| 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 |
| 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 |
| e3cd4c3 | APipe Tester | 12 July 2016, 12:14:05 UTC | Updated class browser cache. | 12 July 2016, 12:14:05 UTC |
| 1729336 | Thomas B. Mooney | 11 July 2016, 13:09:42 UTC | Merge pull request #1498 from tmooney/disk_usage_summary_command_for_software_results Command to summarize disk usage of SoftwareResults by Sponsor. | 11 July 2016, 13:09:42 UTC |
| ce6f1b3 | APipe Tester | 08 July 2016, 12:16:59 UTC | Updated `gmt` tab completion. | 08 July 2016, 12:16:59 UTC |
| d142b06 | APipe Tester | 08 July 2016, 12:16:20 UTC | Updated `genome` tab completion. | 08 July 2016, 12:16:20 UTC |
| 5185ebc | Thomas B. Mooney | 07 July 2016, 19:56:16 UTC | Command to summarize disk usage of SoftwareResults by Sponsor. This is a slightly polished-up version of a script from past meetings. | 07 July 2016, 19:57:47 UTC |
| 164b644 | Thomas B. Mooney | 07 July 2016, 12:42:37 UTC | Merge pull request #1492 from tmooney/specify_queue_in_plot_segments Specify a default LSF queue in CopyNumber PlotSegments | 07 July 2016, 12:42:37 UTC |
| 3e84bc5 | Thomas B. Mooney | 06 July 2016, 21:56:29 UTC | Use config to decide the LSF queue. | 06 July 2016, 21:56:29 UTC |
| e9d7ce6 | Thomas B. Mooney | 05 July 2016, 15:51:08 UTC | Specify a default LSF queue if the command doesn't have one. | 06 July 2016, 14:09:34 UTC |
| 69dc2f7 | APipe Tester | 06 July 2016, 12:18:29 UTC | Updated `gmt` tab completion. | 06 July 2016, 12:18:29 UTC |
| 75243d7 | APipe Tester | 06 July 2016, 12:17:44 UTC | Updated `genome` tab completion. | 06 July 2016, 12:17:44 UTC |
| 33f82f3 | APipe Tester | 06 July 2016, 12:16:18 UTC | Updated class browser cache. | 06 July 2016, 12:16:18 UTC |
| 08e9509 | Thomas B. Mooney | 05 July 2016, 18:24:57 UTC | Ignore any LSF queue specifications. | 05 July 2016, 18:27:00 UTC |
| eade6d2 | Thomas B. Mooney | 05 July 2016, 18:23:30 UTC | Spelling: mathes => matches | 05 July 2016, 18:27:00 UTC |
| b02fcff | Thomas B. Mooney | 05 July 2016, 15:51:46 UTC | Ignore LSF queue and resource specification when diffing XML. | 05 July 2016, 15:52:21 UTC |
| dd59a10 | Thomas B. Mooney | 05 July 2016, 13:46:15 UTC | Specify a default LSF queue. | 05 July 2016, 13:46:15 UTC |
| 3f9657b | Thomas B. Mooney | 05 July 2016, 13:16:36 UTC | Merge pull request #1491 from tmooney/cache_username_result Cache the username in Genome::Sys->username. | 05 July 2016, 13:16:36 UTC |
| 31adf3a | Thomas B. Mooney | 05 July 2016, 13:15:45 UTC | Merge pull request #1486 from tmooney/remove_unused_use_workflow_includes Remove `gmt bwa align-reads` and unused "use Workflow;" includes. | 05 July 2016, 13:15:45 UTC |
| c1d68ed | Thomas B. Mooney | 30 June 2016, 21:51:56 UTC | Cache the username. Since getpwuid is being unreliable, save the answer if we do succeed to save us from further travails. | 30 June 2016, 21:51:56 UTC |
| c4912e0 | Thomas B. Mooney | 30 June 2016, 20:35:32 UTC | Merge pull request #1490 from tmooney/if_at_first_you_dont_succeed_getting_a_username If we don't get a username back from `getpwuid`, try again! | 30 June 2016, 20:35:32 UTC |
| bbdaf40 | Thomas B. Mooney | 30 June 2016, 19:14:36 UTC | Add a comment explaining why we're sleeping. | 30 June 2016, 19:14:36 UTC |
| 59ea7f7 | Thomas B. Mooney | 30 June 2016, 19:10:38 UTC | Pull the ENV check out of the loop. | 30 June 2016, 19:10:38 UTC |
| d1f8802 | Thomas B. Mooney | 30 June 2016, 16:27:43 UTC | Merge pull request #1483 from tmooney/instrument_data_import_helper_doesnt_use_workflow Remove unused Workflow helpers in InstrumentData Import. | 30 June 2016, 16:27:43 UTC |
| 5fd16f5 | Thomas B. Mooney | 30 June 2016, 16:26:45 UTC | Merge pull request #1485 from tmooney/clinseq_tells_no_lies_about_workflow ClinSeq: Remove false comment. | 30 June 2016, 16:26:45 UTC |
| 3fe5407 | Thomas B. Mooney | 30 June 2016, 16:26:23 UTC | Merge pull request #1477 from tmooney/remove_batchrun_eptiopepred_script Remove EpitopePrediction batchrun script. | 30 June 2016, 16:26:23 UTC |
| 21378b7 | Thomas B. Mooney | 30 June 2016, 16:14:59 UTC | Make it fatal to not find the username. | 30 June 2016, 16:14:59 UTC |
| 2532750 | Thomas B. Mooney | 30 June 2016, 13:54:20 UTC | If we don't get a username back from `getpwuid`, try again! It seems our systems are sometimes unreliable at returning a value here, causing some build failures. In my testing, it will fail to return a value on the first attempt, but the second attempt will succeed. Trying this five times is thus probably overkill(!), but hopefully is sufficient to make `Genome::Sys->username` reliable. If things really go poorly, the user_id is often "good enough" as a unique per-user value... just one less friendly to the viewer. However, it's insufficient to locate a `Genome::Sys::User` object, so anything depending on real user objects would still fail. | 30 June 2016, 13:54:20 UTC |
| 719cc3e | Thomas B. Mooney | 29 June 2016, 19:57:20 UTC | Add default LSF queues to small indels workflow steps. | 29 June 2016, 19:57:20 UTC |
| 891cad4 | Thomas B. Mooney | 29 June 2016, 19:40:31 UTC | Specify default LSF queue for various SomVal tasks. | 29 June 2016, 19:40:31 UTC |
| 01e9aee | Thomas B. Mooney | 29 June 2016, 18:21:40 UTC | Remove unused "use Workflow" in ViromeEvent GMTs. Do these tools even need to stick around? | 29 June 2016, 18:21:40 UTC |
| baa5bf2 | Thomas B. Mooney | 29 June 2016, 18:17:19 UTC | Remove unused "use Workflow" in GenePrediction commands. Some of these were already commented-out, anyway! | 29 June 2016, 18:17:19 UTC |
| 8775626 | Thomas B. Mooney | 29 June 2016, 18:14:15 UTC | Remove unused "use Workflow;" from build failure report. | 29 June 2016, 18:14:15 UTC |
| 328b8f1 | Thomas B. Mooney | 29 June 2016, 18:12:46 UTC | Remove unused "use Workflow" includes in `gmt pindel` tools. | 29 June 2016, 18:12:46 UTC |
| 1ffd092 | Thomas B. Mooney | 29 June 2016, 18:10:43 UTC | Remove unused "use Workflow;" in Somatic GMTs. | 29 June 2016, 18:10:43 UTC |
| 2fa9639 | Thomas B. Mooney | 29 June 2016, 18:07:50 UTC | Remove unused "use Workflow;" in DV2 detectors. | 29 June 2016, 18:07:50 UTC |
| fa3ae93 | Thomas B. Mooney | 29 June 2016, 18:06:15 UTC | Remove unused `gmt bwa align-reads` that has spurious `use Workflow;`. | 29 June 2016, 18:06:15 UTC |
| 6d401d8 | Thomas B. Mooney | 29 June 2016, 18:02:25 UTC | Remove unused "use Workflow" in Pindel indel conversion. | 29 June 2016, 18:02:25 UTC |
| a35f74c | Thomas B. Mooney | 29 June 2016, 17:59:57 UTC | Remove "use Workflow;" since these don't. | 29 June 2016, 17:59:57 UTC |
| 37ab2f9 | Thomas B. Mooney | 29 June 2016, 17:52:32 UTC | Remove false comment. This was converted to WorkflowBuilder in #1326. | 29 June 2016, 17:52:32 UTC |
| 8a2b766 | Thomas B. Mooney | 29 June 2016, 17:48:16 UTC | Remove `genome individual cpu-disk-summary`. This command is coupled to Workflow builds and so it does not work in our new more Ptero-iffic world. The usage log reports no uses, so remove it rather than fixing it up. | 29 June 2016, 17:48:16 UTC |
| c0d44e9 | Thomas B. Mooney | 29 June 2016, 17:26:38 UTC | Remove unused Workflow helpers. | 29 June 2016, 17:28:45 UTC |
| 52d7ccb | APipe Tester | 29 June 2016, 12:18:44 UTC | Updated `gmt` tab completion. | 29 June 2016, 12:18:44 UTC |
| f8fce48 | APipe Tester | 29 June 2016, 12:17:59 UTC | Updated `genome` tab completion. | 29 June 2016, 12:17:59 UTC |
| cd8b800 | APipe Tester | 29 June 2016, 12:16:29 UTC | Updated class browser cache. | 29 June 2016, 12:16:29 UTC |
| d02ddd5 | Thomas B. Mooney | 28 June 2016, 21:01:52 UTC | Remove GMTs that relied on Workflow integration. These used a Workflow-specific way of parallel_by that effectively made them workflows unto themselves. The underlying commands are still around for use if needed for now. | 28 June 2016, 21:02:42 UTC |
| e0c9b63 | Thomas B. Mooney | 28 June 2016, 20:36:23 UTC | Replace hard-coded NHLBI and 1000 Genomes files with parameters. The hard-coded versions are on volumes slated for removal, and hardcoded paths are bad, anyway! CHANGELOG: `gmt germline filtering` now requires that the 1000 Genomes and NHLBI files be specified as parameters. This change is to faciliate the removal of old volumes where these files have historically been located. | 28 June 2016, 20:39:05 UTC |
| 9f1f1e0 | Thomas B. Mooney | 28 June 2016, 20:25:45 UTC | Remove EpitopePrediction batchrun script. This references volumes that are being eliminated. | 28 June 2016, 20:25:45 UTC |
| e27c8bf | Thomas B. Mooney | 28 June 2016, 20:05:59 UTC | Remove old `gmt pindel run-pindel-model-group` command. | 28 June 2016, 20:05:59 UTC |
| e360b94 | Thomas B. Mooney | 28 June 2016, 19:23:49 UTC | Merge pull request #1459 from tmooney/ber_uses_workflowbuilder BER/Prediction Workflow uses WorkflowBuilder | 28 June 2016, 19:23:49 UTC |
| db2584e | Thomas B. Mooney | 28 June 2016, 19:19:47 UTC | Merge pull request #1460 from tmooney/remove_gene_prediction_workflow_model_uses Remove uses of Workflow::Model in GenePrediction. | 28 June 2016, 19:19:47 UTC |
| f92660d | Thomas B. Mooney | 28 June 2016, 19:17:30 UTC | Merge pull request #1464 from tmooney/remove_references_to_deprecated_volumes Remove References to Volumes Being Retired | 28 June 2016, 19:17:30 UTC |
| 7e7be6d | Thomas B. Mooney | 28 June 2016, 19:16:37 UTC | Merge pull request #1467 from tmooney/remove_plotsv_script Remove old plotSV.pl script. | 28 June 2016, 19:16:37 UTC |
| f2c994a | Thomas B. Mooney | 28 June 2016, 19:16:17 UTC | Merge pull request #1466 from tmooney/remove_capture_processmodels Remove old `gmt capture process-models`. | 28 June 2016, 19:16:17 UTC |
| 94bc7a8 | Thomas B. Mooney | 28 June 2016, 18:58:39 UTC | Merge pull request #1462 from tmooney/specify_queues_in_mutect_and_verifybam Specify queues in Mutect and SomVal's VerifyBam. | 28 June 2016, 18:58:39 UTC |
| ccd9576 | Jason Walker | 28 June 2016, 18:31:14 UTC | Merge pull request #1469 from jasonwalker80/skip_sort_speedseq_sv Speedseq SV remove sort and symlink VCF. | 28 June 2016, 18:31:14 UTC |
| bf89f4d | Thomas B. Mooney | 28 June 2016, 13:26:58 UTC | Merge pull request #1473 from tmooney/sys_lsf_bsub_works_with_docker Add Genome::Sys::LSF::bsub Docker Support | 28 June 2016, 13:26:58 UTC |
| 52adfce | APipe Tester | 28 June 2016, 12:16:53 UTC | Updated `gmt` tab completion. | 28 June 2016, 12:16:53 UTC |
| 8171024 | APipe Tester | 28 June 2016, 12:16:10 UTC | Updated `genome` tab completion. | 28 June 2016, 12:16:10 UTC |
| 221e91a | APipe Tester | 28 June 2016, 12:14:42 UTC | Updated class browser cache. | 28 June 2016, 12:14:42 UTC |
| 1563be0 | Thomas B. Mooney | 27 June 2016, 22:09:18 UTC | Get around docker_run.py's overzealous assuming we've got a TTY. | 27 June 2016, 22:09:18 UTC |
| 08f37c8 | Jason Walker | 27 June 2016, 20:13:21 UTC | Add test for presence of expected symlinks. | 27 June 2016, 20:13:21 UTC |
| 4d931cb | Susanna Kiwala | 27 June 2016, 20:05:32 UTC | Merge pull request #1442 from susannasiebert/clinseq_igv Use tumor_bam and normal_bam subroutines instead of RefAlign builds | 27 June 2016, 20:05:32 UTC |
| 3fe39e0 | Thomas B. Mooney | 27 June 2016, 18:59:32 UTC | Let's not hit home directories in this test. | 27 June 2016, 18:59:32 UTC |
| 58f1392 | Thomas B. Mooney | 27 June 2016, 15:16:05 UTC | Merge pull request #1475 from tmooney/better_processingprofile_denovoassembly_t_diffs Don't worry about matching queues and resource requests. | 27 June 2016, 15:16:05 UTC |
| 5021890 | Thomas B. Mooney | 27 June 2016, 15:15:57 UTC | Merge pull request #1474 from tmooney/better_model_rnaseq_t_diffs Better Model/RnaSeq.t Diffs | 27 June 2016, 15:15:57 UTC |
| 8985ba4 | Thomas B. Mooney | 27 June 2016, 13:00:17 UTC | Merge pull request #1465 from tmooney/remove_old_copynumber_tools Remove old CopyNumber tools that depend on volumes being retired. | 27 June 2016, 13:00:17 UTC |
| e8ad09a | Thomas B. Mooney | 23 June 2016, 22:11:34 UTC | Merge pull request #1471 from tmooney/feature_list_importer_strips_blank_lines FeatureList Import: Skip blank lines instead of crashing. | 23 June 2016, 22:11:34 UTC |
| c1bd277 | Jason Walker | 23 June 2016, 17:38:36 UTC | Merge pull request #1472 from acoffman/fix_clinseq_wgs_exome_check Only check for the annotated vcf if the build exists Merging for @acoffman | 23 June 2016, 17:38:36 UTC |
| 708ecce | Thomas B. Mooney | 23 June 2016, 14:44:46 UTC | Don't worry about matching queues and resource requests. | 23 June 2016, 14:44:46 UTC |
| 3e13af4 | Thomas B. Mooney | 23 June 2016, 14:17:05 UTC | Don't care what the resource requests are when doing the diffs. | 23 June 2016, 14:19:50 UTC |
| a16a0c8 | Thomas B. Mooney | 23 June 2016, 14:14:09 UTC | Don't care what the queues are when doing the diffs. | 23 June 2016, 14:14:09 UTC |
| 0eb42e5 | Thomas B. Mooney | 23 June 2016, 14:02:02 UTC | Stop notifying when apipe-builder uses the apipe queue. It's normal for that to happen these days. This effectively reverts commits: fc8f689d8a2e7db52cec37ea6c0992558e2367cc f04749e10c650ca8463ad5d3ec847b3ce0609140 | 23 June 2016, 14:04:24 UTC |
| 07d00f6 | Thomas B. Mooney | 23 June 2016, 13:58:03 UTC | Set LSB_SUB_ADDITIONAL when bsubbing if configured. | 23 June 2016, 13:58:03 UTC |
| c6845ac | Adam Coffman | 22 June 2016, 22:09:21 UTC | remove need for outer check and hash | 22 June 2016, 22:09:21 UTC |
| 251b903 | Adam Coffman | 22 June 2016, 21:28:26 UTC | only check for the annotated vcf if the build exists | 22 June 2016, 21:28:26 UTC |
| 226f545 | Thomas B. Mooney | 22 June 2016, 19:22:33 UTC | Merge pull request #1470 from tmooney/use_gdc_web_portal_instead_of_tcga_portal Use GDC Portal instead of TCGA Portal | 22 June 2016, 19:22:33 UTC |
| 2965c37 | Thomas B. Mooney | 22 June 2016, 18:49:01 UTC | FeatureList Import: Skip blank lines instead of crashing. | 22 June 2016, 18:49:01 UTC |
| b54d38a | APipe Tester | 22 June 2016, 12:17:51 UTC | Updated `gmt` tab completion. | 22 June 2016, 12:17:51 UTC |
| 5ca96d7 | APipe Tester | 22 June 2016, 12:15:28 UTC | Updated `genome` tab completion. | 22 June 2016, 12:15:28 UTC |
| 1619a92 | APipe Tester | 22 June 2016, 12:13:57 UTC | Updated class browser cache. | 22 June 2016, 12:13:57 UTC |
| 3e00c8f | Eddie Belter | 21 June 2016, 23:33:28 UTC | Merge pull request #1461 from ebelter/sx-trim-by-pos SX: Trim By Position | 21 June 2016, 23:33:28 UTC |
| d0d77b2 | Jason Walker | 21 June 2016, 20:06:35 UTC | Add index file extension to symlink target | 21 June 2016, 20:06:35 UTC |
| ba3bf6f | Eddie Belter | 21 June 2016, 19:58:36 UTC | Trim By Pos: end "end" support | 21 June 2016, 19:58:36 UTC |
| dfd26c2 | Thomas B. Mooney | 21 June 2016, 18:56:52 UTC | Add test for whether we found the result we wanted. | 21 June 2016, 18:59:36 UTC |
| 33bb414 | Thomas B. Mooney | 21 June 2016, 18:45:39 UTC | Convert to JSON on the fly. Maybe slower but far easier to understand! | 21 June 2016, 18:59:35 UTC |
| de30707 | Thomas B. Mooney | 21 June 2016, 18:23:18 UTC | Make Tier2 and Tier3 optional for benefit of ClinSeq. CreateMutationSpectrum runs this with only a Tier1 file. This implements the desired change in e99186dbc5d6e7865546afa8920b928f9624fdd8. | 21 June 2016, 18:23:18 UTC |
| 1a45ed6 | Thomas B. Mooney | 21 June 2016, 15:48:10 UTC | Sort to mimic ordering of results from TCGA portal. | 21 June 2016, 15:48:10 UTC |
