| 512f7ce | Eddie Belter | 13 May 2014, 20:45:47 UTC | GME Flexbar: add version 2.4 | 13 May 2014, 20:45:47 UTC |
| 2efcc7b | Feiyu Du | 13 May 2014, 18:52:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 May 2014, 18:52:39 UTC |
| 995132f | Thomas Mooney | 13 May 2014, 18:31:53 UTC | Fall back on the BED file stored in the ROI FeatureList. | 13 May 2014, 18:31:53 UTC |
| c7aa44a | Feiyu Du | 13 May 2014, 18:15:38 UTC | Add star unit test | 13 May 2014, 18:16:48 UTC |
| 6bdcd7f | Feiyu Du | 12 May 2014, 17:15:21 UTC | more tweaks to plug star in rna-seq pipeline | 13 May 2014, 18:16:48 UTC |
| 997101e | Feiyu Du | 06 May 2014, 19:03:03 UTC | Add star aligner to rna-seq pipeline | 13 May 2014, 18:16:48 UTC |
| 19f54d2 | Feiyu Du | 25 April 2014, 20:01:23 UTC | Add star aligner for rna-seq model | 13 May 2014, 18:16:47 UTC |
| 6ce4635 | Nathaniel Nutter | 13 May 2014, 17:49:50 UTC | remove transition code for created_by | 13 May 2014, 17:49:50 UTC |
| 6ea6cb9 | Nathaniel Nutter | 13 May 2014, 17:48:52 UTC | can't define with aliased property user_name | 13 May 2014, 17:49:45 UTC |
| 6b3d607 | Nathaniel Nutter | 13 May 2014, 15:17:03 UTC | remove transition code for created_by All snapshots (for awhile now) have created_by/run_as and all models (except 2 that had no user_name) have values. | 13 May 2014, 17:49:44 UTC |
| 0955494 | Thomas Mooney | 13 May 2014, 17:44:51 UTC | Add two more metrics for the benefit of the coverage report views. | 13 May 2014, 17:44:51 UTC |
| 78e3774 | Nathaniel Nutter | 13 May 2014, 15:30:37 UTC | allow run_as to be specified when defining models | 13 May 2014, 15:30:37 UTC |
| 538dca2 | Nathaniel Nutter | 13 May 2014, 15:30:03 UTC | update Genome/Model/Command/Define-docs.t expected output for run-as | 13 May 2014, 15:30:03 UTC |
| d254069 | Nathaniel Nutter | 13 May 2014, 15:07:40 UTC | allow run_as to be specified when defining models It is desired that production managers be able to create SomaticVariation models that can run as the production user (apipe-builder or cle). | 13 May 2014, 15:07:40 UTC |
| 53bea3f | apregier | 13 May 2014, 14:54:03 UTC | Skip useless test that fails all the time | 13 May 2014, 14:56:51 UTC |
| 1e4d29e | Nathaniel Nutter | 13 May 2014, 14:05:55 UTC | no longer need runtime default value for creation_time Remove the runtime default value for creation_time now that values have been backfilled in the database. | 13 May 2014, 14:51:18 UTC |
| 466f052 | Thomas Mooney | 13 May 2014, 14:28:54 UTC | Update due to updated updated_at (again). | 13 May 2014, 14:28:54 UTC |
| a813b85 | Nathaniel Nutter | 12 May 2014, 21:25:43 UTC | hard-code assumption about test Instead of depending on our current GENOME_SYS_UMASK hard-code in the value for the test. | 13 May 2014, 13:36:43 UTC |
| 64f68f3 | Nathaniel Nutter | 12 May 2014, 21:24:17 UTC | add test case Setting GENOME_SYS_UMASK='0027' for 'cle' user revealed that by not casting GENOME_SYS_UMASK as octal we were not using the expected umask. | 13 May 2014, 13:36:42 UTC |
| 8067ad1 | Nathaniel Nutter | 12 May 2014, 21:23:47 UTC | refactor test to use Genome::Utility::Test::Stat | 13 May 2014, 13:36:40 UTC |
| cf37205 | Nathaniel Nutter | 12 May 2014, 21:10:57 UTC | give tests default names | 13 May 2014, 13:36:39 UTC |
| f32fb72 | Nathaniel Nutter | 12 May 2014, 20:47:00 UTC | add Genome::Utility::Test::Stat | 13 May 2014, 13:36:37 UTC |
| 18f9fb3 | Thomas Mooney | 13 May 2014, 13:31:03 UTC | Newline at end of file. | 13 May 2014, 13:31:03 UTC |
| 91f5d4c | Thomas Mooney | 13 May 2014, 13:24:30 UTC | Update expected to account for updated updated_at time. | 13 May 2014, 13:24:30 UTC |
| 7727fae | Thomas Mooney | 13 May 2014, 13:07:44 UTC | Mark properties as transient to avoid triggering updated_at. | 13 May 2014, 13:07:44 UTC |
| 4327662 | APipe Tester | 13 May 2014, 12:20:31 UTC | Updated `genome` tab completion. | 13 May 2014, 12:20:31 UTC |
| aad808d | APipe Tester | 13 May 2014, 12:18:54 UTC | Updated class browser cache. | 13 May 2014, 12:18:54 UTC |
| dbf180a | Thomas Mooney | 12 May 2014, 22:59:13 UTC | Don't trigger circular updated_at update due to update of updated_at. | 12 May 2014, 22:59:13 UTC |
| 95daf3b | Nathaniel Nutter | 12 May 2014, 22:56:45 UTC | update help synopsis | 12 May 2014, 22:56:55 UTC |
| e2292d9 | apregier | 12 May 2014, 20:32:09 UTC | Handle read_group ids with colons | 12 May 2014, 21:55:30 UTC |
| 8179e71 | apregier | 12 May 2014, 19:43:47 UTC | Add debug messages | 12 May 2014, 21:55:29 UTC |
| 955db4b | apregier | 12 May 2014, 19:43:22 UTC | Add debug messages | 12 May 2014, 21:55:29 UTC |
| d7c6a8a | Avinash Ramu | 12 May 2014, 21:40:50 UTC | add minimum test | 12 May 2014, 21:40:50 UTC |
| 4185502 | Avinash Ramu | 12 May 2014, 21:37:34 UTC | update number of tests | 12 May 2014, 21:37:34 UTC |
| 78d8289 | Avinash Ramu | 12 May 2014, 21:17:39 UTC | modify check for mrkdup file | 12 May 2014, 21:18:37 UTC |
| bd87f4c | Avinash Ramu | 12 May 2014, 21:17:13 UTC | update clin-seq blessed build | 12 May 2014, 21:18:36 UTC |
| c326045 | Avinash Ramu | 12 May 2014, 21:16:49 UTC | add plot cnv convergence tool | 12 May 2014, 21:18:36 UTC |
| f93e700 | Avinash Ramu | 12 May 2014, 21:02:12 UTC | update clinseq cnv dir | 12 May 2014, 21:18:35 UTC |
| f6b9b04 | Avinash Ramu | 12 May 2014, 19:00:59 UTC | fix cnv diff | 12 May 2014, 21:18:35 UTC |
| d58686b | Avinash Ramu | 12 May 2014, 19:00:22 UTC | format awk command | 12 May 2014, 21:18:34 UTC |
| 5b2c953 | Avinash Ramu | 12 May 2014, 00:11:16 UTC | small tweak to makecircos test | 12 May 2014, 21:18:34 UTC |
| 38bd1a2 | Avinash Ramu | 11 May 2014, 23:57:32 UTC | update microarray cnvs Use the CNV calls from the HMM algorithm, they seem to work better in terms of determining local sequence context than naively calling CN from LRR and then segmenting. | 12 May 2014, 21:18:33 UTC |
| d79e42c | Avinash Ramu | 10 May 2014, 22:13:06 UTC | add checks to glob results | 12 May 2014, 21:18:33 UTC |
| b4ecaf7 | Avinash Ramu | 10 May 2014, 22:09:30 UTC | update microarray cnv results | 12 May 2014, 21:18:32 UTC |
| a9231d2 | Avinash Ramu | 09 May 2014, 16:39:47 UTC | add files to manifest | 12 May 2014, 21:18:32 UTC |
| 5311d0d | Avinash Ramu | 09 May 2014, 16:35:42 UTC | change cnv dir structure | 12 May 2014, 21:18:31 UTC |
| 7e42bb1 | Avinash Ramu | 09 May 2014, 16:35:04 UTC | update microarray cnv calling | 12 May 2014, 21:18:30 UTC |
| cd89418 | Ian Ferguson | 12 May 2014, 19:30:27 UTC | Try using C++ bam-errorrate for bwamem alignments BamQC now tries to use an in-development C++ rewrite of bam-errorrate for bwamem alignments. Previously it would skip bam-errorrate when the aligner was bwamem. | 12 May 2014, 19:41:25 UTC |
| 6c26cf7 | Thomas Mooney | 12 May 2014, 19:40:12 UTC | The database changed, so change the expected result again. | 12 May 2014, 19:40:12 UTC |
| c88447a | Thomas Mooney | 12 May 2014, 19:07:24 UTC | Remove $DB::single = 1; | 12 May 2014, 19:07:24 UTC |
| add5f61 | dmorton | 12 May 2014, 18:27:29 UTC | Make buffer_size specifiable in Vep | 12 May 2014, 18:28:30 UTC |
| cde3a9d | dmorton | 12 May 2014, 18:27:09 UTC | Remove redundant line. | 12 May 2014, 18:28:29 UTC |
| 9f51cdd | APipe Tester | 12 May 2014, 18:02:18 UTC | updated ur submodule to d2f68f4 | 12 May 2014, 18:02:18 UTC |
| 7a2144e | apregier | 12 May 2014, 17:10:45 UTC | Should be debug, not error message | 12 May 2014, 17:10:45 UTC |
| 2cfd515 | apregier | 12 May 2014, 17:08:43 UTC | Build ids are no longer numeric | 12 May 2014, 17:08:43 UTC |
| 8c37fa1 | Thomas Mooney | 08 May 2014, 13:48:22 UTC | Status and related columns are now directly stored on builds. | 12 May 2014, 14:45:20 UTC |
| dc69835 | APipe Tester | 10 May 2014, 12:19:39 UTC | Updated `genome` tab completion. | 10 May 2014, 12:19:39 UTC |
| 1cd8ae3 | APipe Tester | 10 May 2014, 12:18:04 UTC | Updated class browser cache. | 10 May 2014, 12:18:04 UTC |
| e4c0271 | dmorton | 09 May 2014, 21:45:58 UTC | Update genome_base_dir after file move | 09 May 2014, 21:45:58 UTC |
| ac4d15a | dmorton | 09 May 2014, 21:24:26 UTC | Move base class We have to 'hide' this base class in a folder to keep the model define subcommand factory from attempting to generate a subcommand. | 09 May 2014, 21:39:10 UTC |
| ebf5e50 | dmorton | 09 May 2014, 19:37:56 UTC | Bugfix: stop use_ok'ing non-existent class | 09 May 2014, 21:39:10 UTC |
| a12533b | dmorton | 09 May 2014, 18:18:06 UTC | Replaced temp-variables with methods | 09 May 2014, 21:39:09 UTC |
| 0b40f85 | dmorton | 09 May 2014, 17:56:12 UTC | Make sure we create the output_directory | 09 May 2014, 21:39:09 UTC |
| ce389a9 | dmorton | 08 May 2014, 21:53:46 UTC | Remove MasterCommand | 09 May 2014, 21:39:09 UTC |
| bcaf786 | dmorton | 08 May 2014, 21:32:11 UTC | Create Dag module to generate the annotation-dag This will soon replace the MasterCommand->dag method | 09 May 2014, 21:39:09 UTC |
| 7d75188 | dmorton | 08 May 2014, 20:58:45 UTC | Remove unused (dummy) input from GetInitialVcfResult | 09 May 2014, 21:39:09 UTC |
| be79e10 | dmorton | 08 May 2014, 20:06:43 UTC | Integrate Annotation Plan into Somatic Validation/Variation builds | 09 May 2014, 21:39:09 UTC |
| d0f861e | dmorton | 08 May 2014, 19:56:52 UTC | Params shouldn't be listed as inputs for commands They are for SoftwareResults, but not for commands | 09 May 2014, 21:39:09 UTC |
| 806ad52 | dmorton | 08 May 2014, 17:23:11 UTC | Make command for getting the vcf-result from DV2 at runtime We couldn't pass this in when we launch the workflow because it hasn't been created yet at that point. | 09 May 2014, 21:39:08 UTC |
| a39f030 | dmorton | 08 May 2014, 17:22:04 UTC | Add use statements for WorkflowBuilder | 09 May 2014, 21:39:08 UTC |
| 9bf1665 | Anthony Brummett | 09 May 2014, 18:39:35 UTC | remove debugging variable causing a void context warning | 09 May 2014, 20:27:58 UTC |
| 7ff5390 | Eddie Belter | 09 May 2014, 20:23:01 UTC | MC16s: adjust est kb usage | 09 May 2014, 20:23:01 UTC |
| 715f103 | Nathaniel Nutter | 09 May 2014, 19:56:36 UTC | exit prevents TestTracker from working | 09 May 2014, 19:56:36 UTC |
| c8a7085 | Nathaniel Nutter | 09 May 2014, 19:02:54 UTC | refactor has_bit to reuse mode | 09 May 2014, 19:35:55 UTC |
| f4fe221 | Nathaniel Nutter | 09 May 2014, 19:02:34 UTC | add missing dependency | 09 May 2014, 19:35:53 UTC |
| 98c6832 | Nathaniel Nutter | 09 May 2014, 18:47:48 UTC | refactor all_results to use ancestors, remove duplicate code | 09 May 2014, 19:35:18 UTC |
| e63f317 | Nathaniel Nutter | 09 May 2014, 17:39:54 UTC | remove unused variable | 09 May 2014, 19:35:17 UTC |
| 68afe6e | Nathaniel Nutter | 09 May 2014, 17:36:24 UTC | convert eval to subtest | 09 May 2014, 19:35:15 UTC |
| 1511d24 | Nathaniel Nutter | 09 May 2014, 17:32:10 UTC | refactor has_group_write for reuse of has_bit | 09 May 2014, 19:35:14 UTC |
| 1adfe0a | Nathaniel Nutter | 09 May 2014, 17:29:22 UTC | s/has_group_write/group_write/ | 09 May 2014, 19:35:12 UTC |
| d9327ae | Nathaniel Nutter | 09 May 2014, 18:58:41 UTC | blacklist genome-re.pl | 09 May 2014, 18:58:41 UTC |
| 32623c6 | Anthony Brummett | 09 May 2014, 17:50:34 UTC | remove properties corresponding to dropped columns analysis_menu_item_id and configuration_set_id | 09 May 2014, 17:50:34 UTC |
| cef18af | Anthony Brummett | 09 May 2014, 15:26:57 UTC | Remove the table name override - The class has the right table after all | 09 May 2014, 17:30:15 UTC |
| 0e9a045 | Adam Coffman | 09 May 2014, 16:11:26 UTC | migration for removing unused apconfig tables | 09 May 2014, 16:11:26 UTC |
| 751b713 | APipe Tester | 09 May 2014, 14:14:49 UTC | updated ur submodule to fdb054f | 09 May 2014, 14:14:49 UTC |
| 7f0cba1 | Anthony Brummett | 08 May 2014, 18:44:52 UTC | use autogenerated IDs instead of IDs that already exist in the DB | 09 May 2014, 14:13:35 UTC |
| ca52cfd | Anthony Brummett | 07 May 2014, 21:37:50 UTC | Populate the validation values in the timeline.analysis_project_event_type table | 09 May 2014, 14:13:34 UTC |
| d1f9e48 | Anthony Brummett | 07 May 2014, 21:28:46 UTC | Populate the validation values in the timeline.allocation_event_type table | 09 May 2014, 14:13:34 UTC |
| 4910151 | Anthony Brummett | 01 May 2014, 14:43:58 UTC | Pass in the alternate DB details in the env var instead of hard-coding it Also, we don't need the GENOME_TEST_USEDB env var - just use the existing env vars for server, user, passwd | 09 May 2014, 14:13:33 UTC |
| 1085ffa | Anthony Brummett | 01 May 2014, 14:42:48 UTC | Show the STDERR output when the test fails | 09 May 2014, 14:13:32 UTC |
| 01d79f8 | Anthony Brummett | 04 April 2014, 21:43:23 UTC | WIP getting the Genome tests to create the seed data for a test database Changes in Config/AnalysisProject.pm are to get the alternate DB loader to see some foreign keys that didn't have delegated properties. | 09 May 2014, 14:13:32 UTC |
| be97fe0 | Anthony Brummett | 14 March 2014, 22:26:03 UTC | Enviroment variables to fill and use test databases | 09 May 2014, 14:13:31 UTC |
| 1ebe4a8 | APipe Tester | 09 May 2014, 12:19:10 UTC | Updated `gmt` tab completion. | 09 May 2014, 12:19:10 UTC |
| ca19339 | APipe Tester | 09 May 2014, 12:18:29 UTC | Updated `genome` tab completion. | 09 May 2014, 12:18:29 UTC |
| c26d698 | APipe Tester | 09 May 2014, 12:17:09 UTC | Updated class browser cache. | 09 May 2014, 12:17:09 UTC |
| ce95801 | Thomas Mooney | 08 May 2014, 22:16:32 UTC | Enable no-commit to avoid locking in dummy library creation. | 08 May 2014, 22:16:32 UTC |
| 011798b | Gabriel Sanderson | 08 May 2014, 21:21:01 UTC | another place where instrument_data_segment_id could be 0 | 08 May 2014, 21:21:01 UTC |
| 64c26da | Gabriel Sanderson | 08 May 2014, 21:06:02 UTC | account for instrument_data_segment_id being 0 sometimes. | 08 May 2014, 21:06:16 UTC |
| 0e35264 | Thomas Mooney | 08 May 2014, 20:59:28 UTC | Use the segment if it's defined even if it's not truthy. | 08 May 2014, 20:59:28 UTC |
| 73e25b8 | Thomas Mooney | 08 May 2014, 20:14:57 UTC | Save the error before $@ is overwritten. | 08 May 2014, 20:14:57 UTC |
