| 118f82c | Thomas B. Mooney | 16 August 2016, 20:05:45 UTC | Bugfix: destination_property should be output_property. | 16 August 2016, 20:05:45 UTC |
| 2962bca | Thomas B. Mooney | 16 August 2016, 17:54:04 UTC | Merge pull request #1532 from tmooney/fix_rnaseq_wf_generation RNASeq: Create the operation before adding it. | 16 August 2016, 17:54:04 UTC |
| c38ec62 | APipe Tester | 16 August 2016, 12:18:08 UTC | Updated `genome` tab completion. | 16 August 2016, 12:18:08 UTC |
| 9c1405f | Thomas B. Mooney | 15 August 2016, 21:43:46 UTC | Bugfix: create the operation before adding it. | 15 August 2016, 21:43:46 UTC |
| 99711bf | Thomas B. Mooney | 15 August 2016, 20:45:30 UTC | Merge pull request #1531 from tmooney/remove_unused_workflow_includes Remove "use Workflow;" from modules that didn't really use it. | 15 August 2016, 20:45:30 UTC |
| d13f3c5 | Thomas B. Mooney | 15 August 2016, 20:45:16 UTC | Merge pull request #1527 from tmooney/make_alignmentsummaryv2_default Make AlignmentSummaryV2 the default in Coverage Reports | 15 August 2016, 20:45:16 UTC |
| 3fe6fd7 | Thomas B. Mooney | 15 August 2016, 18:15:30 UTC | Merge pull request #1528 from tmooney/subject_mapping_crud_commands Institute a delete command and lister for subject mappings. | 15 August 2016, 18:15:30 UTC |
| d0e6716 | Thomas B. Mooney | 11 August 2016, 22:51:41 UTC | Remove "use Workflow;" from modules that didn't really use it. | 11 August 2016, 22:51:41 UTC |
| 2e96b66 | APipe Tester | 11 August 2016, 22:06:26 UTC | updated ur submodule to 6bfeb56 | 11 August 2016, 22:06:26 UTC |
| 41efc78 | Thomas B. Mooney | 11 August 2016, 20:17:46 UTC | Merge pull request #1482 from tmooney/rnaseq_uses_workflowbuilder Convert RnaSeq Workflow Generation to WorkflowBuilder. | 11 August 2016, 20:17:46 UTC |
| 229025f | Thomas B. Mooney | 11 August 2016, 19:35:42 UTC | Institute a delete command and lister for subject mappings. The lister is less friendly but more powerful than the view command. | 11 August 2016, 19:35:42 UTC |
| 4ff8285 | Thomas B. Mooney | 10 August 2016, 19:56:51 UTC | Make AlignmentSummaryV2 the default. | 10 August 2016, 19:56:51 UTC |
| feba8bf | APipe Tester | 10 August 2016, 15:56:54 UTC | updated jenkins submodule to 8f32daf | 10 August 2016, 15:56:54 UTC |
| 5a5620d | APipe Tester | 10 August 2016, 15:56:39 UTC | updated ur submodule to aad936a | 10 August 2016, 15:56:39 UTC |
| 6eef43c | APipe Tester | 10 August 2016, 12:19:16 UTC | Updated `gmt` tab completion. | 10 August 2016, 12:19:16 UTC |
| 79fe990 | APipe Tester | 10 August 2016, 12:18:35 UTC | Updated `genome` tab completion. | 10 August 2016, 12:18:35 UTC |
| 68bdc20 | APipe Tester | 10 August 2016, 12:17:08 UTC | Updated class browser cache. | 10 August 2016, 12:17:08 UTC |
| 3d18ce5 | Thomas B. Mooney | 09 August 2016, 19:03:30 UTC | Merge pull request #1508 from tmooney/stop_warning_us_about_environment_variables_with_no_value Stop warning about undefined environment variables. | 09 August 2016, 19:03:30 UTC |
| aed68b1 | Thomas B. Mooney | 09 August 2016, 19:03:18 UTC | Merge pull request #1523 from tmooney/allow_nonexistent_instrument_data Allow Running Builds with Missing Instrument Data BAMs | 09 August 2016, 19:03:18 UTC |
| 75fad5c | Thomas B. Mooney | 09 August 2016, 19:02:59 UTC | Merge pull request #1507 from tmooney/refseq_convertedbed_result_uses_displayname_in_error_message RefSeq Converter: Use names of references instead of object hashes in error message. | 09 August 2016, 19:02:59 UTC |
| 90c1e11 | Thomas B. Mooney | 09 August 2016, 19:02:44 UTC | Merge pull request #1468 from tmooney/reference_sequence_ucsc_files_are_in_build_dir UCSC annotation file changes for ReferenceSequence | 09 August 2016, 19:02:44 UTC |
| d0e2692 | Thomas B. Mooney | 09 August 2016, 19:01:50 UTC | Merge pull request #1495 from tmooney/reuse_rederivable_references Reuse "rederivable" Reference Sequences | 09 August 2016, 19:01:50 UTC |
| c8f58d0 | Thomas B. Mooney | 09 August 2016, 18:55:30 UTC | Merge pull request #1518 from tmooney/convert_chrm_to_mt Convert chrM to MT. | 09 August 2016, 18:55:30 UTC |
| dcd1e8c | Thomas B. Mooney | 09 August 2016, 18:55:14 UTC | Merge pull request #1385 from tmooney/viromescreening_uses_workflowbuilder ViromeScreening uses WorkflowBuilder | 09 August 2016, 18:55:14 UTC |
| b761bf4 | Thomas B. Mooney | 09 August 2016, 18:51:00 UTC | Merge pull request #1522 from tmooney/remove_capturelist_scripts Remove old scripts in "CaptureList" directory. | 09 August 2016, 18:51:00 UTC |
| 598b49b | APipe Tester | 09 August 2016, 12:17:55 UTC | Updated `genome` tab completion. | 09 August 2016, 12:17:55 UTC |
| 9bfd564 | Thomas B. Mooney | 08 August 2016, 20:19:35 UTC | Merge pull request #1514 from tmooney/prioritize_new_data_in_cqid CQID: Give all the "new" things a try first. | 08 August 2016, 20:19:35 UTC |
| ba459eb | Eddie Belter | 08 August 2016, 20:14:41 UTC | Merge pull request #1520 from ebelter/instdata-import-working-dir InstData Import: allow the specification of working directory | 08 August 2016, 20:14:41 UTC |
| 38ca62e | Thomas B. Mooney | 08 August 2016, 17:49:10 UTC | Default to a low temp request if the BAM is missing. If we end up running the step it will fail (and use little temp!). If we end up shortcutting the step the value is irrelevant and we won't care that we couldn't find the BAM. | 08 August 2016, 17:49:10 UTC |
| 241622a | Thomas B. Mooney | 08 August 2016, 17:46:52 UTC | Allow builds to start even if the source instrument data cannot be found. If the steps of the build which depend upon the BAM have already generated results, we might be able to shortcut past them even though the data are unavailable. | 08 August 2016, 17:46:52 UTC |
| 3348631 | Thomas B. Mooney | 08 August 2016, 17:30:51 UTC | Remove old scripts in "CaptureList" directory. | 08 August 2016, 17:30:51 UTC |
| f5ebd08 | Eddie Belter | 05 August 2016, 22:19:45 UTC | InstData Import: allow the specification of working directory | 05 August 2016, 22:19:45 UTC |
| b93808c | Feiyu Du | 04 August 2016, 20:10:56 UTC | Merge pull request #1519 from dufeiyu/update_cle Update blessed process for CLE regression test | 04 August 2016, 20:10:56 UTC |
| cad1c6b | Feiyu Du | 04 August 2016, 19:16:21 UTC | Update blessed process for CLE test | 04 August 2016, 19:16:21 UTC |
| 020244e | Thomas B. Mooney | 04 August 2016, 14:18:02 UTC | Convert chrM to MT. | 04 August 2016, 14:18:02 UTC |
| ec50914 | Thomas B. Mooney | 03 August 2016, 17:25:19 UTC | Merge pull request #1517 from tmooney/use_simpler_translation_variable_in_lsf_paths Use %J (LSF's standard) instead of %%JOB_ID%%. | 03 August 2016, 17:25:19 UTC |
| 3e016d2 | Thomas B. Mooney | 02 August 2016, 20:39:07 UTC | Use %J (LSF's standard) instead of %%JOB_ID%%. LSF will translate this for us to be the LSF Job ID. | 02 August 2016, 20:39:07 UTC |
| f716fad | Thomas B. Mooney | 02 August 2016, 19:56:16 UTC | Merge pull request #1509 from tmooney/ptero_builder_doesnt_determine_final_logdir Defer to new Ptero feature to decide the log paths. | 02 August 2016, 19:56:16 UTC |
| 67fa0b6 | Feiyu Du | 29 July 2016, 19:54:00 UTC | Merge pull request #1516 from dufeiyu/update_process Update blessed process for Jenkins genome-process-test | 29 July 2016, 19:54:00 UTC |
| edf290e | Feiyu Du | 29 July 2016, 18:30:42 UTC | Update blessed process | 29 July 2016, 18:30:42 UTC |
| 6c545be | Feiyu Du | 28 July 2016, 21:27:04 UTC | Merge pull request #1515 from dufeiyu/vcf_description Update vcf description with more info | 28 July 2016, 21:27:04 UTC |
| 58f4521 | Feiyu Du | 28 July 2016, 20:48:28 UTC | Give better vcf description | 28 July 2016, 20:48:28 UTC |
| 0eefeb3 | Thomas B. Mooney | 28 July 2016, 15:39:56 UTC | Merge pull request #1512 from tmooney/sort_before_running_bedtools_merge bedtools merge requires the file to be sorted. | 28 July 2016, 15:39:56 UTC |
| 8734993 | Thomas B. Mooney | 27 July 2016, 22:50:22 UTC | CQID: Give all the "new" things a try first. If someone manually resets the status to "new" (for example, via `genome analysis-project reprocess`) they probably expect us to try their instrument data at least once in short order! This is also a good clue that they may have corrected whatever issues were causing the previous failures. | 27 July 2016, 22:50:22 UTC |
| 2e27636 | Thomas B. Mooney | 27 July 2016, 18:59:24 UTC | Merge pull request #1489 from tmooney/more_correct_somatic_filter_workflow_test SomaticFilterWorkflow test: Quote parameters to `diff`. | 27 July 2016, 18:59:24 UTC |
| a7ede01 | Thomas B. Mooney | 27 July 2016, 18:59:05 UTC | Merge pull request #1494 from tmooney/refalign_bamqc_server_uses_lower_queue Use lower queue for BamQc "server" process. | 27 July 2016, 18:59:05 UTC |
| 9688ecb | Thomas B. Mooney | 27 July 2016, 18:58:46 UTC | Merge pull request #1488 from tmooney/find_fewer_irrelevant_results AlignmentResult: Check the reference and annotation builds when seeking our Merged result(s) | 27 July 2016, 18:58:46 UTC |
| 7a04ba2 | Thomas B. Mooney | 05 July 2016, 19:16:47 UTC | Reuse "rederivable" Reference Sequences This will save us from creating extra copies of reference sequences and spending time indexing them for alignment when they match a reference we've already created. | 27 July 2016, 17:25:10 UTC |
| 3279ff3 | Thomas B. Mooney | 27 July 2016, 15:45:59 UTC | Merge pull request #1510 from tmooney/make_logging_revision_failures_nonfatal Don't die just because we can't revert the logging. | 27 July 2016, 15:45:59 UTC |
| 83196e6 | Thomas B. Mooney | 27 July 2016, 15:00:50 UTC | Merge pull request #1511 from tmooney/disable_tcga_queries_for_old_systems Require a newer SSL implementation to perform the web queries. | 27 July 2016, 15:00:50 UTC |
| 1bfb161 | APipe Tester | 27 July 2016, 12:16:18 UTC | Updated `gmt` tab completion. | 27 July 2016, 12:16:18 UTC |
| 3645600 | APipe Tester | 27 July 2016, 12:15:31 UTC | Updated `genome` tab completion. | 27 July 2016, 12:15:31 UTC |
| 2a7e7b0 | Thomas B. Mooney | 26 July 2016, 22:00:21 UTC | bedtools merge requires the file to be sorted. Although imported feature-lists often are sorted, we don't guarantee that, so better sort here. | 26 July 2016, 22:02:33 UTC |
| dfcdaf3 | Eddie Belter | 26 July 2016, 19:26:15 UTC | Merge pull request #1503 from ebelter/sx-trim-by-pos-with-ns Trim by positions can handle scaffold/supercontigs | 26 July 2016, 19:26:15 UTC |
| 1933bba | Thomas B. Mooney | 25 July 2016, 18:26:17 UTC | Require a newer SSL implementation to perform the web queries. The GDC portal now requires newer SSL to perform the handshake, so disable the TCGA support for older systems. (Running with an outdated OpenSSL is scary, and one probably shouldn't do it, anyway!) | 25 July 2016, 18:26:17 UTC |
| fbda4f7 | Feiyu Du | 21 July 2016, 20:30:09 UTC | Merge pull request #1506 from dufeiyu/plan_file Update CLE plan files with new filters | 21 July 2016, 20:30:09 UTC |
| 65f6cfc | Thomas B. Mooney | 21 July 2016, 18:59:47 UTC | Don't die just because we can't revert the logging. Letting a few messages leak into the task's log files is far better than throwing out all of our work when there's an issue reopening the original log file! | 21 July 2016, 18:59:47 UTC |
| beeaab2 | Thomas B. Mooney | 20 July 2016, 19:51:15 UTC | Don't warn when there's no LSB_SUB_ADDITIONAL variable defined. | 20 July 2016, 19:51:15 UTC |
| 9f3365d | Thomas B. Mooney | 20 July 2016, 19:47:13 UTC | Stop warning about undefined environment variables. Users don't really care about the limitations of the environment compared to Perl hashes. | 20 July 2016, 19:47:13 UTC |
| 4c0127d | Thomas B. Mooney | 20 July 2016, 19:37:07 UTC | Defer to new Ptero feature to decide the log paths. This uses genome/ptero-lsf#124 and genome/ptero-perl-sdk#117 to ensure a unique filename is chosen for each job, even during a parallel-by. As a bonus that filename's UUID will now be the Job ID making it easier to match to the job to which it belongs. | 20 July 2016, 19:37:07 UTC |
| dd261bd | Thomas B. Mooney | 20 July 2016, 19:35:23 UTC | Stop redirecting output of post-exec. This was supposedly for debugging, but we never looked at it, and until recently it was written to /tmp/ where it vanished anyway. | 20 July 2016, 19:36:54 UTC |
| 591ccce | Thomas B. Mooney | 19 July 2016, 13:45:13 UTC | Merge pull request #1480 from tmooney/somvar_uses_workflowbuilder SomVar uses WorkflowBuilder | 19 July 2016, 13:45:13 UTC |
| ebcc5d1 | Thomas B. Mooney | 19 July 2016, 13:44:47 UTC | Merge pull request #1481 from tmooney/mc16s_uses_workflowbuilder Convert MC16s workflow generation to WorkflowBuilder. | 19 July 2016, 13:44:47 UTC |
| 6a6dcbd | APipe Tester | 19 July 2016, 12:19:21 UTC | Updated `gmt` tab completion. | 19 July 2016, 12:19:21 UTC |
| 93199bf | APipe Tester | 19 July 2016, 12:18:37 UTC | Updated `genome` tab completion. | 19 July 2016, 12:18:37 UTC |
| 640bc03 | Thomas B. Mooney | 18 July 2016, 19:34:28 UTC | Merge pull request #1499 from tmooney/add_error_to_instantation_failure_message Add error to instantiation failure message. | 18 July 2016, 19:34:28 UTC |
| 3462b8e | Jason Walker | 18 July 2016, 18:07:38 UTC | Merge pull request #1500 from jasonwalker80/remove_sata132_jwalker Remove references to sata132/jwalker file paths. | 18 July 2016, 18:07:38 UTC |
| e62168a | Thomas B. Mooney | 18 July 2016, 17:48:14 UTC | Print display names of references instead of object hashes. | 18 July 2016, 17:48:14 UTC |
| 09212f6 | Feiyu Du | 18 July 2016, 16:30:12 UTC | Merge pull request #1504 from dufeiyu/empty_bed_merge Make trio wrapper merge work if one of input reports is empty | 18 July 2016, 16:30:12 UTC |
| 7c7af8e | Malachi Griffith | 18 July 2016, 16:16:56 UTC | Merge pull request #1505 from malachig/master clean up all references to gscmnt paths | 18 July 2016, 16:16:56 UTC |
| 2204b1f | Jason Walker | 18 July 2016, 14:58:08 UTC | correct syntax for example_values | 18 July 2016, 14:58:08 UTC |
| c52ff64 | Malachi Griffith | 15 July 2016, 21:28:56 UTC | update test to use cancer gene list instead of aml rmg list | 15 July 2016, 21:28:56 UTC |
| 1ee96eb | Malachi Griffith | 15 July 2016, 20:08:38 UTC | clean up references to specific gscmnt paths | 15 July 2016, 20:08:38 UTC |
| 1c3e45a | Malachi Griffith | 15 July 2016, 19:25:22 UTC | remove old readme | 15 July 2016, 19:25:22 UTC |
| c481ed2 | Feiyu Du | 14 July 2016, 21:25:36 UTC | add test case to unit test | 14 July 2016, 21:25:36 UTC |
| c2c4522 | Feiyu Du | 14 July 2016, 17:41:51 UTC | Add vaf-cutoff filter to cle snv plan files | 14 July 2016, 17:41:51 UTC |
| e816435 | Feiyu Du | 14 July 2016, 15:52:06 UTC | Make merge work if base or supplemental report is empty | 14 July 2016, 15:52:06 UTC |
| c1aa03c | Thomas B. Mooney | 14 July 2016, 15:03:41 UTC | Merge pull request #1496 from tmooney/remove_lsf_queue_alignment_prod Remove "lsf_queue_alignment_prod" config. | 14 July 2016, 15:03:41 UTC |
| e961086 | Eddie Belter | 13 July 2016, 21:46:19 UTC | Trim by positions can handle scaffold/supercontigs | 13 July 2016, 21:47:40 UTC |
| fb18469 | Thomas B. Mooney | 13 July 2016, 16:57:40 UTC | Merge pull request #1449 from tmooney/keep_logs_around_when_ptero_postexec_fails Keep logs around when Ptero's post-exec fails. | 13 July 2016, 16:57:40 UTC |
| 15092b9 | Thomas B. Mooney | 13 July 2016, 16:57:34 UTC | Merge pull request #1501 from tmooney/remember_the_annotate_snvs_vcf_op Only create one annotate_snvs_vcf_op per type. | 13 July 2016, 16:57:34 UTC |
| 2be846e | Thomas B. Mooney | 13 July 2016, 15:25:18 UTC | Use the passed-in log directory. | 13 July 2016, 15:25:18 UTC |
| 37fa620 | APipe Tester | 13 July 2016, 12:18:35 UTC | Updated `gmt` tab completion. | 13 July 2016, 12:18:35 UTC |
| 85b9378 | APipe Tester | 13 July 2016, 12:17:53 UTC | Updated `genome` tab completion. | 13 July 2016, 12:17:53 UTC |
| 5c102db | APipe Tester | 13 July 2016, 12:16:25 UTC | Updated class browser cache. | 13 July 2016, 12:16:25 UTC |
| 95dc9f7 | Thomas B. Mooney | 12 July 2016, 20:53:21 UTC | Merge pull request #1479 from tmooney/remove_parallel_commands Remove GMTs that relied on Workflow integration. | 12 July 2016, 20:53:21 UTC |
| f12d105 | Thomas B. Mooney | 12 July 2016, 20:21:16 UTC | Merge pull request #1484 from tmooney/remove_old_individual_cpudisksummary_command Remove `genome individual cpu-disk-summary`. | 12 July 2016, 20:21:16 UTC |
| 71a6825 | Thomas B. Mooney | 12 July 2016, 19:25:52 UTC | Merge pull request #1452 from tmooney/ptero_prepostexec_uses_docker Fix ptero-lsf-{pre,post}-exec within docker | 12 July 2016, 19:25:52 UTC |
| 97ac184 | Thomas B. Mooney | 12 July 2016, 19:02:14 UTC | Merge pull request #1497 from tmooney/ptero_null_command_uses_queue_config Use config to decide the LSF queue (Ptero NullCommand) | 12 July 2016, 19:02:14 UTC |
| ebd0033 | Thomas B. Mooney | 12 July 2016, 19:01:25 UTC | Merge pull request #1478 from tmooney/parameterize_files_in_germline_filtering Replace hard-coded NHLBI and 1000 Genomes files with parameters. | 12 July 2016, 19:01:25 UTC |
| 3fb2e19 | Thomas B. Mooney | 09 June 2016, 22:06:11 UTC | Update expected pre and post-exec strings in JSON. | 12 July 2016, 19:00:05 UTC |
| b88c75c | Thomas B. Mooney | 12 July 2016, 18:48:13 UTC | Only create one annotate_snvs_vcf_op per type. | 12 July 2016, 18:48:13 UTC |
| 9ed95be | Thomas B. Mooney | 12 July 2016, 18:33:12 UTC | Merge pull request #1476 from tmooney/remove_pindel_modelgroup_command Remove old `gmt pindel run-pindel-model-group` command. | 12 July 2016, 18:33:12 UTC |
| 69e442f | Thomas B. Mooney | 09 June 2016, 18:04:00 UTC | Use full path to pre and post-exec commands. | 12 July 2016, 18:24:00 UTC |
| 0dae693 | Thomas B. Mooney | 08 June 2016, 21:15:13 UTC | Make sure pre- and post-exec run within the docker container, too. | 12 July 2016, 18:24:00 UTC |
| a6068ba | Thomas B. Mooney | 12 July 2016, 18:23:01 UTC | Merge pull request #1453 from tmooney/remove_old_assembly_tools_that_use_workflow Remove old Assembly tools that use Workflow. | 12 July 2016, 18:23:01 UTC |
| d0e9910 | Thomas B. Mooney | 12 July 2016, 18:17:49 UTC | Merge pull request #1493 from tmooney/workflow_builder_default_queue Use Config to Select a Default LSF Queue if None Specified | 12 July 2016, 18:17:49 UTC |
| 332e187 | Thomas B. Mooney | 12 July 2016, 18:15:34 UTC | Merge pull request #1454 from tmooney/remove_old_polymuttpipeline Remove old "PolymuttPipeline" workflow tool. | 12 July 2016, 18:15:34 UTC |
| 597a6dc | Thomas B. Mooney | 12 July 2016, 18:15:20 UTC | Merge pull request #1487 from tmooney/validate_svs_steps_specify_lsf_queues Specify a default queue in several SomVal steps. | 12 July 2016, 18:15:20 UTC |
| f0a0496 | APipe Tester | 12 July 2016, 12:15:38 UTC | Updated `genome` tab completion. | 12 July 2016, 12:15:38 UTC |
