013, 23:18:36 UTC | updated workflow submodule to 522b38e | 28 May 2013, 23:18:36 UTC |
| 96289d5 | APipe Tester | 28 May 2013, 23:11:32 UTC | updated ur submodule to 7c26259 | 28 May 2013, 23:11:32 UTC |
| 836cada | APipe Tester | 28 May 2013, 23:06:35 UTC | updated workflow submodule to ee35758 | 28 May 2013, 23:06:35 UTC |
| 0df8671 | APipe Tester | 28 May 2013, 22:59:13 UTC | updated ur submodule to bd16283 | 28 May 2013, 22:59:13 UTC |
| 4ca4cdb | APipe Tester | 28 May 2013, 22:55:05 UTC | updated workflow submodule to 243ce9f | 28 May 2013, 22:55:05 UTC |
| b7d0e31 | APipe Tester | 28 May 2013, 22:46:07 UTC | updated ur submodule to 8dc3b36 | 28 May 2013, 22:46:07 UTC |
| 775fbb6 | APipe Tester | 28 May 2013, 22:43:36 UTC | updated workflow submodule to 08d2689 | 28 May 2013, 22:43:36 UTC |
| 7d383ce | APipe Tester | 28 May 2013, 22:33:03 UTC | updated ur submodule to d74433c | 28 May 2013, 22:33:03 UTC |
| dbd2f46 | APipe Tester | 28 May 2013, 22:31:03 UTC | updated workflow submodule to e003bcc | 28 May 2013, 22:31:03 UTC |
| ac3a448 | APipe Tester | 28 May 2013, 22:20:05 UTC | updated ur submodule to 6575555 | 28 May 2013, 22:20:05 UTC |
| c9c432f | APipe Tester | 28 May 2013, 22:18:55 UTC | updated workflow submodule to ff530b5 | 28 May 2013, 22:18:55 UTC |
| dd047cb | APipe Tester | 28 May 2013, 22:08:11 UTC | updated ur submodule to 70a76bc | 28 May 2013, 22:08:11 UTC |
| 7b03aec | APipe Tester | 28 May 2013, 22:06:56 UTC | updated workflow submodule to e1a15a8 | 28 May 2013, 22:06:56 UTC |
| 20462a2 | APipe Tester | 28 May 2013, 21:57:10 UTC | updated ur submodule to 7e15ff4 | 28 May 2013, 21:57:10 UTC |
| a72e59d | APipe Tester | 28 May 2013, 21:55:03 UTC | updated workflow submodule to 434cb15 | 28 May 2013, 21:55:03 UTC |
| 589f7c1 | APipe Tester | 28 May 2013, 21:45:21 UTC | updated ur submodule to 47e5811 | 28 May 2013, 21:45:21 UTC |
| b930032 | APipe Tester | 28 May 2013, 21:42:59 UTC | updated workflow submodule to 8f4684c | 28 May 2013, 21:42:59 UTC |
| cbe4dc7 | APipe Tester | 28 May 2013, 21:33:02 UTC | updated ur submodule to 09a25d1 | 28 May 2013, 21:33:02 UTC |
| cf05364 | APipe Tester | 28 May 2013, 21:30:44 UTC | updated workflow submodule to 0487908 | 28 May 2013, 21:30:44 UTC |
| 43006d3 | APipe Tester | 28 May 2013, 21:20:06 UTC | updated ur submodule to fc67cda | 28 May 2013, 21:20:06 UTC |
| 789588d | APipe Tester | 28 May 2013, 21:18:48 UTC | updated workflow submodule to 6c08ac0 | 28 May 2013, 21:18:48 UTC |
| 9eadae5 | APipe Tester | 28 May 2013, 21:07:24 UTC | updated ur submodule to 4531b84 | 28 May 2013, 21:07:24 UTC |
| c8f2b88 | APipe Tester | 28 May 2013, 21:06:31 UTC | updated workflow submodule to 6bb7ed6 | 28 May 2013, 21:06:31 UTC |
| 75b895a | APipe Tester | 28 May 2013, 20:56:45 UTC | updated ur submodule to 423d080 | 28 May 2013, 20:56:45 UTC |
| 4737f70 | APipe Tester | 28 May 2013, 20:54:28 UTC | updated workflow submodule to a2bb1a6 | 28 May 2013, 20:54:28 UTC |
| efae205 | APipe Tester | 28 May 2013, 20:43:27 UTC | updated workflow submodule to fb9f25c | 28 May 2013, 20:43:27 UTC |
| 744a823 | APipe Tester | 28 May 2013, 20:43:23 UTC | updated ur submodule to 4a4466b | 28 May 2013, 20:43:23 UTC |
| adf4ec5 | APipe Tester | 28 May 2013, 20:31:01 UTC | updated workflow submodule to 022362b | 28 May 2013, 20:31:01 UTC |
| 7ac76d4 | APipe Tester | 28 May 2013, 20:30:15 UTC | updated ur submodule to adb2273 | 28 May 2013, 20:30:15 UTC |
| 2f0b728 | APipe Tester | 28 May 2013, 20:19:21 UTC | updated workflow submodule to 586485a | 28 May 2013, 20:19:21 UTC |
| 4c41ed6 | APipe Tester | 28 May 2013, 20:18:02 UTC | updated ur submodule to d95fe24 | 28 May 2013, 20:18:02 UTC |
| 2b6c744 | APipe Tester | 28 May 2013, 20:07:03 UTC | updated workflow submodule to e0def01 | 28 May 2013, 20:07:03 UTC |
| f567b09 | APipe Tester | 28 May 2013, 20:04:01 UTC | updated ur submodule to 9c19c6e | 28 May 2013, 20:04:01 UTC |
| 15199d4 | APipe Tester | 28 May 2013, 19:54:44 UTC | updated workflow submodule to 3bc5567 | 28 May 2013, 19:54:44 UTC |
| 4f19b8c | APipe Tester | 28 May 2013, 19:51:20 UTC | updated ur submodule to 973660c | 28 May 2013, 19:51:20 UTC |
| 4ac5c7e | APipe Tester | 28 May 2013, 19:43:16 UTC | updated workflow submodule to ccfd670 | 28 May 2013, 19:43:16 UTC |
| 5c58ea0 | APipe Tester | 28 May 2013, 19:39:44 UTC | updated ur submodule to 1ee90d3 | 28 May 2013, 19:39:44 UTC |
| 95117fb | APipe Tester | 28 May 2013, 19:31:10 UTC | updated workflow submodule to 0c6d228 | 28 May 2013, 19:31:10 UTC |
| 2fc3f62 | APipe Tester | 28 May 2013, 19:27:26 UTC | updated ur submodule to 76c2d33 | 28 May 2013, 19:27:26 UTC |
| 72fe1ce | APipe Tester | 28 May 2013, 19:18:44 UTC | updated workflow submodule to 0887379 | 28 May 2013, 19:18:44 UTC |
| a4970ac | APipe Tester | 28 May 2013, 19:14:51 UTC | updated ur submodule to 03ca4a2 | 28 May 2013, 19:14:51 UTC |
| 58d989f | APipe Tester | 28 May 2013, 19:06:45 UTC | updated workflow submodule to 937041d | 28 May 2013, 19:06:45 UTC |
| b7ee59d | APipe Tester | 28 May 2013, 19:02:48 UTC | updated ur submodule to 14806a8 | 28 May 2013, 19:02:48 UTC |
| bdcd76c | APipe Tester | 28 May 2013, 18:54:45 UTC | updated workflow submodule to f236e7a | 28 May 2013, 18:54:45 UTC |
| ec0bae2 | APipe Tester | 28 May 2013, 18:49:53 UTC | updated ur submodule to 36a08fd | 28 May 2013, 18:49:53 UTC |
| 044f711 | APipe Tester | 28 May 2013, 18:42:48 UTC | updated workflow submodule to aabd90b | 28 May 2013, 18:42:48 UTC |
| 7660060 | APipe Tester | 28 May 2013, 18:33:02 UTC | updated ur submodule to 773f705 | 28 May 2013, 18:33:02 UTC |
| 889067c | APipe Tester | 28 May 2013, 18:31:22 UTC | updated workflow submodule to 5c5b60a | 28 May 2013, 18:31:22 UTC |
| 24e6383 | Nathan Nutter | 28 May 2013, 18:12:20 UTC | initial class browser cache | 28 May 2013, 18:12:20 UTC |
| 4e3d48b | APipe Tester | 24 May 2013, 20:28:11 UTC | Updated `gmt` tab completion. | 24 May 2013, 20:28:11 UTC |
| e7fc3e7 | APipe Tester | 24 May 2013, 20:27:24 UTC | Updated `genome` tab completion. | 24 May 2013, 20:27:24 UTC |
| 20f6f3a | Jasreet Hundal | 24 May 2013, 20:20:20 UTC | Removing old tests | 24 May 2013, 20:20:20 UTC |
| eb1e7fb | Jasreet Hundal | 24 May 2013, 20:05:33 UTC | epitope prediction updates Merge branch 'master' of ssh://git/srv/git/genome | 24 May 2013, 20:05:33 UTC |
| 9dc9779 | Jasreet Hundal | 24 May 2013, 20:04:04 UTC | epitope prediction module updates | 24 May 2013, 20:04:04 UTC |
| 4433946 | Veena Bhonagiri | 24 May 2013, 14:34:28 UTC | Added Snap model files for O. dentatum | 24 May 2013, 14:34:28 UTC |
| dc97e7a | dmorton | 23 May 2013, 21:32:38 UTC | Make gmb view log-preview not read in the whole file. It was possible to eat up all your memory the old way. | 23 May 2013, 21:32:38 UTC |
| d6edf63 | dmorton | 23 May 2013, 19:41:07 UTC | Unarchiving a build now fixes symlinks for input builds It was previously only fixing its own symlinks even though it unarchived its input build's allocations. (how selfish right?) | 23 May 2013, 20:36:17 UTC |
| d9ff482 | dmorton | 23 May 2013, 19:21:10 UTC | Added input_builds method to Model::Build | 23 May 2013, 20:36:17 UTC |
| 7d69d40 | Chris Miller | 23 May 2013, 17:53:54 UTC | handle headers on files better | 23 May 2013, 17:54:13 UTC |
| 5ad4682 | Thomas Mooney | 23 May 2013, 17:38:15 UTC | Expand test for compatibility of references. This was previously failing when there was a chain of references with "coordinates_from" so #1 and #2 led to a comparison of #2 and #3, even though #1 pointing to #2 should definitely be compatible with #2 itself. | 23 May 2013, 17:38:15 UTC |
| 31207ef | APipe Tester | 23 May 2013, 16:43:46 UTC | Updated `genome` tab completion. | 23 May 2013, 16:43:46 UTC |
| 9199acf | dmorton | 23 May 2013, 01:42:08 UTC | Update ClinSeq test expected output | 23 May 2013, 01:42:08 UTC |
| 618aa59 | dmorton | 22 May 2013, 23:08:13 UTC | Update ClinSeq data for test | 22 May 2013, 23:08:47 UTC |
| f403b8a | dmorton | 22 May 2013, 22:16:22 UTC | Make the GMTCuffDiffWrapper take different input It now takes condition_model_ids_string instead of bam_file_paths. This change was brought on by a 1000 character limit on the oracle database column which stores software result inputs. | 22 May 2013, 23:08:47 UTC |
| ba579e5 | Scott Smith | 22 May 2013, 22:46:43 UTC | fix typo in docs causing module compile fail | 22 May 2013, 22:46:43 UTC |
| 5316bd9 | Scott Smith | 22 May 2013, 22:45:48 UTC | updated docs for new "genome model copy" feature to take indirect params | 22 May 2013, 22:45:48 UTC |
| 02a894d | Scott Smith | 22 May 2013, 22:39:44 UTC | updated "genome model copy" to support input_model.other_input_model.blah=foo, and recursively make new underlying models as needed | 22 May 2013, 22:40:24 UTC |
| 9c9d506 | Scott Smith | 06 May 2013, 20:07:01 UTC | rename $exit_code variable to $sytem_retval, since this another variable actually contains the exit code | 22 May 2013, 22:40:23 UTC |
| 99c3cbd | dmorton | 22 May 2013, 22:09:54 UTC | Revert "update diag() code on diff failure for Strelka" This reverts commit 45073ff67d47621fd73bae4a4f43f4211bf7b838. | 22 May 2013, 22:14:52 UTC |
| 05db458 | dmorton | 22 May 2013, 21:40:58 UTC | Fix Test Sys-sw not doing what was intended. | 22 May 2013, 22:14:51 UTC |
| 7ee6ef2 | Eddie Belter | 22 May 2013, 15:52:19 UTC | Sample: remove is_control property | 22 May 2013, 18:31:38 UTC |
| 45073ff | Scott Smith | 22 May 2013, 18:25:24 UTC | update diag() code on diff failure for Strelka | 22 May 2013, 18:25:24 UTC |
| bbe74bc | Scott Smith | 22 May 2013, 18:24:03 UTC | don't complain about inputs w/o values when they are optional | 22 May 2013, 18:24:03 UTC |
| 684c364 | Scott Smith | 22 May 2013, 18:22:31 UTC | add Genome::Sys concatenate_files(), quote_for_shell() | 22 May 2013, 18:22:31 UTC |
| 371e7af | Eddie Belter | 22 May 2013, 14:44:33 UTC | DeNovo: scalar context bug in merge sx results | 22 May 2013, 14:55:54 UTC |
| b8cccd8 | Jim Weible | 22 May 2013, 13:15:09 UTC | wrapper for joinx vcf-normalize-indels | 22 May 2013, 13:15:21 UTC |
| 2c07fdb | Eddie Belter | 21 May 2013, 19:55:48 UTC | SX Processor: properly propogate DEFAULT processor | 21 May 2013, 19:55:48 UTC |
| 33e232f | Thomas Mooney | 21 May 2013, 18:17:31 UTC | Handle multiple BAM files since this is an "is_many" property. | 21 May 2013, 18:17:31 UTC |
| deb79c1 | Ian Ferguson | 20 May 2013, 20:33:32 UTC | Fix vcf symlinking in DV2 Don't unlink a vcf symlink and then recreate an identical symlink. Just leave the link alone if it already has the desired target. This should help prevent builds from failing because they tried to create symlinks on read-only volumes. | 20 May 2013, 20:33:32 UTC |
| f88bc72 | Thomas Mooney | 20 May 2013, 19:25:26 UTC | Defer checking inputs so build can be created (but unstartable). | 20 May 2013, 19:25:26 UTC |
| 5b8fe3c | dmorton | 18 May 2013, 13:14:43 UTC | Fix typo in DifferentialExpression pipeline | 18 May 2013, 13:15:39 UTC |
| 968b833 | Eddie Belter | 17 May 2013, 21:00:07 UTC | Sync RMU: run region 454 inherits from base | 17 May 2013, 21:00:07 UTC |
| d9f2b75 | Eddie Belter | 17 May 2013, 20:59:41 UTC | Sync RMU: handle setting attribute value to undef | 17 May 2013, 20:59:41 UTC |
| ba2aa8d | Eddie Belter | 17 May 2013, 20:59:01 UTC | Sync: rm db::single | 17 May 2013, 20:59:01 UTC |
| 106ed1a | Chris Miller | 17 May 2013, 17:01:38 UTC | removed incorrect default | 17 May 2013, 17:01:51 UTC |
| 662eb14 | Veena Bhonagiri | 17 May 2013, 14:55:22 UTC | Added code to copy contigs.cmt and gap.txt file to Sequence/Unmasked dirwhile running MGAP | 17 May 2013, 14:55:22 UTC |
| 6cb819f | APipe Tester | 17 May 2013, 03:53:42 UTC | Updated `genome` tab completion. | 17 May 2013, 03:53:42 UTC |
| 16fda3e | dmorton | 17 May 2013, 03:34:16 UTC | Fix missing param in GMTCuffdiffWrapper | 17 May 2013, 03:34:43 UTC |
| 454dca1 | Thomas Mooney | 16 May 2013, 15:44:30 UTC | Convert to absolute paths before creating the result. (If the user supplied a relative path or other whatnot, result generation would fail.) | 16 May 2013, 21:02:56 UTC |
| 8d7bd8b | dmorton | 16 May 2013, 19:34:50 UTC | Fix where we look for the new DifferentialExpression command | 16 May 2013, 19:35:37 UTC |
| e31ea72 | Gabriel Sanderson | 16 May 2013, 19:04:08 UTC | Merge branch 'master' into gb_master | 16 May 2013, 19:04:08 UTC |
| c196edd | Gabriel Sanderson | 16 May 2013, 19:03:24 UTC | improved error messages | 16 May 2013, 19:03:24 UTC |
| ac4bf6e | APipe Tester | 16 May 2013, 17:48:59 UTC | Updated `genome` tab completion. | 16 May 2013, 17:50:01 UTC |
| d574b71 | Eddie Belter | 16 May 2013, 17:38:54 UTC | DeNovo: special diff for metrics files | 16 May 2013, 17:49:02 UTC |
| ae269eb | dmorton | 16 May 2013, 17:20:20 UTC | Fix check of stage_output in SoftwareResult::Default | 16 May 2013, 17:35:06 UTC |
| b2a4772 | dmorton | 15 May 2013, 22:54:07 UTC | SoftwareResultify DifferentialExpression's Cuffdiff | 16 May 2013, 17:35:06 UTC |
| 302ccfe | APipe Tester | 16 May 2013, 17:12:14 UTC | Updated `gmt` tab completion. | 16 May 2013, 17:12:14 UTC |
| b03da8f | APipe Tester | 16 May 2013, 17:11:11 UTC | Updated `genome` tab completion. | 16 May 2013, 17:11:11 UTC |
