| 02423fb | Gabriel Sanderson | 27 August 2013, 17:57:21 UTC | Merge branch 'master' into gb_master | 27 August 2013, 17:57:21 UTC |
| a88ea93 | Gabriel Sanderson | 27 August 2013, 17:56:26 UTC | Add a VERY rudimentary check to the beginning that will look for the common problem that we have "chr" chromosomes without a nimblegen reference sequence. | 27 August 2013, 17:56:26 UTC |
| 1eb3b61 | APipe Tester | 27 August 2013, 15:47:05 UTC | updated graphite submodule to 1629c7e | 27 August 2013, 15:47:05 UTC |
| 05b227e | Mark Burnett | 27 August 2013, 15:37:38 UTC | G:D:Allocation test -- seed RNG on fork This should fix the bug related to my previous commit. | 27 August 2013, 15:37:38 UTC |
| d98687b | Mark Burnett | 27 August 2013, 15:30:16 UTC | change G:D:A test allocation_paths This is an attempt to fix this error: ERROR: Failed to create directory (/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing//tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/allocation_lock_testing_1_pKhDg6d) with return value = '', and error: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 ERROR: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 I could not reproduce the error, but this change should fix the odd, nested path. | 27 August 2013, 15:32:18 UTC |
| 4c1b012 | Thomas Mooney | 27 August 2013, 15:23:44 UTC | Take fail count into consideration when deciding which data to process. | 27 August 2013, 15:23:44 UTC |
| 1e078c6 | Mark Burnett | 27 August 2013, 13:33:39 UTC | G:M:T:Picard monitors both stdout and stderr for activity | 27 August 2013, 14:09:50 UTC |
| cf50bfc | Mark Burnett | 27 August 2013, 13:32:55 UTC | make sure InstrumentData::delete removes BamQc results | 27 August 2013, 14:09:49 UTC |
| c0325c1 | Mark Burnett | 23 August 2013, 14:56:16 UTC | add note indicating a build is run using flow | 27 August 2013, 14:09:49 UTC |
| 61bcd43 | Thomas Mooney | 27 August 2013, 14:05:30 UTC | Updates to account for transition to UUIDs. | 27 August 2013, 14:05:30 UTC |
| 29bd72e | Thomas Mooney | 27 August 2013, 13:49:27 UTC | Improve error message--print just class name instead of metaobject hash. | 27 August 2013, 13:49:27 UTC |
| 9cda567 | APipe Tester | 26 August 2013, 23:22:02 UTC | updated workflow submodule to f9affd1 | 26 August 2013, 23:22:02 UTC |
| 62ea041 | Feiyu Du | 26 August 2013, 22:22:39 UTC | add output default to STDOUT | 26 August 2013, 22:22:39 UTC |
| 8b473d9 | APipe Tester | 26 August 2013, 20:48:40 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:48:40 UTC |
| 9dfa0d2 | APipe Tester | 26 August 2013, 20:47:39 UTC | Updated `genome` tab completion. | 26 August 2013, 20:47:39 UTC |
| 050a1f8 | APipe Tester | 26 August 2013, 20:45:49 UTC | Updated class browser cache. | 26 August 2013, 20:45:49 UTC |
| 18f5021 | Dan Koboldt | 26 August 2013, 20:21:36 UTC | Writing something here. Merge branch 'master' of git+ssh://git/srv/git/genome | 26 August 2013, 20:21:36 UTC |
| f85d020 | APipe Tester | 26 August 2013, 20:19:12 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:19:12 UTC |
| 0af579a | APipe Tester | 26 August 2013, 20:18:06 UTC | Updated `genome` tab completion. | 26 August 2013, 20:18:06 UTC |
| d8af0fa | APipe Tester | 26 August 2013, 20:15:43 UTC | Updated class browser cache. | 26 August 2013, 20:15:43 UTC |
| 06a4444 | Dan Koboldt | 26 August 2013, 20:11:12 UTC | Updates to Mendelian analysis tools | 26 August 2013, 20:11:12 UTC |
| 3f18253 | Nathan Nutter | 26 August 2013, 19:26:48 UTC | Merge Postgres transition branch | 26 August 2013, 19:26:48 UTC |
| 810d6bf | Nathan Nutter | 23 August 2013, 20:26:50 UTC | remove Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
| 3134ae7 | Nathan Nutter | 23 August 2013, 20:26:41 UTC | remove use of Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
| ef4bca8 | Nathan Nutter | 23 August 2013, 19:00:09 UTC | remove Genome::DataSource::PGTest | 26 August 2013, 19:18:29 UTC |
| f36c89b | Nathan Nutter | 23 August 2013, 18:59:31 UTC | remove GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:29 UTC |
| 32a3b9c | Nathan Nutter | 23 August 2013, 18:59:10 UTC | remove use of GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:28 UTC |
| 8b03865 | Anthony Brummett | 22 August 2013, 20:38:23 UTC | Data source pointed to the old Oracle schema The graphite metrics collector will use this to look up session info. We'd like to see the session count drop to 0 | 26 August 2013, 19:18:27 UTC |
| d1227d1 | Anthony Brummett | 20 August 2013, 23:47:17 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:27 UTC |
| ef4425e | Anthony Brummett | 20 August 2013, 23:28:40 UTC | Make Model/Command/Import/Metadata.t test pass This replays part of commit 89ebc0cbd7398ca5e8c31445e46ea6a8afc336de which was undone by commit 65e970fb2b36deef08d1773fafec1b419dd892eb | 26 August 2013, 19:18:26 UTC |
| 38a760e | Nathan Nutter | 13 August 2013, 20:08:38 UTC | add OldGMSchema | 26 August 2013, 19:18:26 UTC |
| 6a92d5a | Nathan Nutter | 02 August 2013, 03:46:40 UTC | update Meta DB for Postgres | 26 August 2013, 19:18:25 UTC |
| dbd6ab0 | Ben Oberkfell | 30 July 2013, 23:43:02 UTC | columns are case sensitive | 26 August 2013, 19:18:24 UTC |
| f1d449d | Ben Oberkfell | 30 July 2013, 17:15:07 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:24 UTC |
| 94f1bd9 | Nathan Nutter | 26 July 2013, 21:44:18 UTC | update channel_for_model to work with UUIDs | 26 August 2013, 19:18:23 UTC |
| 54cac01 | Nathan Nutter | 14 August 2013, 01:39:35 UTC | IDs are now 32 character text (UUID) | 26 August 2013, 19:18:23 UTC |
| 947fbc6 | Nathan Nutter | 15 August 2013, 17:37:24 UTC | all classes now use UUID generators | 26 August 2013, 19:18:21 UTC |
| 69525a8 | Nathan Nutter | 15 August 2013, 17:36:19 UTC | update table_names to match Postgres schema | 26 August 2013, 19:18:21 UTC |
| 449cc3e | Nathan Nutter | 23 August 2013, 20:23:37 UTC | remove GMSchemaOracle | 26 August 2013, 19:18:20 UTC |
| bf9bf19 | Ben Oberkfell | 11 July 2013, 21:39:16 UTC | switch GMSchema to Postgres | 26 August 2013, 19:18:19 UTC |
| 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 |
