| d136f32 | Thomas B. Mooney | 20 April 2016, 20:49:46 UTC | Merge pull request #1164 from tmooney/farewell_convergence_models Remove "Convergence" model type. | 20 April 2016, 20:49:46 UTC |
| c63546f | Thomas B. Mooney | 20 April 2016, 17:43:13 UTC | Merge pull request #1371 from tmooney/use_genome_in_path_test Use Genome so test-tracker succeeds. | 20 April 2016, 17:43:13 UTC |
| 2cf30d5 | sleongmgi | 20 April 2016, 16:05:21 UTC | Merge pull request #1372 from sleongmgi/sleong-deal-with-warning-message deal with warning message | 20 April 2016, 16:05:21 UTC |
| d7d0af5 | Avi Ramu | 20 April 2016, 16:02:25 UTC | Merge pull request #1367 from gatoravi/clinseq_workflow_fix Add wgs/exome only if input builds exist | 20 April 2016, 16:02:25 UTC |
| 44c88e9 | Thomas B. Mooney | 20 April 2016, 15:38:03 UTC | Merge pull request #1369 from tmooney/refalign_summary_test_doesnt_lock RefAlign Summary Test Doesn't Lock | 20 April 2016, 15:38:03 UTC |
| b0b1890 | sleongmgi | 20 April 2016, 12:32:40 UTC | Merge pull request #1370 from sleongmgi/sleong-files-do-not-exist-cause-wait-forever fix the test that wait forever for input if the files do not exist. | 20 April 2016, 12:32:40 UTC |
| 631c689 | APipe Tester | 20 April 2016, 12:16:35 UTC | Updated `genome` tab completion. | 20 April 2016, 12:16:35 UTC |
| 27eff02 | Shin Leong | 19 April 2016, 17:43:38 UTC | default the $unfiltered_snp_calls to $filtered_snp_calls. Move the lq_snp_calls in the block. | 19 April 2016, 17:43:38 UTC |
| dd4385f | Shin Leong | 19 April 2016, 17:20:34 UTC | deal with the warning logger message and turn print to diag. | 19 April 2016, 17:31:46 UTC |
| 663535f | Thomas Mooney | 19 April 2016, 17:13:08 UTC | Use Genome so test-tracker succeeds. | 19 April 2016, 17:13:08 UTC |
| cd51c9e | Jason Walker | 19 April 2016, 17:00:16 UTC | Merge pull request #1350 from jasonwalker80/sv_annotation_build38 Add build38 options for downloading SV annotation files. | 19 April 2016, 17:00:16 UTC |
| f819d91 | Shin Leong | 19 April 2016, 16:06:11 UTC | fix the test that wait forever for input if the files do not exist. | 19 April 2016, 16:06:11 UTC |
| 610cb37 | sleongmgi | 19 April 2016, 16:01:54 UTC | Merge pull request #1368 from sleongmgi/sleong-update-config-file-not-to-use-sata420 update the config file that uses sata420. | 19 April 2016, 16:01:54 UTC |
| 6a0a3a1 | Thomas Mooney | 19 April 2016, 15:40:29 UTC | Use an actual tempdir instead of hard-coding /tmp. | 19 April 2016, 15:40:29 UTC |
| 0d708a2 | Jason Walker | 19 April 2016, 15:25:26 UTC | Add hg38 table name. | 19 April 2016, 15:25:26 UTC |
| 1db82a4 | Thomas Mooney | 19 April 2016, 15:19:11 UTC | Set NO_COMMIT to make doubly sure we're not really doing work! | 19 April 2016, 15:19:11 UTC |
| 2f1d5d7 | Thomas Mooney | 19 April 2016, 15:17:39 UTC | Set a custom lock directory for testing. We aren't really setting metrics, so don't need to lock. | 19 April 2016, 15:17:39 UTC |
| e326e1c | Avinash Ramu | 18 April 2016, 20:21:57 UTC | Move mutation spectrum into the if-block | 18 April 2016, 20:21:57 UTC |
| d169774 | Avinash Ramu | 18 April 2016, 20:16:25 UTC | Revert "Add wgs/exome only if input builds exist" This reverts commit 00711c6188d9707487ed6229908cdbea6d858308. | 18 April 2016, 20:16:25 UTC |
| 9d9e62a | Shin Leong | 18 April 2016, 19:57:12 UTC | update the config file that uses sata420. | 18 April 2016, 19:57:12 UTC |
| 00711c6 | Avinash Ramu | 18 April 2016, 19:56:21 UTC | Add wgs/exome only if input builds exist Currently if a clin-seq build only has a exome_model as an input, the wgs version of create-mutation-spectrum is still added as a step in the workflow. This pull-request hopes to fix that. | 18 April 2016, 19:56:21 UTC |
| 6cb00bf | Jason Walker | 18 April 2016, 17:47:59 UTC | Merge pull request #1365 from jasonwalker80/mouse_84_38_annotation Annotator updates for Ensembl 84 | 18 April 2016, 17:47:59 UTC |
| 7fbe17b | Feiyu Du | 14 April 2016, 21:32:53 UTC | Merge pull request #1357 from dufeiyu/cle_test_update Update CLE Test | 14 April 2016, 21:32:53 UTC |
| 3284c0b | Jason Walker | 14 April 2016, 16:42:13 UTC | Add IG_pseudogene as a coding pseudogene biotype. Also move biotype_class as a class method useful for debugging and troubleshooting missing biotypes. | 14 April 2016, 16:42:13 UTC |
| 3b2460c | Jason Walker | 14 April 2016, 16:00:31 UTC | Add scRNA to the list of ncrna, non-coding RNA. | 14 April 2016, 16:00:31 UTC |
| 2ae575b | Thomas B. Mooney | 14 April 2016, 14:08:41 UTC | Merge pull request #1362 from tmooney/somvar_reports_lsf_resource_config Make LSF resource for SomaticVariation report step configurable. | 14 April 2016, 14:08:41 UTC |
| 3a07f7b | Thomas B. Mooney | 14 April 2016, 13:27:03 UTC | Merge pull request #1361 from tmooney/dont_mail_prodbuilder_reports Don't send out build reports for any production users. | 14 April 2016, 13:27:03 UTC |
| c01fdfb | APipe Tester | 14 April 2016, 12:18:34 UTC | Updated `genome` tab completion. | 14 April 2016, 12:18:34 UTC |
| 132ff5a | Avi Ramu | 13 April 2016, 21:20:09 UTC | Merge pull request #1346 from gatoravi/clinseq_junctions_fix Use Genome::Utility | 13 April 2016, 21:20:09 UTC |
| 2ec552c | Jason Walker | 13 April 2016, 19:17:38 UTC | Add bidirectional_promoter_lncRNA as a ncrna to biotype hash. | 13 April 2016, 19:17:38 UTC |
| b3eb025 | Thomas B. Mooney | 13 April 2016, 18:13:06 UTC | Merge pull request #1355 from tmooney/apipebuilder_in_build_commands Allow apipe-builder to use AbandonAndQueue. | 13 April 2016, 18:13:06 UTC |
| 2227bde | Avinash Ramu | 13 April 2016, 16:10:20 UTC | use Genome::Utility::Text first | 13 April 2016, 16:10:20 UTC |
| 9cb1bfb | Thomas Mooney | 13 April 2016, 14:35:01 UTC | Improve comment accuracy. | 13 April 2016, 14:35:01 UTC |
| f700129 | Thomas Mooney | 13 April 2016, 13:44:24 UTC | Make LSF resource for SomaticVariation report step configurable. | 13 April 2016, 13:44:24 UTC |
| 4f0c46d | Thomas B. Mooney | 13 April 2016, 13:25:57 UTC | Merge pull request #1354 from tmooney/queue_specification_for_instrumentdata_merge_command MergeAlignments: Specify an LSF queue configuration. | 13 April 2016, 13:25:57 UTC |
| dfc191c | Thomas B. Mooney | 13 April 2016, 13:25:36 UTC | Merge pull request #1339 from tmooney/ensembl_commands_use_inline_workflow Use inline workflow backend instead of NO_LSF environment variable. | 13 April 2016, 13:25:36 UTC |
| 8ce157d | Thomas Mooney | 13 April 2016, 13:23:12 UTC | Don't send out reports for any production users. | 13 April 2016, 13:23:12 UTC |
| ef048f1 | sleongmgi | 13 April 2016, 12:30:58 UTC | Merge pull request #1356 from sleongmgi/sleong-run-blast-path-fix fix the path. | 13 April 2016, 12:30:58 UTC |
| bd2b00b | APipe Tester | 13 April 2016, 12:18:28 UTC | Updated `genome` tab completion. | 13 April 2016, 12:18:28 UTC |
| af26352 | APipe Tester | 13 April 2016, 12:16:44 UTC | Updated class browser cache. | 13 April 2016, 12:16:44 UTC |
| 82edf40 | Avinash Ramu | 12 April 2016, 21:15:49 UTC | Add use File::Spec; | 12 April 2016, 21:15:49 UTC |
| 20940ef | Avinash Ramu | 12 April 2016, 21:08:43 UTC | Make fetching backwards compatible | 12 April 2016, 21:08:43 UTC |
| ba8a0e0 | Feiyu Du | 12 April 2016, 19:28:24 UTC | Update blessed process for CLE test | 12 April 2016, 19:28:24 UTC |
| a21cdb4 | Shin Leong | 12 April 2016, 18:59:39 UTC | fix the path. | 12 April 2016, 18:59:39 UTC |
| 3b9c5d8 | Thomas B. Mooney | 12 April 2016, 18:54:03 UTC | Merge pull request #1351 from tmooney/stop_testing_on_old_perl Remove some old Perl 5.8 tests. | 12 April 2016, 18:54:03 UTC |
| 1d0118f | sleongmgi | 12 April 2016, 18:44:28 UTC | Merge pull request #1343 from tmooney/correct_fasta_access_in_bsmap_tests Use correct accessor to get FASTA for bsmap tests. | 12 April 2016, 18:44:28 UTC |
| b3cb13d | Eddie Belter | 12 April 2016, 17:41:56 UTC | Merge pull request #1349 from ebelter/qc-config-cmds View and Diff Commands for QC Config | 12 April 2016, 17:41:56 UTC |
| 1667c86 | sleongmgi | 12 April 2016, 17:17:06 UTC | Merge pull request #1347 from sleongmgi/change-bsub-wait-for-completion Change bsub wait for completion | 12 April 2016, 17:17:06 UTC |
| e099796 | Thomas Mooney | 12 April 2016, 15:01:10 UTC | This list now matches the inheritance, so remove the check. | 12 April 2016, 15:01:10 UTC |
| 36cf282 | Thomas Mooney | 12 April 2016, 14:43:48 UTC | Remove "Start" from list--it doesn't even inherit from this! | 12 April 2016, 14:43:48 UTC |
| afc05f4 | Thomas Mooney | 12 April 2016, 14:43:21 UTC | Remove reference to non-existent "Remove" command. | 12 April 2016, 14:43:21 UTC |
| 69ab9eb | Thomas Mooney | 12 April 2016, 14:42:55 UTC | Add AbandonAndQueue to apipe-builderable commands. | 12 April 2016, 14:42:55 UTC |
| 36b9573 | Thomas Mooney | 12 April 2016, 14:41:40 UTC | Remove old SVN noise. | 12 April 2016, 14:41:40 UTC |
| 2b57382 | Thomas Mooney | 12 April 2016, 13:47:16 UTC | MergeAlignments: Specify an LSF queue configuration. | 12 April 2016, 13:47:16 UTC |
| a281a0b | APipe Tester | 12 April 2016, 12:17:24 UTC | Updated `gmt` tab completion. | 12 April 2016, 12:17:24 UTC |
| e0a62a1 | APipe Tester | 12 April 2016, 12:16:41 UTC | Updated `genome` tab completion. | 12 April 2016, 12:16:41 UTC |
| d580976 | APipe Tester | 12 April 2016, 12:15:04 UTC | Updated class browser cache. | 12 April 2016, 12:15:04 UTC |
| 9f18d09 | Eddie Belter | 11 April 2016, 22:46:18 UTC | Basic test for qc config view cmd | 11 April 2016, 22:46:18 UTC |
| 08881c0 | Eddie Belter | 11 April 2016, 22:43:59 UTC | Save to file uses config_to_yaml; remove white space in expected output | 11 April 2016, 22:43:59 UTC |
| 115ea5a | Thomas B. Mooney | 11 April 2016, 20:53:42 UTC | Merge pull request #1353 from tmooney/remove_gmt_lims_tree Remove `gmt lims` tree. | 11 April 2016, 20:53:42 UTC |
| e830c5e | Thomas Mooney | 11 April 2016, 20:22:06 UTC | Remove commented-out reference to old GMT Lims tree. | 11 April 2016, 20:22:06 UTC |
| d4a08fe | Thomas Mooney | 11 April 2016, 20:21:49 UTC | Remove GMT Lims tree. | 11 April 2016, 20:21:49 UTC |
| c3d62f3 | Jason Walker | 11 April 2016, 20:20:09 UTC | Add known_by_projection as valid transcript_transcript_status for structures. | 11 April 2016, 20:20:09 UTC |
| 5e60d26 | Susanna Kiwala | 11 April 2016, 17:09:19 UTC | Merge pull request #1326 from susannasiebert/clinseq_workflow_builder Port ClinSeq to use WorkflowBuilder | 11 April 2016, 17:09:19 UTC |
| 676c927 | Susanna Kiwala | 11 April 2016, 14:37:16 UTC | Rename iterator to index where appropriate | 11 April 2016, 16:40:15 UTC |
| a8a01ee | Susanna Kiwala | 11 April 2016, 14:36:40 UTC | Remove unused iterator variables | 11 April 2016, 16:40:15 UTC |
| f83d981 | Thomas Mooney | 11 April 2016, 14:35:39 UTC | Use same perl interpreter as test is using. | 11 April 2016, 14:47:54 UTC |
| d8cf2c1 | Thomas Mooney | 11 April 2016, 14:27:55 UTC | Remove test of loading reference sequences in Perl 5.8. The real test of refseqs is in Genome/Model/Build/ReferenceSequence.t | 11 April 2016, 14:47:08 UTC |
| 61ece50 | Thomas B. Mooney | 11 April 2016, 14:42:30 UTC | Merge pull request #1340 from tmooney/build_view_shows_ptero_lsf_jobs Add LSF ID to the Ptero workflow display. | 11 April 2016, 14:42:30 UTC |
| 3115c29 | Susanna Kiwala | 11 April 2016, 14:36:09 UTC | Don't assign the return op return value to a variable if it isn't used later | 11 April 2016, 14:36:09 UTC |
| 9a05bd0 | Thomas B. Mooney | 11 April 2016, 14:23:38 UTC | Merge pull request #1337 from tmooney/genotype_microarray_uses_workflowbuilder GenotypeMicroarray uses WorkflowBuilder. | 11 April 2016, 14:23:38 UTC |
| a8142c7 | Thomas B. Mooney | 11 April 2016, 14:23:19 UTC | Merge pull request #1338 from tmooney/remove_unfinished_phenotypecorrelation_familybased_workflow PhenotypeCorrelation Remove Unfinished Mendelian "Family-Based" Workflow. | 11 April 2016, 14:23:19 UTC |
| af10580 | Shin Leong | 11 April 2016, 13:08:22 UTC | add the retry to get the group information. | 11 April 2016, 13:08:22 UTC |
| 83bcc4b | Eddie Belter | 09 April 2016, 00:39:48 UTC | Merge pull request #1 from tmooney/qc-config-cmds Quick test for the new QC config diff command. | 09 April 2016, 00:39:48 UTC |
| 8d66db9 | Jason Walker | 08 April 2016, 18:48:02 UTC | Add a sort position to sort these files by chromosome, start and end. | 08 April 2016, 18:48:02 UTC |
| 68c6a5e | Jason Walker | 08 April 2016, 17:06:07 UTC | Add build38 options for downloading SV annotation files. | 08 April 2016, 17:06:07 UTC |
| 61f2c15 | Shin Leong | 08 April 2016, 12:26:43 UTC | use the lsf_queue_short queue. | 08 April 2016, 12:26:43 UTC |
| 36fd49b | APipe Tester | 08 April 2016, 12:18:56 UTC | Updated `gmt` tab completion. | 08 April 2016, 12:18:56 UTC |
| 69a2f68 | APipe Tester | 08 April 2016, 12:18:12 UTC | Updated `genome` tab completion. | 08 April 2016, 12:18:12 UTC |
| 579ef8f | APipe Tester | 08 April 2016, 12:16:34 UTC | Updated class browser cache. | 08 April 2016, 12:16:34 UTC |
| b17fe7e | Thomas Mooney | 07 April 2016, 22:20:25 UTC | Quick test of the QC config diff command. | 07 April 2016, 22:20:25 UTC |
| 7a806f4 | Thomas B. Mooney | 07 April 2016, 22:03:11 UTC | Merge pull request #1344 from tmooney/model_creator_info_is_required Model: created_by/run_as/creation_date are required. | 07 April 2016, 22:03:11 UTC |
| 91dfbd5 | Thomas B. Mooney | 07 April 2016, 21:58:48 UTC | Merge pull request #1341 from tmooney/remove_gmt_contaminationscreen_tree Remove "ContaminationScreen" GMT tree. | 07 April 2016, 21:58:48 UTC |
| 5b6efce | Thomas B. Mooney | 07 April 2016, 21:58:19 UTC | Merge pull request #1332 from tmooney/genomeenv_has_option_to_not_rebuild_metadb Add option to not rebuild the meta DB. | 07 April 2016, 21:58:19 UTC |
| 6f33dd4 | Thomas B. Mooney | 07 April 2016, 21:53:40 UTC | Merge pull request #1328 from tmooney/set_empty_default_for_parent_workflow_log_directory Set a default empty value for parent_workflow_log_directory. | 07 April 2016, 21:53:40 UTC |
| 12eeabb | Eddie Belter | 07 April 2016, 21:41:35 UTC | QC Config has a simple diff command | 07 April 2016, 21:41:35 UTC |
| d4d35d6 | Eddie Belter | 07 April 2016, 21:41:05 UTC | QC Config has a view command | 07 April 2016, 21:41:05 UTC |
| 4a175a8 | Eddie Belter | 07 April 2016, 21:31:40 UTC | QC Config has config_to_yaml | 07 April 2016, 21:31:40 UTC |
| 58fe0cd | Eddie Belter | 07 April 2016, 21:29:22 UTC | QC Config has __display_name__ | 07 April 2016, 21:29:22 UTC |
| 926809c | Thomas B. Mooney | 07 April 2016, 20:18:41 UTC | Merge pull request #1333 from tmooney/remove_old_modelgroup_commands Remove old ModelGroup commands. | 07 April 2016, 20:18:41 UTC |
| 5076938 | APipe Tester | 07 April 2016, 18:18:57 UTC | updated graphite submodule to 00710ee | 07 April 2016, 19:28:34 UTC |
| 23a8afb | APipe Tester | 07 April 2016, 18:18:49 UTC | updated jenkins submodule to f5af37b | 07 April 2016, 19:28:33 UTC |
| 3863a1f | Jason Walker | 07 April 2016, 19:16:34 UTC | Merge pull request #1322 from jasonwalker80/true_csv_support True CSV parsing support. | 07 April 2016, 19:16:34 UTC |
| a526c6f | Jason Walker | 07 April 2016, 18:46:58 UTC | Add known_by_projection as a valid transcript_status | 07 April 2016, 18:46:58 UTC |
| 94b6fa0 | Thomas B. Mooney | 07 April 2016, 18:37:32 UTC | Merge pull request #1312 from tmooney/heartbeat_check_for_ptero Support Heartbeat Check for PTero-based Builds. | 07 April 2016, 18:37:32 UTC |
| a35d58b | Shin Leong | 07 April 2016, 18:04:13 UTC | add the on_submit and on_complete callbacks back. | 07 April 2016, 18:04:13 UTC |
| f56fb95 | Shin Leong | 07 April 2016, 16:54:50 UTC | remove the _bsub_and_wait_for_completion__wait_on_jobs and put the perl callbacks back and only pass the queue parameter for the wait job. | 07 April 2016, 16:54:50 UTC |
| 8a2c325 | Avinash Ramu | 07 April 2016, 16:08:34 UTC | add use Genome::Utility::Text | 07 April 2016, 16:08:34 UTC |
| e5c098f | Avinash Ramu | 07 April 2016, 16:01:43 UTC | Use Genome::Utility | 07 April 2016, 16:01:43 UTC |
| f4f9c91 | Dan Koboldt | 07 April 2016, 15:43:18 UTC | New module for running germline SNP/indel calling in parallel | 07 April 2016, 15:43:18 UTC |
