| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| abbeec7 | Dan Koboldt | 07 April 2016, 15:42:50 UTC | Allowed manual provision of data ratio | 07 April 2016, 15:42:50 UTC |
| 7336f8e | Shin Leong | 07 April 2016, 15:35:23 UTC | change the bsub and wait to use the -K LSF flag instead of doing LSF pre/post callback. | 07 April 2016, 15:35:23 UTC |
| 4271375 | Thomas Mooney | 06 April 2016, 20:55:42 UTC | Model: created_by/run_as/creation_date are required. | 06 April 2016, 22:36:47 UTC |
| a4ddd30 | Thomas Mooney | 06 April 2016, 22:36:20 UTC | Add creation info to model mock. | 06 April 2016, 22:36:46 UTC |
| 782face | Thomas Mooney | 05 April 2016, 17:58:26 UTC | Use correct accessor to get FASTA for tests. "fasta_file" is the original import location of the file, not the current location. | 05 April 2016, 17:58:26 UTC |
| 8f5796a | Thomas Mooney | 31 March 2016, 21:57:53 UTC | Remove "ContaminationScreen" GMT tree. | 31 March 2016, 21:57:53 UTC |
| 372c447 | Thomas Mooney | 31 March 2016, 21:07:46 UTC | Add LSF ID to the Ptero workflow display. Now that PTero is configured to pass the job ID back to the execution, we can get this info without an additional API call per job. Instead it's in the info we're already pulling back! | 31 March 2016, 21:07:46 UTC |
| a9917c4 | Eddie Belter | 31 March 2016, 19:43:24 UTC | Merge pull request #1330 from ebelter/instdata-import-sanitize InstData Import: Merge and Modify Sanitize and Split Bam | 31 March 2016, 19:43:24 UTC |
| 6d7fb8d | Thomas Mooney | 30 March 2016, 22:18:04 UTC | Update silly error message. | 30 March 2016, 22:18:04 UTC |
| 58bd94d | Thomas Mooney | 30 March 2016, 22:16:36 UTC | Remove top of "genome model phenotype-correlation mendelian" tree. | 30 March 2016, 22:16:36 UTC |
| a580295 | Thomas Mooney | 30 March 2016, 22:11:57 UTC | PhenotypeCorrelation: Remove unfinished "family-based" mendelian tool One of the tools this workflow called was never put into a functioning state and was removed in 2270930dd281e28f1924d856f3275e26660aa4a0 in July 2012, so this mustn't have been used since then! | 30 March 2016, 22:12:43 UTC |
| e906d54 | Thomas Mooney | 30 March 2016, 21:20:05 UTC | GenotypeMicroarray uses WorkflowBuilder. | 30 March 2016, 21:20:05 UTC |
| ff3402d | Eddie Belter | 30 March 2016, 21:01:09 UTC | SanAndSplit Bam: PR updates | 30 March 2016, 21:01:09 UTC |
| efda77f | Thomas Mooney | 30 March 2016, 20:03:06 UTC | Remove old model-group commands. | 30 March 2016, 20:03:06 UTC |
| 68df760 | Thomas B. Mooney | 30 March 2016, 18:35:41 UTC | Merge pull request #1329 from tmooney/fix_else_cases_for_1316 PteroWorkflowMixin: Pass correct number of parameters in the "else" cases as well. | 30 March 2016, 18:35:41 UTC |
| 53c13e0 | Feiyu Du | 30 March 2016, 18:14:50 UTC | Merge pull request #1331 from dufeiyu/update_trio Update blessed process object for Jenkins genome-process-test | 30 March 2016, 18:14:50 UTC |
| 30e9e1c | Thomas Mooney | 30 March 2016, 18:09:21 UTC | Add option to not rebuild the meta DB. This facilitates running `genome-env` from a snapshot directory. | 30 March 2016, 18:09:21 UTC |
| 7fa8730 | Feiyu Du | 30 March 2016, 17:31:54 UTC | update with new process | 30 March 2016, 17:31:54 UTC |
| 9af80de | Thomas B. Mooney | 30 March 2016, 14:27:23 UTC | Merge pull request #1327 from tmooney/determine_error_checks_one_more_line_properly DetermineError: Properly handle case where dies on next line of logs. | 30 March 2016, 14:27:23 UTC |
| fac6b12 | Eddie Belter | 29 March 2016, 21:56:17 UTC | Update tests and data | 29 March 2016, 21:56:17 UTC |
| 78c7beb | Feiyu Du | 29 March 2016, 21:44:41 UTC | Merge pull request #1323 from dufeiyu/c_position Add c_position to variant report | 29 March 2016, 21:44:41 UTC |
| 04f2016 | Thomas Mooney | 29 March 2016, 21:01:45 UTC | Need to add a blank parameter in the "else" cases as well. This corrects an omission from #1316. | 29 March 2016, 21:02:08 UTC |
| 6b05eeb | APipe Tester | 29 March 2016, 20:32:41 UTC | updated graphite submodule to 91c31cf | 29 March 2016, 20:32:41 UTC |
| 9ff7d47 | Thomas B. Mooney | 29 March 2016, 18:54:24 UTC | Merge pull request #1316 from tmooney/ptero_workflow_output_includes_id Add an ID column to the Ptero Workflow display. | 29 March 2016, 18:54:24 UTC |
| a93dacc | Eddie Belter | 29 March 2016, 18:52:02 UTC | Switch to picard sort so picard downsample does not fail | 29 March 2016, 18:52:10 UTC |
| f8e09dd | Thomas Mooney | 29 March 2016, 18:49:56 UTC | Tests should "use above". | 29 March 2016, 18:49:56 UTC |
| b35c917 | Thomas Mooney | 29 March 2016, 18:46:49 UTC | Set a default empty value for parent_workflow_log_directory. This fixes `genome config list`, which chokes on undefined values. | 29 March 2016, 18:46:49 UTC |
| d62c70e | Thomas B. Mooney | 29 March 2016, 17:55:15 UTC | Merge pull request #1306 from tmooney/use_job_group_with_ptero Specify a default job group for PTero-launched jobs. | 29 March 2016, 17:55:15 UTC |
| c9f9c5c | Thomas Mooney | 29 March 2016, 14:24:39 UTC | Carry over no-PID status from #1287. | 29 March 2016, 14:24:39 UTC |
| 1664bdb | Thomas Mooney | 17 March 2016, 20:37:43 UTC | Really get all the executions. get_all_executions doesn't! | 29 March 2016, 14:23:42 UTC |
| 4f18547 | Thomas Mooney | 16 March 2016, 14:40:28 UTC | Support Heartbeat Check for Ptero-based Builds. | 29 March 2016, 14:23:42 UTC |
| 4d6e42a | Thomas B. Mooney | 29 March 2016, 14:16:48 UTC | Merge pull request #1287 from tmooney/heartbeatcheck_missing_pids_isnt_fatal Don't die in HeartbeatCheck if no PIDs Found. | 29 March 2016, 14:16:48 UTC |
| 29781f6 | Thomas Mooney | 28 March 2016, 22:50:34 UTC | Need to check the one more line in the next iteration. Otherwise we're really checking the same line a second time, which doesn't get us any additional information. | 28 March 2016, 22:57:12 UTC |
| a07cb35 | Eddie Belter | 25 March 2016, 23:08:56 UTC | SanAndSplit: update tests and convert to subtests | 25 March 2016, 23:27:18 UTC |
| 40c7ec2 | Eddie Belter | 25 March 2016, 23:08:05 UTC | SanAndSplit: add metrics | 25 March 2016, 23:08:05 UTC |
| bf410fb | Eddie Belter | 25 March 2016, 22:01:20 UTC | SanAndSplit: streamline rg id for reads | 25 March 2016, 22:01:20 UTC |
| 80c257a | Jason Walker | 29 February 2016, 20:35:25 UTC | The necessary changes simply based on model class to get a build to start. Conflicts: lib/perl/Genome/Model/ClinSeq.pm | 25 March 2016, 17:17:54 UTC |
| 0214717 | David Morton | 25 March 2016, 17:04:41 UTC | Merge pull request #1325 from davidlmorton/serviceDataFeature Use new 'service_data_to_save' feature of PTero | 25 March 2016, 17:04:41 UTC |
| 2947c5e | Susanna Kiwala | 11 March 2016, 16:44:42 UTC | Refactor copy_fusion_files | 25 March 2016, 17:04:07 UTC |
| 12877bb | Susanna Kiwala | 25 March 2016, 14:44:10 UTC | Group tophat_junctions_absolute_op, cufflinks_expression_absolute_op, and intersect_tumor_fusion_sv_op together | 25 March 2016, 14:44:29 UTC |
| adedcfe | Susanna Kiwala | 25 March 2016, 14:30:59 UTC | Subroutine for annotate_genes_by_dgidb_op | 25 March 2016, 14:37:36 UTC |
| ec7f100 | Susanna Kiwala | 25 March 2016, 14:11:50 UTC | Subroutine for identify_loh_op | 25 March 2016, 14:11:50 UTC |
| f92fe61 | Susanna Kiwala | 25 March 2016, 14:09:45 UTC | Subroutine for sciclone_op | 25 March 2016, 14:09:45 UTC |
| 496c654 | Susanna Kiwala | 25 March 2016, 13:57:16 UTC | Subroutine for create_mutation_spectrum_op | 25 March 2016, 13:57:16 UTC |
| 2748799 | Susanna Kiwala | 25 March 2016, 13:48:21 UTC | Subroutine for converge_snv_indel_report_op | 25 March 2016, 13:48:21 UTC |
| c34af0c | Susanna Kiwala | 25 March 2016, 13:33:38 UTC | Subroutine for make_circos_plot_op | 25 March 2016, 13:33:38 UTC |
| 153ed45 | Susanna Kiwala | 24 March 2016, 19:47:49 UTC | Subroutine for summarize_tier1_snv_support_op | 25 March 2016, 13:29:08 UTC |
| 0eabc9f | Eddie Belter | 25 March 2016, 00:20:26 UTC | SanAndSplit: rework getting fh to write reads | 25 March 2016, 00:20:36 UTC |
| a198347 | Eddie Belter | 24 March 2016, 23:20:24 UTC | SanAndSplit: add tag removal to sanitize function | 24 March 2016, 23:20:24 UTC |
| aad32b7 | Eddie Belter | 24 March 2016, 23:17:13 UTC | SanAndSplit: create _sanitze_read funciton | 24 March 2016, 23:17:13 UTC |
| ed2689f | Eddie Belter | 24 March 2016, 23:05:02 UTC | SanAndSplit: merge detrermine type and get new flag functions | 24 March 2016, 23:05:35 UTC |
| 10a7023 | Eddie Belter | 24 March 2016, 22:54:39 UTC | SanAndSplit: test get new flag function | 24 March 2016, 22:54:39 UTC |
| 2dfb15d | Eddie Belter | 23 March 2016, 23:55:39 UTC | SanAndSplit: test correct seq and qual function | 24 March 2016, 22:36:15 UTC |
| f826fb3 | Eddie Belter | 23 March 2016, 23:41:22 UTC | SanAndSplit: test determine type function | 24 March 2016, 22:36:14 UTC |
| 9ea9fc4 | Eddie Belter | 22 March 2016, 20:25:14 UTC | SanSplit: add test for separate reads function | 24 March 2016, 22:36:13 UTC |
| 93f4a08 | Eddie Belter | 22 March 2016, 19:46:04 UTC | Revcomp sequence/qualities if needed | 24 March 2016, 22:36:13 UTC |
