| 12210a8 | APipe Tester | 19 December 2013, 13:16:05 UTC | Updated `genome` tab completion. | 19 December 2013, 13:16:05 UTC |
| 86795fc | APipe Tester | 19 December 2013, 13:14:35 UTC | Updated class browser cache. | 19 December 2013, 13:14:35 UTC |
| aef08fc | Gabriel Sanderson | 19 December 2013, 00:00:56 UTC | Merge branch 'backfill' into gb_master | 19 December 2013, 00:00:56 UTC |
| 8a629e1 | Gabriel Sanderson | 03 December 2013, 20:42:06 UTC | Fixed a bug introduced by renaming variables where a statement always evaluated to true and caused AD/BQ miscalculations | 18 December 2013, 23:57:26 UTC |
| 18af6ed | Gabriel Sanderson | 18 December 2013, 23:50:28 UTC | Merge branch 'master' into gb_master | 18 December 2013, 23:50:28 UTC |
| fea9c6e | Gabriel Sanderson | 18 December 2013, 23:49:21 UTC | Improved error messages | 18 December 2013, 23:49:33 UTC |
| ac37837 | Adam Coffman | 18 December 2013, 22:29:52 UTC | add compile test for subject pairing command tree | 18 December 2013, 22:29:52 UTC |
| 113e0e7 | Adam Coffman | 18 December 2013, 22:26:20 UTC | add test for config profile items | 18 December 2013, 22:26:20 UTC |
| 43c728e | Adam Coffman | 18 December 2013, 21:58:43 UTC | add compile test for empty class | 18 December 2013, 21:58:43 UTC |
| e94065f | Adam Coffman | 18 December 2013, 21:44:23 UTC | enable analysis project name changes via cli | 18 December 2013, 21:44:23 UTC |
| 89e4b48 | Adam Coffman | 18 December 2013, 20:43:35 UTC | add test for add-config-file command | 18 December 2013, 20:43:35 UTC |
| c6c4bfc | Jim Weible | 18 December 2013, 20:34:13 UTC | set pipefail | 18 December 2013, 20:34:26 UTC |
| 608367c | Adam Coffman | 18 December 2013, 20:16:53 UTC | add tests for config commands | 18 December 2013, 20:16:53 UTC |
| 071ac79 | Mark Burnett | 18 December 2013, 19:33:05 UTC | squelch annoying status messages | 18 December 2013, 19:34:17 UTC |
| 3ab702a | Adam Coffman | 18 December 2013, 19:08:07 UTC | add command for associating imported inst data with analysis projects | 18 December 2013, 19:08:07 UTC |
| bda29e5 | APipe Tester | 18 December 2013, 18:48:03 UTC | updated workflow submodule to 551fe8a | 18 December 2013, 18:48:03 UTC |
| 3f115d9 | Avinash Ramu | 18 December 2013, 17:38:52 UTC | updated clinseq blessed build to one with RNA fusions | 18 December 2013, 17:39:08 UTC |
| 1f1c2fe | Anthony Brummett | 17 December 2013, 22:54:57 UTC | Remove unused class Genome::Site::TGI::PseErrorLogEntry | 18 December 2013, 16:32:02 UTC |
| 47a06d5 | Anthony Brummett | 17 December 2013, 22:44:30 UTC | Remove unused class Genome::Model::Build::ErrorLogEntry This also removes Genome::Site::TGI::Observers::Command, the only place that mentioned the removed class | 18 December 2013, 16:32:01 UTC |
| c25d96f | Feiyu Du | 18 December 2013, 16:29:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 December 2013, 16:29:27 UTC |
| 26cbfac | Feiyu Du | 18 December 2013, 16:29:15 UTC | bug fix to make property value overwritable | 18 December 2013, 16:29:15 UTC |
| 82cda29 | Susanna Siebert | 18 December 2013, 14:16:28 UTC | test data updated | 18 December 2013, 14:16:28 UTC |
| ff85315 | Susanna Siebert | 18 December 2013, 14:12:34 UTC | test data updated | 18 December 2013, 14:12:34 UTC |
| ac6a581 | APipe Tester | 18 December 2013, 13:16:38 UTC | Updated `genome` tab completion. | 18 December 2013, 13:16:38 UTC |
| f6eb256 | Malachi Griffith | 17 December 2013, 23:53:33 UTC | standalone gms: fix tool for importing file based databases stored as git repos on github | 17 December 2013, 23:53:33 UTC |
| 8815ef5 | Anthony Brummett | 17 December 2013, 17:44:20 UTC | remove hard-coded address from bsub command | 17 December 2013, 17:44:20 UTC |
| 16b961f | Anthony Brummett | 17 December 2013, 17:44:04 UTC | add configuration for annotation report email address | 17 December 2013, 17:44:04 UTC |
| 159465a | APipe Tester | 17 December 2013, 13:17:24 UTC | Updated `gmt` tab completion. | 17 December 2013, 13:17:24 UTC |
| 5b081df | APipe Tester | 17 December 2013, 13:16:38 UTC | Updated `genome` tab completion. | 17 December 2013, 13:16:38 UTC |
| 78b182d | APipe Tester | 17 December 2013, 13:15:00 UTC | Updated class browser cache. | 17 December 2013, 13:15:00 UTC |
| 06f6053 | Dave Larson | 13 December 2013, 22:40:30 UTC | updated data to point to new v1.1.4 native output | 17 December 2013, 03:35:40 UTC |
| 035a76e | Dave Larson | 13 December 2013, 22:27:02 UTC | updated data to point to new v1.1.4 native output | 17 December 2013, 03:35:39 UTC |
| 15a478f | Dave Larson | 13 December 2013, 22:26:41 UTC | update the version in the test to correspond to new default | 17 December 2013, 03:35:38 UTC |
| f258d95 | Dave Larson | 13 December 2013, 22:18:15 UTC | Update expected output comparison and test data to handle muTect v1.1.4 | 17 December 2013, 03:35:38 UTC |
| df3a8aa | Dave Larson | 13 December 2013, 22:16:05 UTC | remove test updating lines. whoops. | 17 December 2013, 03:35:37 UTC |
| 6d6bd57 | Dave Larson | 13 December 2013, 17:53:37 UTC | Update muTect and its immediate test for version 1.1.4 Other code dependent on muTect may have broken tests after this commit | 17 December 2013, 03:35:36 UTC |
| 32ae9fa | Anthony Brummett | 16 December 2013, 22:19:30 UTC | remove long-obsolete email sending | 16 December 2013, 22:19:30 UTC |
| 33d3b60 | Gabriel Sanderson | 16 December 2013, 21:44:42 UTC | Merge branch 'master' into gb_master | 16 December 2013, 21:44:42 UTC |
| 0fdee6e | Gabriel Sanderson | 16 December 2013, 21:43:04 UTC | When looking for existing software results and allocations, automatically clean up the symlink if a test name is set on the result. | 16 December 2013, 21:43:31 UTC |
| 48e5891 | Malachi Griffith | 16 December 2013, 21:25:11 UTC | ClinSeq: temporary fix for problematic workflow setup in clinseq for circos plot generation | 16 December 2013, 21:25:11 UTC |
| 85bcde3 | Anthony Brummett | 16 December 2013, 20:51:26 UTC | remove the email option for bsub invocations | 16 December 2013, 20:51:26 UTC |
| ed9649f | Anthony Brummett | 16 December 2013, 20:50:39 UTC | preserve the ability to send the email but do not send it anymore | 16 December 2013, 20:50:39 UTC |
| 7d1fd78 | Adam Coffman | 16 December 2013, 19:15:03 UTC | add command for adding config files to an analysis project | 16 December 2013, 19:15:03 UTC |
| 8e5bff2 | Adam Coffman | 16 December 2013, 18:49:44 UTC | add support for holding/releasing analysis project model creation | 16 December 2013, 18:49:44 UTC |
| 39cbb28 | Jim Weible | 16 December 2013, 18:34:18 UTC | make post chimera-scan annotation optional | 16 December 2013, 18:34:33 UTC |
| d5b407e | Obi Griffith | 16 December 2013, 17:29:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 December 2013, 17:29:07 UTC |
| 08e710d | Nathan Nutter | 16 December 2013, 15:59:12 UTC | remove dependency on Git::Repository | 16 December 2013, 15:59:12 UTC |
| 1c65a1a | Obi Griffith | 15 December 2013, 03:52:04 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 December 2013, 03:52:04 UTC |
| 3bf1414 | Avinash Ramu | 14 December 2013, 15:25:19 UTC | copy over unfiltered fusion, fix small error in copying annotated fusions | 14 December 2013, 15:25:36 UTC |
| 5fcb784 | APipe Tester | 14 December 2013, 13:17:07 UTC | Updated `gmt` tab completion. | 14 December 2013, 13:17:07 UTC |
| 2d07103 | APipe Tester | 14 December 2013, 13:16:22 UTC | Updated `genome` tab completion. | 14 December 2013, 13:16:22 UTC |
| 8e83b83 | Nathan Nutter | 13 December 2013, 21:51:08 UTC | mark many GENOME_* variables as required If we defined a value in Genome::Site::TGI and a default_value was not supplied then these are now "required" configuration. A few exceptions were: GENOME_DEV_MODE GENOME_STATSD_HOST GENOME_STATSD_PORT We can decide later whether not having these set should be a compile-time or run-time error. For now we have to be careful about failing when they are not set since the code that uses them is probably not very defensive about it. | 13 December 2013, 22:13:41 UTC |
| 7ff790b | Nathan Nutter | 13 December 2013, 21:37:51 UTC | add missing package declarations | 13 December 2013, 21:37:51 UTC |
| 249ce49 | Nathan Nutter | 13 December 2013, 20:11:18 UTC | inherit import from Genome::Env::Required Instead of using side effect of `use Genome::Env::Required` inherit the import method with the requirement check. | 13 December 2013, 20:11:18 UTC |
| 8c1f0dd | Nathan Nutter | 13 December 2013, 20:10:01 UTC | add NAME | 13 December 2013, 20:10:01 UTC |
| 6b0b5e2 | Nathan Nutter | 13 December 2013, 19:58:43 UTC | rename to make consistent with others | 13 December 2013, 19:58:43 UTC |
| d5607a9 | Nathan Nutter | 13 December 2013, 19:49:46 UTC | remove Env tests since they don't define classes | 13 December 2013, 19:49:46 UTC |
| 8c93642 | Nathan Nutter | 13 December 2013, 19:03:39 UTC | add test to catch and case sensitive files | 13 December 2013, 19:03:54 UTC |
| 76c1d98 | Anthony Brummett | 13 December 2013, 17:20:13 UTC | Switch to using Genome::Utility::Email from MIME::Lite Also added function Genome::Utility::Email::construct_address() | 13 December 2013, 17:23:51 UTC |
| 289f600 | Anthony Brummett | 13 December 2013, 17:16:58 UTC | add configuration for the email domain name | 13 December 2013, 17:23:32 UTC |
| 2e07e44 | Anthony Brummett | 11 December 2013, 23:17:46 UTC | add configuration for the apipe mail alias | 13 December 2013, 17:23:26 UTC |
| 2abf7b1 | Anthony Brummett | 11 December 2013, 23:14:17 UTC | add configuration for the SMTP server name | 13 December 2013, 17:23:25 UTC |
| 302808f | Anthony Brummett | 11 December 2013, 23:03:01 UTC | add configuration for a test email address | 13 December 2013, 17:23:23 UTC |
| 6f4178a | Anthony Brummett | 11 December 2013, 22:47:16 UTC | add configuration for a "noisy" system generated mail address | 13 December 2013, 17:23:20 UTC |
| 22ef7e0 | Anthony Brummett | 11 December 2013, 22:44:35 UTC | add configuration for a "no reply" email address | 13 December 2013, 17:23:19 UTC |
| 3610867 | Anthony Brummett | 11 December 2013, 22:43:07 UTC | add configuration for illumina bwa report mail alias | 13 December 2013, 17:23:18 UTC |
| 27d86d1 | Anthony Brummett | 11 December 2013, 22:27:39 UTC | Add configuration for the virome screening email alias | 13 December 2013, 17:23:17 UTC |
| 4884daf | Anthony Brummett | 10 December 2013, 22:56:40 UTC | replace example email addresses with non-tgi addresses | 13 December 2013, 17:23:16 UTC |
| c86eb5a | Anthony Brummett | 10 December 2013, 21:13:50 UTC | utility module to send email | 13 December 2013, 17:23:15 UTC |
| 8217929 | Anthony Brummett | 10 December 2013, 20:27:25 UTC | remove large commented-out section | 13 December 2013, 17:23:14 UTC |
| 978b9c6 | Anthony Brummett | 10 December 2013, 17:30:21 UTC | Add method to construct an owner_id from the USER and GENOME_EMAIL_DOMAIN env vars | 13 December 2013, 17:23:12 UTC |
| 330b634 | Obi Griffith | 13 December 2013, 17:00:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 December 2013, 17:00:17 UTC |
| 04a6258 | Kyung Kim | 13 December 2013, 16:56:51 UTC | Added additional params | 13 December 2013, 16:56:51 UTC |
| aaf5ca5 | Avinash Ramu | 13 December 2013, 15:44:11 UTC | updated arguments to Genome::Sys->copy(takes only files, not dirs as params). create fusion dir even if WGS build does not exist. | 13 December 2013, 15:45:52 UTC |
| 5435890 | APipe Tester | 13 December 2013, 13:17:20 UTC | Updated `gmt` tab completion. | 13 December 2013, 13:17:20 UTC |
| b58e7cf | APipe Tester | 13 December 2013, 13:16:36 UTC | Updated `genome` tab completion. | 13 December 2013, 13:16:36 UTC |
| d40b847 | Obi Griffith | 13 December 2013, 02:16:56 UTC | added option to CNview | 13 December 2013, 02:16:56 UTC |
| 656e09c | Obi Griffith | 13 December 2013, 00:23:57 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 December 2013, 00:23:57 UTC |
| a93c6a0 | Obi Griffith | 13 December 2013, 00:23:29 UTC | updated usage and docs for CView | 13 December 2013, 00:23:29 UTC |
| 4621349 | Chris Miller | 12 December 2013, 23:56:01 UTC | igv reference shouldn't default to b36, should be required param | 12 December 2013, 23:56:33 UTC |
| f1c8ea8 | Avinash Ramu | 12 December 2013, 23:46:21 UTC | copy over fusion files even when there are no SV files | 12 December 2013, 23:46:39 UTC |
| 8acd064 | Kyung Kim | 12 December 2013, 23:37:04 UTC | Added ability to use flexbar v230 which has different params than earlier versions | 12 December 2013, 23:37:04 UTC |
| 01f146f | Avinash Ramu | 12 December 2013, 23:29:19 UTC | update clinseq.pm to not do filtering(this is now done in the RNAseq pipeline), just do intersection of fusion calls with SVs | 12 December 2013, 23:29:48 UTC |
| 7538b60 | apregier | 12 December 2013, 20:08:11 UTC | Merge branch 'copy' into gb_master | 12 December 2013, 20:08:11 UTC |
| 12bc286 | apregier | 12 December 2013, 19:43:47 UTC | Must cbind before the order changes cbind assumes that the arrays will be in the same order, but topTags changes the order. cbind must happen first. | 12 December 2013, 20:05:54 UTC |
| 245b0ff | apregier | 11 December 2013, 21:09:57 UTC | Add sdrf file to idf output Set the sdrf file name on the idf object Add additional required IDF row headers | 12 December 2013, 20:05:53 UTC |
| e0d8247 | Malachi Griffith | 12 December 2013, 17:43:24 UTC | ClinSeq: minor update to documentation | 12 December 2013, 17:43:24 UTC |
| 080e2ac | APipe Tester | 12 December 2013, 13:16:20 UTC | Updated `genome` tab completion. | 12 December 2013, 13:16:20 UTC |
| 470b464 | APipe Tester | 12 December 2013, 13:14:38 UTC | Updated class browser cache. | 12 December 2013, 13:14:38 UTC |
| 5b0f66c | Susanna Siebert | 09 December 2013, 14:32:02 UTC | removed debug breakpoint | 11 December 2013, 21:06:07 UTC |
| 4c8ce81 | Susanna Siebert | 06 December 2013, 22:48:36 UTC | added wrapper to run EdgeR for ClinSeq including making the gene counts file and filtering | 11 December 2013, 21:06:01 UTC |
| 8efdb73 | Susanna Siebert | 06 December 2013, 21:46:56 UTC | added filtering functionality for gene counts files | 11 December 2013, 21:05:51 UTC |
| 2692834 | Susanna Siebert | 06 December 2013, 20:51:15 UTC | Make parameter names more intuitive | 11 December 2013, 21:05:42 UTC |
| 86f27b5 | Susanna Siebert | 11 December 2013, 20:43:07 UTC | empty genotype file is not a failure just return early | 11 December 2013, 20:43:17 UTC |
| b4a5a2a | Eddie Belter | 11 December 2013, 18:45:16 UTC | MC16s: get SX results ind for each instdata when merging | 11 December 2013, 18:45:16 UTC |
| 33919c0 | APipe Tester | 11 December 2013, 13:18:19 UTC | Updated `gmt` tab completion. | 11 December 2013, 13:18:19 UTC |
| ea9d10e | APipe Tester | 11 December 2013, 13:17:36 UTC | Updated `genome` tab completion. | 11 December 2013, 13:17:36 UTC |
| 4e2fbd9 | APipe Tester | 11 December 2013, 13:16:05 UTC | Updated class browser cache. | 11 December 2013, 13:16:05 UTC |
| d00cef8 | Mark Burnett | 10 December 2013, 21:47:32 UTC | add support for Converge to WorkflowBuilder | 10 December 2013, 21:48:37 UTC |
| 0f00623 | Mark Burnett | 10 December 2013, 20:42:57 UTC | move responsibility for sorting input/output properties This will allow us to add new operation types that depend on particular sort order for their inputs and outputs (like Converge). | 10 December 2013, 21:48:36 UTC |
