| 1fb8816 | Jason Walker | 14 October 2014, 16:02:01 UTC | Add gold reports for CLE validation without ft-keep filter. | 14 October 2014, 16:02:01 UTC |
| cb1b1e6 | Thomas B. Mooney | 14 October 2014, 14:30:23 UTC | Merge pull request #99 from tmooney/cleanup_instrument_data_properties Cleanup instrument data properties | 14 October 2014, 14:30:23 UTC |
| 4088de2 | Thomas B. Mooney | 14 October 2014, 12:57:28 UTC | Merge pull request #98 from tmooney/speed_up_setting_extra_columns Switch property to be "ARRAY" typed instead of is_many. | 14 October 2014, 12:57:28 UTC |
| 412b006 | APipe Tester | 14 October 2014, 12:17:55 UTC | Updated `gmt` tab completion. | 14 October 2014, 12:17:55 UTC |
| 2e65544 | APipe Tester | 14 October 2014, 12:17:12 UTC | Updated `genome` tab completion. | 14 October 2014, 12:17:12 UTC |
| 2f27e09 | APipe Tester | 14 October 2014, 12:15:32 UTC | Updated class browser cache. | 14 October 2014, 12:15:32 UTC |
| 42abf10 | APipe Tester | 13 October 2014, 22:03:55 UTC | updated jenkins submodule to 32e0bd5 | 13 October 2014, 22:03:55 UTC |
| 29a3f51 | Chris Miller | 13 October 2014, 20:19:23 UTC | Merge pull request #94 from chrisamiller/master removing requirement for bam_readcount_version param - default will be set in | 13 October 2014, 20:19:23 UTC |
| c3dec32 | Nathaniel Nutter | 13 October 2014, 20:14:15 UTC | Merge pull request #80 from gsanders/build_view Improve responsiveness when encountering large log files | 13 October 2014, 20:14:15 UTC |
| 5010a0d | Thomas Mooney | 22 September 2014, 22:35:06 UTC | Add data types for attributes | 13 October 2014, 14:16:44 UTC |
| 71422b8 | Thomas Mooney | 22 September 2014, 22:25:44 UTC | Clean up attributes to use is_attribute to avoid duplication. | 13 October 2014, 14:16:43 UTC |
| 0d8a21e | Thomas Mooney | 22 September 2014, 22:18:48 UTC | Clean up attributes to use is_attribute to avoid duplication. | 13 October 2014, 14:16:43 UTC |
| d90e35f | Thomas Mooney | 13 October 2014, 14:16:22 UTC | Remove duplicate downsample_ratio declaration. | 13 October 2014, 14:16:43 UTC |
| 11da3fc | Thomas Mooney | 22 September 2014, 22:13:15 UTC | Remove duplicate taxon declaration. | 13 October 2014, 13:32:09 UTC |
| 656a29c | Thomas B. Mooney | 13 October 2014, 13:26:24 UTC | Merge pull request #55 from tmooney/remove_phenotype_measurable Remove use of PHENOTYPE_MEASURABLE and related old Site::TGI modules | 13 October 2014, 13:26:24 UTC |
| 1799363 | Thomas Mooney | 11 October 2014, 04:00:34 UTC | Switch property to be "ARRAY" instead of is_many. | 11 October 2014, 04:00:34 UTC |
| eab1293 | APipe Tester | 10 October 2014, 23:01:38 UTC | updated jenkins submodule to 38d1832 | 10 October 2014, 23:38:44 UTC |
| 19a4654 | Thomas B. Mooney | 10 October 2014, 23:38:32 UTC | Merge pull request #92 from tmooney/remove_ssmith_mail Send notifications to apipe-builder instead of specific users. | 10 October 2014, 23:38:32 UTC |
| f90c070 | Adam Coffman | 10 October 2014, 22:33:18 UTC | Merge pull request #95 from acoffman/change_file_summary_size_width Remove width restriction on size_in_bytes | 10 October 2014, 22:33:18 UTC |
| a78392a | apregier | 10 October 2014, 20:20:07 UTC | Merge pull request #93 from apregier/dont_wait_to_remove_bad_lock Don't wait to remove bad lock | 10 October 2014, 20:20:07 UTC |
| d397993 | Adam Coffman | 10 October 2014, 19:38:52 UTC | remove width restriction | 10 October 2014, 19:38:52 UTC |
| 03051c0 | Chris Miller | 10 October 2014, 19:11:06 UTC | removing repetitive code chunks | 10 October 2014, 19:11:06 UTC |
| 7bb640b | Chris Miller | 10 October 2014, 18:04:25 UTC | removing requirement for bam_readcount_version param - default will be set in GMT::Sam::Readcounts and propogate up, unless otherwise specified | 10 October 2014, 18:04:25 UTC |
| 5fea3a3 | apregier | 10 October 2014, 16:23:45 UTC | Remove env variable that is no longer needed | 10 October 2014, 16:23:45 UTC |
| 032cd6a | apregier | 10 October 2014, 16:22:09 UTC | Remove outdated comment | 10 October 2014, 16:22:09 UTC |
| 51ede50 | David Morton | 10 October 2014, 16:00:13 UTC | Merge pull request #90 from davidlmorton/AT-624-second-attempt Allow for create to return undef | 10 October 2014, 16:00:13 UTC |
| 5756072 | apregier | 09 October 2014, 20:08:40 UTC | Remove e-mail and sleep when removing invalid lock | 09 October 2014, 20:08:40 UTC |
| b5248ff | apregier | 09 October 2014, 19:14:58 UTC | Indentation | 09 October 2014, 19:14:58 UTC |
| 6b7dd14 | Thomas B. Mooney | 09 October 2014, 18:57:21 UTC | Merge pull request #87 from tmooney/simplify_sample_type Replace calculated "sample_type" property with an alias | 09 October 2014, 18:57:21 UTC |
| 0833c00 | Thomas Mooney | 09 October 2014, 18:55:28 UTC | Merge branch 'master' into remove_phenotype_measurable Conflicts: lib/perl/Genome/Site/TGI/Sample.pm | 09 October 2014, 18:55:28 UTC |
| a2c4d38 | Gabriel Sanderson | 09 October 2014, 18:47:01 UTC | Remove extraneous grep. Warn when a grep is skipped due to size. | 09 October 2014, 18:47:01 UTC |
| 034581c | Thomas Mooney | 09 October 2014, 18:37:10 UTC | Mail to apipe-builder instead of a specific set of users. | 09 October 2014, 18:37:10 UTC |
| e3c0953 | Ian Ferguson | 09 October 2014, 18:26:05 UTC | Merge pull request #81 from tmooney/find_result_for_variants_directory Use the build directory to decide which result is the correct one. | 09 October 2014, 18:26:05 UTC |
| bd5a483 | Thomas B. Mooney | 09 October 2014, 17:40:44 UTC | Merge pull request #83 from tmooney/simplify_clinseq_workflow Remove duplicative _as_array workflow inputs in ClinSeq | 09 October 2014, 17:40:44 UTC |
| 0840e6e | Thomas Mooney | 09 October 2014, 15:59:30 UTC | Remove ssmith from slow merge notifications. | 09 October 2014, 15:59:30 UTC |
| 4b61c41 | dmorton | 09 October 2014, 13:10:52 UTC | Allow for create to return undef This happens when SoftwareResult::create fails to create the result because another process has already created it. Then SoftwareResult::get_or_create will look for and find the already created result. | 09 October 2014, 13:10:52 UTC |
| 1119a46 | APipe Tester | 09 October 2014, 12:17:54 UTC | Updated `gmt` tab completion. | 09 October 2014, 12:17:54 UTC |
| 507b756 | APipe Tester | 09 October 2014, 12:17:04 UTC | Updated `genome` tab completion. | 09 October 2014, 12:17:04 UTC |
| 5af1c29 | APipe Tester | 09 October 2014, 12:15:00 UTC | Updated class browser cache. | 09 October 2014, 12:15:00 UTC |
| 47fa08e | apregier | 08 October 2014, 22:05:01 UTC | Merge pull request #85 from apregier/rename_trio_samples Rename trio samples | 08 October 2014, 22:05:01 UTC |
| 7b815af | Jim Eldred | 08 October 2014, 20:56:50 UTC | Merge pull request #88 from jeldred/htseq changing gmt htseq count to use the new individual attribut of genome sa... | 08 October 2014, 20:56:50 UTC |
| 24d9c84 | Thomas Mooney | 08 October 2014, 18:45:37 UTC | Use a "via" __self__ property instead of a calculated property. The calculated property implementation was returning the old value when running updates. Rather than fix it, just stop using it altogether. | 08 October 2014, 18:45:37 UTC |
| 257ea35 | Ian Ferguson | 08 October 2014, 18:40:02 UTC | Merge pull request #86 from iferguson90/remove-maize-blast-test Remove ancient MaizeBlast.pm and its failing tests | 08 October 2014, 18:40:02 UTC |
| cda3528 | Ian Ferguson | 08 October 2014, 18:30:25 UTC | Remove ancient MaizeBlast.pm and its failing tests | 08 October 2014, 18:30:25 UTC |
| 7918a90 | Thomas B. Mooney | 08 October 2014, 15:36:34 UTC | Merge pull request #82 from tmooney/revert_event_changes Remove Redundant Property Declarations in Events | 08 October 2014, 15:36:34 UTC |
| 942f419 | apregier | 08 October 2014, 15:26:38 UTC | Remove confusing d30 variable name | 08 October 2014, 15:26:38 UTC |
| 20c60e8 | apregier | 08 October 2014, 15:24:34 UTC | Use blank placeholder files The Trio.t test does not actually compare the content of the output files, only the existance. By using blank files, we stop providing the false impression that the test verifies the content of the files, and we make the test easier to maintain. | 08 October 2014, 15:24:34 UTC |
| 98ce2d1 | apregier | 08 October 2014, 15:05:11 UTC | Remove unused plan files | 08 October 2014, 15:05:11 UTC |
| 7507613 | apregier | 08 October 2014, 14:51:28 UTC | Rename method | 08 October 2014, 14:51:28 UTC |
| 8a9f233 | apregier | 08 October 2014, 14:50:19 UTC | Mixed up discovery and followup | 08 October 2014, 14:50:19 UTC |
| cea798a | Avinash Ramu | 08 October 2014, 03:39:17 UTC | update clinseq blessed Looks like 6 new models were added for the AML109 subject(some new experiments perhaps) and this results in some metrics changing. | 08 October 2014, 03:39:17 UTC |
| 779686d | APipe Tester | 07 October 2014, 18:22:35 UTC | updated jenkins submodule to 6a3e96c | 07 October 2014, 22:53:16 UTC |
| 16a425b | apregier | 30 September 2014, 18:26:47 UTC | Rename how samples are referred to validation => followup d0_tumor => discovery_tumor d30_tumor => followup_tumor d0_normal => normal | 07 October 2014, 21:10:42 UTC |
| 370ce3f | apregier | 30 September 2014, 17:28:01 UTC | Rename additional to followup | 07 October 2014, 20:34:58 UTC |
| 0f482ce | Eddie Belter | 07 October 2014, 19:38:44 UTC | Merge pull request #77 from ebelter/tcga-metadata Tcga metadata | 07 October 2014, 19:38:44 UTC |
| ed96a54 | apregier | 07 October 2014, 16:28:38 UTC | Merge pull request #71 from apregier/warning-message-fix Fix warning message for undefined entry | 07 October 2014, 16:28:38 UTC |
| 2dadb01 | apregier | 07 October 2014, 16:28:12 UTC | Merge pull request #73 from apregier/refactor-with-svr Refactor with separated value reader/writer | 07 October 2014, 16:28:12 UTC |
| e972130 | Thomas Mooney | 07 October 2014, 15:52:31 UTC | Remove duplicative _as_array workflow inputs. Now that UR will auto-box these when passed to commands expecting is_many properties, we can simplify this to pass the same input to all commands requiring it. | 07 October 2014, 15:52:31 UTC |
| ebc741b | Thomas Mooney | 07 October 2014, 15:39:44 UTC | Use canonical names to make Ghosts happy. | 07 October 2014, 15:39:44 UTC |
| 045f094 | Thomas Mooney | 07 October 2014, 14:54:00 UTC | Move id property into id_by section. | 07 October 2014, 15:00:34 UTC |
| e3b76cc | Thomas Mooney | 07 October 2014, 14:51:38 UTC | Remove redundant property declarations. | 07 October 2014, 15:00:34 UTC |
| 4adbdd0 | APipe Tester | 07 October 2014, 02:30:06 UTC | Merge pull request #79 from nnutter/bam_readcount_ver_clinseq | 07 October 2014, 02:30:06 UTC |
| 7dca88b | Eddie Belter | 06 October 2014, 19:26:12 UTC | InstData Import: add cghub to env path to run cgquery | 06 October 2014, 19:26:12 UTC |
| e5a9e50 | Thomas Mooney | 06 October 2014, 15:58:08 UTC | Check if we got an allocation and an owner. | 06 October 2014, 15:58:08 UTC |
| 0abc019 | Eddie Belter | 06 October 2014, 15:49:43 UTC | InstData Import: tcga metadata dies if not library strategy exists when determining target region | 06 October 2014, 15:49:43 UTC |
| 9dd3ade | Thomas Mooney | 06 October 2014, 15:31:01 UTC | Allow export of our new function. | 06 October 2014, 15:31:01 UTC |
| 62837d8 | Thomas Mooney | 06 October 2014, 15:21:44 UTC | Use List::Util::first instead of a homespun version. | 06 October 2014, 15:21:44 UTC |
| a531892 | Thomas Mooney | 06 October 2014, 15:00:32 UTC | Use the build directory to decide which result is the correct one. If the indel_detection_strategy contains an unfiltered detector that also detects snvs, the previous logic would get confused about which result is the correct one. The final result symlinked in the variants directory knows the one true result. (In SomVal a different label is set on the SR::User--this would be a better solution, but it isn't backwards-compatible.) | 06 October 2014, 15:00:32 UTC |
| 1042c33 | James Eldred | 06 October 2014, 14:23:39 UTC | changing gmt htseq count to use the new individual attribut of genome sample | 06 October 2014, 14:23:39 UTC |
| 1ba07e5 | Gabriel Sanderson | 03 October 2014, 21:38:48 UTC | Improve responsiveness when encountering large log files | 03 October 2014, 21:39:26 UTC |
| 59867d8 | APipe Tester | 03 October 2014, 14:13:14 UTC | Merge pull request #65 from jeldred/master | 03 October 2014, 14:13:14 UTC |
| 592d507 | Eddie Belter | 02 October 2014, 20:31:58 UTC | InstData Import: tcga bam uses metadata module | 02 October 2014, 20:31:58 UTC |
| 1a65321 | Eddie Belter | 02 October 2014, 20:31:18 UTC | InstData Import: add ref name and version & update target region in tcga metadata | 02 October 2014, 20:31:18 UTC |
| c2312fe | James Eldred | 02 October 2014, 20:11:31 UTC | reverting inadvertent changes to variable names in a ClinSeq module | 02 October 2014, 20:11:31 UTC |
| b7a3399 | Nathaniel Nutter | 02 October 2014, 19:23:36 UTC | hard-code secondary bam-readcount version The last passing builds ClinSeq was using 0.4 in "Run clonality analysis and produce clonality plots" while using 0.6 in "Produce a report using DOCM" and "Generate SnvIndel Report". This change preserves that behavior while not just using a default value. | 02 October 2014, 19:23:36 UTC |
| 2408038 | Thomas Mooney | 02 October 2014, 18:37:42 UTC | Remove disused/duplicate LIMS subject hierarchy classes. | 02 October 2014, 18:37:42 UTC |
| fc54b7a | Thomas Mooney | 02 October 2014, 18:20:52 UTC | Use Synchronize::Classes version of sample. | 02 October 2014, 18:20:52 UTC |
| 2d94e18 | Thomas Mooney | 02 October 2014, 18:17:25 UTC | Whitespace. | 02 October 2014, 18:17:25 UTC |
| 5082a62 | Eddie Belter | 01 October 2014, 23:23:50 UTC | InstData Import: add tcga metadata module | 01 October 2014, 23:43:35 UTC |
| f3a02e7 | Avinash Ramu | 01 October 2014, 21:05:19 UTC | Merge 4d9c0df4e0fef85199c463e8f9eb2f358e38abac into 618c9e8a7bd3194ae89fa9d345be4056f3637128 | 01 October 2014, 21:05:19 UTC |
| 618c9e8 | Eddie Belter | 01 October 2014, 21:04:52 UTC | InstData Import: rm prematurely pushed tcga load metadata module | 01 October 2014, 21:04:52 UTC |
| e3d0844 | James Eldred | 01 October 2014, 20:41:24 UTC | changed 4 ClinSeq scripts that were used by 4 ClinSeq converge tests to not use the patient accessor on Sample | 01 October 2014, 20:41:24 UTC |
| 4d9c0df | Avinash Ramu | 01 October 2014, 18:08:03 UTC | pass b-r-c version to clinseq steps | 01 October 2014, 18:08:03 UTC |
| e5ec3a2 | APipe Tester | 01 October 2014, 17:44:02 UTC | Merge pull request #72 from amb43790/column | 01 October 2014, 17:44:02 UTC |
| 273f8b3 | APipe Tester | 01 October 2014, 17:34:53 UTC | Merge pull request #59 from jasonwalker80/trio_with_homopolymer | 01 October 2014, 17:34:53 UTC |
| 7180a0f | Jason Walker | 01 October 2014, 17:15:38 UTC | Replace vcf-homopolymer filter with vcf | 01 October 2014, 17:15:38 UTC |
| f84a582 | APipe Tester | 01 October 2014, 16:38:04 UTC | updated ur submodule to 15cfd98 | 01 October 2014, 16:38:04 UTC |
| 10894c4 | APipe Tester | 01 October 2014, 14:51:11 UTC | Merge pull request #74 from nnutter/search_queue | 01 October 2014, 14:51:11 UTC |
| c2111ab | APipe Tester | 01 October 2014, 12:16:51 UTC | Updated `gmt` tab completion. | 01 October 2014, 12:16:51 UTC |
| 7fd4df9 | APipe Tester | 01 October 2014, 12:16:11 UTC | Updated `genome` tab completion. | 01 October 2014, 12:16:11 UTC |
| d6d620e | APipe Tester | 01 October 2014, 12:14:38 UTC | Updated class browser cache. | 01 October 2014, 12:14:38 UTC |
| 491c4c3 | Gabriel Sanderson | 01 October 2014, 01:18:51 UTC | Merge pull request #75 from gsanders/typo Fix typo in module name | 01 October 2014, 01:18:51 UTC |
| 554c353 | Malachi Griffith | 01 October 2014, 00:07:01 UTC | Merge pull request #70 from malachig/master Update/add to various brief docs shown when user does genome --help, genome model --help, etc | 01 October 2014, 00:07:01 UTC |
| bfa7fc9 | Malachi Griffith | 30 September 2014, 23:21:04 UTC | remove color mixin doc that is appearing in various undesired locations in the help docs | 30 September 2014, 23:21:04 UTC |
| 2fe4ba4 | Jason Walker | 30 September 2014, 21:49:35 UTC | Merge remote-tracking branch 'origin/master' into trio_with_homopolymer | 30 September 2014, 21:49:35 UTC |
| db24da0 | Gabriel Sanderson | 30 September 2014, 21:44:53 UTC | Fix typo in module name | 30 September 2014, 21:44:53 UTC |
| fdaef75 | Gabriel Sanderson | 30 September 2014, 21:44:03 UTC | Fix typo in module name | 30 September 2014, 21:44:03 UTC |
| 74e4540 | Nathaniel Nutter | 30 September 2014, 19:27:10 UTC | wrap modify_index in a transaction If we failed to add an object it could leave the view in an inconsistent state which caused the whole process transaction to fail. | 30 September 2014, 21:40:26 UTC |
| 7fdd97a | apregier | 30 September 2014, 21:19:59 UTC | Refactor to use SeparatedValueReader | 30 September 2014, 21:23:46 UTC |
| e471826 | apregier | 30 September 2014, 21:08:29 UTC | Refactor split_file to use SeparatedValue{Reader,Writer} | 30 September 2014, 21:23:45 UTC |
