| eaaad3c | APipe Tester | 26 August 2013, 14:46:47 UTC | updated ur submodule to f88cc7d | 26 August 2013, 14:46:47 UTC |
| 5cd7c6b | Nathan Nutter | 25 August 2013, 16:18:17 UTC | Revert "factor in GENOME_SOFTWARE_RESULT_TEST_NAME into the version" This reverts commit b76311302c51a1c82828e8f1f00a5ca498f9566d. GENOME_SOFTWARE_RESULT_TEST_NAME is not always set so this had no effect. Will look for an alternative solution. | 25 August 2013, 16:18:17 UTC |
| b763113 | Nathan Nutter | 25 August 2013, 01:13:55 UTC | factor in GENOME_SOFTWARE_RESULT_TEST_NAME into the version | 25 August 2013, 01:14:21 UTC |
| 7894d8f | Nathan Nutter | 25 August 2013, 01:07:17 UTC | extract repeated expression into temp variable | 25 August 2013, 01:14:20 UTC |
| 2362379 | Nathan Nutter | 25 August 2013, 01:04:24 UTC | whitespace | 25 August 2013, 01:14:19 UTC |
| 79aa1fa | Nathan Nutter | 24 August 2013, 05:06:25 UTC | whitespace | 24 August 2013, 05:06:25 UTC |
| 8e30c22 | Nathan Nutter | 24 August 2013, 05:04:55 UTC | silence 'Build * For Model' emails in these tests | 24 August 2013, 05:04:55 UTC |
| e3d6e39 | Nathan Nutter | 24 August 2013, 01:45:39 UTC | add ability to silence 'Build * For Model' emails | 24 August 2013, 01:45:39 UTC |
| adf3b56 | Nathan Nutter | 23 August 2013, 20:24:23 UTC | Genome::DataSource::OldPostgres | 23 August 2013, 22:13:07 UTC |
| 07b71f2 | Nathan Nutter | 23 August 2013, 20:25:49 UTC | Genome::DataSource::Dgidb | 23 August 2013, 22:13:06 UTC |
| 2271eed | Adam Coffman | 23 August 2013, 21:17:05 UTC | update expected | 23 August 2013, 21:17:05 UTC |
| 4c19479 | Eddie Belter | 23 August 2013, 19:06:48 UTC | Sync: create then execute update command | 23 August 2013, 19:07:09 UTC |
| fe267c8 | Eddie Belter | 23 August 2013, 18:49:10 UTC | Fix SQL db links in site sync setup proj seq product | 23 August 2013, 19:07:08 UTC |
| 34181f2 | Eddie Belter | 23 August 2013, 18:48:27 UTC | Inst data tests abandoning builds and deleting associated alignment results upon delete | 23 August 2013, 19:07:08 UTC |
| 936c00e | Eddie Belter | 23 August 2013, 18:45:06 UTC | Alignment results cascade delete their bam qc results | 23 August 2013, 19:07:07 UTC |
| 509fd5e | Adam Coffman | 23 August 2013, 19:00:14 UTC | update expected test output | 23 August 2013, 19:00:14 UTC |
| d720c63 | Dan Koboldt | 23 August 2013, 17:59:59 UTC | Update to allow VCF output option | 23 August 2013, 17:59:59 UTC |
| b36d97c | APipe Tester | 23 August 2013, 17:10:20 UTC | Updated `gmt` tab completion. | 23 August 2013, 17:10:20 UTC |
| 66f485e | APipe Tester | 23 August 2013, 17:09:18 UTC | Updated `genome` tab completion. | 23 August 2013, 17:09:18 UTC |
| 40a566e | APipe Tester | 23 August 2013, 17:07:15 UTC | Updated class browser cache. | 23 August 2013, 17:07:15 UTC |
| 6b771f2 | Travis Abbott | 23 August 2013, 16:49:14 UTC | update PC burden test code | 23 August 2013, 16:49:58 UTC |
| fc0ed6b | Nathan Nutter | 23 August 2013, 14:21:20 UTC | enable nounset later | 23 August 2013, 14:21:38 UTC |
| 9b7653c | APipe Tester | 22 August 2013, 22:48:08 UTC | Updated `genome` tab completion. | 22 August 2013, 22:48:08 UTC |
| 8de3247 | APipe Tester | 22 August 2013, 22:46:24 UTC | Updated class browser cache. | 22 August 2013, 22:46:24 UTC |
| fa2fd54 | Nathan Nutter | 22 August 2013, 22:35:08 UTC | add genome-env CHANGELOG: Moved most of `genome-test-env` to a new command, `genome-env`, so people can use `genome-env` to setup for running builds, etc. with the correct UR and Workflow. They can also continue to use `genome-test-env` to setup for running tests which basically just turns off database commits in addition to running `genome-env`. | 22 August 2013, 22:38:02 UTC |
| 22064a3 | Nathan Nutter | 22 August 2013, 22:13:07 UTC | remove unused/incomplete command | 22 August 2013, 22:38:01 UTC |
| eafe8cf | Feiyu Du | 22 August 2013, 22:18:46 UTC | remove use_error_rate_pileup and add error_rate_version for RnaSeq | 22 August 2013, 22:19:42 UTC |
| 0e5bbfe | APipe Tester | 22 August 2013, 21:38:56 UTC | updated graphite submodule to a20ecce | 22 August 2013, 21:38:56 UTC |
| c3338e7 | Travis Abbott | 22 August 2013, 16:51:51 UTC | Merge commit '47bfd70e20b45afad8fdd4c88bbb0badaa6a6785' as 'lib/perl/Genome/Model/Tools/Germline/BurdenTest' | 22 August 2013, 16:51:51 UTC |
| 47bfd70 | Travis Abbott | 22 August 2013, 16:51:51 UTC | Squashed 'lib/perl/Genome/Model/Tools/Germline/BurdenTest/' content from commit b6d5eb4 git-subtree-dir: lib/perl/Genome/Model/Tools/Germline/BurdenTest git-subtree-split: b6d5eb456b61cada90b07ce9419a4545225bd45b | 22 August 2013, 16:51:51 UTC |
| 7aed89b | APipe Tester | 22 August 2013, 15:47:31 UTC | updated ur submodule to 5f86690 | 22 August 2013, 15:47:31 UTC |
| be99232 | Nathan Nutter | 22 August 2013, 15:45:32 UTC | fixup! remove Genome::Model::Varaint and Genome::Model::BuildVariant Missed a reference to Genome::Model::BuildVariant. | 22 August 2013, 15:46:29 UTC |
| aee7511 | APipe Tester | 22 August 2013, 15:32:51 UTC | Updated `gmt` tab completion. | 22 August 2013, 15:32:51 UTC |
| 89f0f32 | APipe Tester | 22 August 2013, 15:32:01 UTC | Updated `genome` tab completion. | 22 August 2013, 15:32:01 UTC |
| 9422314 | APipe Tester | 22 August 2013, 15:30:17 UTC | Updated class browser cache. | 22 August 2013, 15:30:17 UTC |
| 45a5d9d | Nathan Nutter | 22 August 2013, 15:26:04 UTC | remove Genome::Model::Varaint and Genome::Model::BuildVariant | 22 August 2013, 15:26:21 UTC |
| 7bbe049 | Nathan Nutter | 22 August 2013, 15:21:06 UTC | shorten BamQc workflow name Workflow::Instance's name must be less than 255 characters. Since this was using the full bam_file path in the name it had the potential to be longer than that so shortening name to just use the basename of the bam_file path. | 22 August 2013, 15:21:06 UTC |
| 6523fb1 | Anthony Brummett | 21 August 2013, 22:07:44 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 21 August 2013, 22:07:44 UTC |
| 26b2def | Anthony Brummett | 21 August 2013, 22:06:15 UTC | Fix the test in advance of the switch to Postgres The Postgres datasource will have AutoCommit=1, and something in the test triggers a call to commit() the data source which generates this warning. | 21 August 2013, 22:06:15 UTC |
| 862c0e1 | APipe Tester | 21 August 2013, 21:55:46 UTC | updated ur submodule to c0fd575 | 21 August 2013, 21:55:46 UTC |
| 6e69c59 | Nathan Nutter | 21 August 2013, 18:44:56 UTC | fix for incorrect data_type in results The ALTERNATE_FROM_CLASS lookup stuff leads to objects with the incorrect data_type in the results. Really this whole thing needs to go in favor of people just explicitly "saying" what they need with UR::BoolExpr. | 21 August 2013, 18:46:46 UTC |
| e709235 | Nathan Nutter | 21 August 2013, 18:02:30 UTC | remove duplicate class Genome::Site::TGI::MiscAttribute Genome::Site::TGI::MiscAttribute was a duplicate of Genome::MiscAttribute so I updated the only user of it, Genome::Site::TGI::InstrumentData, to just use Genome::MiscAttribute. | 21 August 2013, 18:02:30 UTC |
| 77ffbf1 | Feiyu Du | 21 August 2013, 15:44:41 UTC | add error_rate_version as bamqc software result param | 21 August 2013, 15:44:41 UTC |
| 861b14c | Adam Coffman | 21 August 2013, 15:02:05 UTC | Mark use_error_rate_pileup as deprecated in RnaSeq error_rate_pileup was removed as a param for the underlying software result. This commit removes references to it in the BamQc command and marks it as deprecated in the RnaSeq model so that current processing profiles should continue to function. | 21 August 2013, 15:02:05 UTC |
| 7982841 | APipe Tester | 21 August 2013, 13:54:24 UTC | updated jenkins submodule to fd135da | 21 August 2013, 13:54:24 UTC |
| 1a063f6 | Dave Larson | 21 August 2013, 13:23:57 UTC | increase memory usage to large levels | 21 August 2013, 13:23:57 UTC |
| 9b4df09 | APipe Tester | 21 August 2013, 02:17:51 UTC | Updated `gmt` tab completion. | 21 August 2013, 02:17:51 UTC |
| 0e5c804 | APipe Tester | 21 August 2013, 02:16:49 UTC | Updated `genome` tab completion. | 21 August 2013, 02:16:49 UTC |
| 87cdf46 | APipe Tester | 21 August 2013, 02:14:56 UTC | Updated class browser cache. | 21 August 2013, 02:14:56 UTC |
| 4147882 | Dave Larson | 21 August 2013, 01:54:07 UTC | This tool is not actually for BED files and is used for DV2. Add an option to skip header lines to handle non-BED files. | 21 August 2013, 01:54:07 UTC |
| 768d060 | Dave Larson | 16 August 2013, 21:44:33 UTC | basic VCF converter for the native mutect output format | 21 August 2013, 01:51:09 UTC |
| 32854bb | Anthony Brummett | 20 August 2013, 22:10:16 UTC | Switch to string comparisons for this test The change works both in the Postgres branch and master | 20 August 2013, 22:10:16 UTC |
| 6c1784d | Anthony Brummett | 20 August 2013, 21:41:37 UTC | Switch to string comparisons for these tests The change works both in the Postgres branch and master | 20 August 2013, 21:41:37 UTC |
| b410c34 | Scott Smith | 20 August 2013, 19:33:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 August 2013, 19:33:11 UTC |
| d2de7ec | Scott Smith | 20 August 2013, 19:30:18 UTC | remove hard-coded expectation that log files are in /gscmnt, and that otherwise we should not log | 20 August 2013, 19:32:42 UTC |
| 41f7a07 | Nathan Nutter | 20 August 2013, 18:34:32 UTC | Update test output for 8e4f17f. | 20 August 2013, 19:32:41 UTC |
| 162d129 | Jim Weible | 20 August 2013, 15:57:47 UTC | Get a real test for GMT/Varscan/ConsensusVcfMatch | 20 August 2013, 19:32:41 UTC |
| c2019fe | Jim Weible | 20 August 2013, 15:57:41 UTC | cleanup | 20 August 2013, 19:32:40 UTC |
| 10813df | Jim Weible | 20 August 2013, 13:10:53 UTC | achieve feature parity with the original script | 20 August 2013, 19:32:40 UTC |
| 4961529 | Nathan Nutter | 20 August 2013, 18:34:32 UTC | Update test output for 8e4f17f. | 20 August 2013, 18:35:29 UTC |
| 6b9aeb3 | Jim Weible | 20 August 2013, 15:57:47 UTC | Get a real test for GMT/Varscan/ConsensusVcfMatch | 20 August 2013, 18:11:19 UTC |
| 8ff4482 | Jim Weible | 20 August 2013, 15:57:41 UTC | cleanup | 20 August 2013, 18:11:19 UTC |
| 9909b3a | Jim Weible | 20 August 2013, 13:10:53 UTC | achieve feature parity with the original script | 20 August 2013, 18:11:18 UTC |
| 0f14163 | Scott Smith | 20 August 2013, 16:24:55 UTC | updated exporter to include feature lists associated with instrument data target_region_set_name | 20 August 2013, 16:24:55 UTC |
| 4bf88ea | Anthony Brummett | 20 August 2013, 15:57:34 UTC | Switch to string comparisons for these tests The change works both in the Postgres branch and master | 20 August 2013, 15:57:34 UTC |
| b11a416 | Chris Miller | 20 August 2013, 13:33:34 UTC | documentation update | 20 August 2013, 13:33:34 UTC |
| 8e4f17f | Nathan Nutter | 20 August 2013, 02:18:34 UTC | make output (sort order) more deterministic when using UUIDs | 20 August 2013, 02:18:34 UTC |
| 507c55e | Nathan Nutter | 20 August 2013, 02:00:33 UTC | fix uninit warning | 20 August 2013, 02:00:33 UTC |
| 9128add | Nathan Nutter | 20 August 2013, 00:05:26 UTC | re-enable now that expected data has been updated | 20 August 2013, 00:05:26 UTC |
| 9439bac | APipe Tester | 19 August 2013, 23:33:06 UTC | Updated `genome` tab completion. | 19 August 2013, 23:33:06 UTC |
| 27597e9 | APipe Tester | 19 August 2013, 23:31:12 UTC | Updated class browser cache. | 19 August 2013, 23:31:12 UTC |
| 4b6ddf7 | Scott Smith | 19 August 2013, 23:20:10 UTC | better warning messages when creating seqdict for refseq | 19 August 2013, 23:21:29 UTC |
| 6033ba8 | Scott Smith | 19 August 2013, 23:19:06 UTC | better error messages in staged profiles | 19 August 2013, 23:21:28 UTC |
| f6f918b | APipe Tester | 19 August 2013, 23:12:24 UTC | updated workflow submodule to 6aaa1ec | 19 August 2013, 23:12:24 UTC |
| c0a25bb | APipe Tester | 19 August 2013, 22:39:22 UTC | updated ur submodule to 6c2d5ce | 19 August 2013, 22:39:22 UTC |
| f693de1 | Scott Smith | 19 August 2013, 22:26:36 UTC | add installer for file based COSMIC database | 19 August 2013, 22:26:36 UTC |
| 6757f4f | Scott Smith | 19 August 2013, 22:21:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 August 2013, 22:21:59 UTC |
| 5c30a7f | Nathan Nutter | 19 August 2013, 20:05:48 UTC | compare with eq so it will work with UUIDs | 19 August 2013, 20:07:37 UTC |
| 06bf8b3 | Nathan Nutter | 16 August 2013, 22:08:51 UTC | add subset_name to avoid the "invalid data for save" warnings | 19 August 2013, 20:07:37 UTC |
| a1fa4ea | Nathan Nutter | 15 August 2013, 20:07:32 UTC | IDs will not always be numeric so compare with eq | 19 August 2013, 20:07:36 UTC |
| 08b2205 | Nathan Nutter | 15 August 2013, 20:00:02 UTC | handle case where lane is not set | 19 August 2013, 20:07:35 UTC |
| cc3490d | Nathan Nutter | 15 August 2013, 19:59:05 UTC | whitespace | 19 August 2013, 20:07:35 UTC |
| c6012d0 | apregier | 16 August 2013, 17:49:36 UTC | Update docs | 19 August 2013, 17:00:57 UTC |
| d421456 | Chris Miller | 19 August 2013, 16:33:55 UTC | correct column uniq-ing | 19 August 2013, 16:34:35 UTC |
| c4839ef | Mark Burnett | 19 August 2013, 14:19:37 UTC | G:M:B:View -> play nice with Flow's running* status | 19 August 2013, 14:23:27 UTC |
| c6a454c | Mark Burnett | 19 August 2013, 14:18:53 UTC | PhenoCorr: wait for NFS cache | 19 August 2013, 14:23:26 UTC |
| 5846712 | apregier | 16 August 2013, 16:50:33 UTC | Vep plugin arguments work with our command line | 16 August 2013, 16:59:24 UTC |
| b31afe5 | APipe Tester | 16 August 2013, 13:53:46 UTC | updated workflow submodule to 92b7450 | 16 August 2013, 13:53:46 UTC |
| 56d23f6 | APipe Tester | 15 August 2013, 21:54:05 UTC | Updated `genome` tab completion. | 15 August 2013, 21:54:05 UTC |
| 1da3863 | APipe Tester | 15 August 2013, 21:51:56 UTC | Updated class browser cache. | 15 August 2013, 21:51:56 UTC |
| e99db69 | apregier | 15 August 2013, 21:38:19 UTC | Merge branch 'generator' into gb_master | 15 August 2013, 21:38:19 UTC |
| 7c61f0a | apregier | 15 August 2013, 21:30:17 UTC | Simplify submission-summary command | 15 August 2013, 21:35:18 UTC |
| 7ea7361 | apregier | 15 August 2013, 21:29:02 UTC | Add somatic validation test objects | 15 August 2013, 21:33:15 UTC |
| b97e1bb | Feiyu Du | 15 August 2013, 18:40:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 August 2013, 18:40:17 UTC |
| 47ffe44 | Feiyu Du | 15 August 2013, 18:37:55 UTC | test more parameters | 15 August 2013, 18:37:55 UTC |
| ac6dadf | APipe Tester | 15 August 2013, 17:54:21 UTC | Updated `genome` tab completion. | 15 August 2013, 17:54:21 UTC |
| 9bd219a | APipe Tester | 15 August 2013, 17:52:15 UTC | Updated class browser cache. | 15 August 2013, 17:52:15 UTC |
| e6d0a3d | Ben Oberkfell | 29 July 2013, 22:50:03 UTC | fix uuid sorting | 15 August 2013, 17:31:15 UTC |
| c027b28 | Ben Oberkfell | 29 July 2013, 20:57:54 UTC | match uuids as well as integers | 15 August 2013, 17:31:14 UTC |
| af72de6 | Nathan Nutter | 15 August 2013, 15:19:16 UTC | remove --newest-first option since it depends on implied information by instrument data IDs | 15 August 2013, 17:31:14 UTC |
