| 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 |
| 034be20 | Thomas B. Mooney | 28 June 2016, 22:28:49 UTC | Convert MC16s workflow generation to WorkflowBuilder. | 28 June 2016, 22:28:49 UTC |
| 9739aab | Thomas B. Mooney | 28 June 2016, 21:26:42 UTC | Resolve a WorkflowBuilder object instead of a Workflow Operation. | 28 June 2016, 21:26:42 UTC |
| d675a0c | Thomas B. Mooney | 28 June 2016, 21:23:26 UTC | Remove unfinished thought. | 28 June 2016, 21:23:26 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 |
| abd45a4 | Thomas B. Mooney | 21 June 2016, 15:18:58 UTC | Updates to use the GDC portal instead of the TCGA portal. | 21 June 2016, 15:47:54 UTC |
| cc8ebf1 | Feiyu Du | 21 June 2016, 15:20:20 UTC | Merge pull request #1463 from dufeiyu/lsf Increase annotation memory usage from 4g to 8g | 21 June 2016, 15:20:20 UTC |
| 481155c | Jason Walker | 21 June 2016, 15:14:10 UTC | use Genome::Sys->create_symlink | 21 June 2016, 15:14:10 UTC |
| 7fac7e6 | Jason Walker | 21 June 2016, 15:12:48 UTC | no need to chdir | 21 June 2016, 15:12:48 UTC |
| 0ed6273 | Jason Walker | 21 June 2016, 15:00:29 UTC | make a relative symlink for the final expected DV2 expected VCF path. | 21 June 2016, 15:00:29 UTC |
| 4c1198e | Thomas B. Mooney | 20 June 2016, 21:45:12 UTC | Remove example on disk being retired. | 20 June 2016, 22:22:10 UTC |
| 7630458 | Thomas B. Mooney | 20 June 2016, 21:36:31 UTC | Remove commented-out references to sata locations. | 20 June 2016, 22:22:10 UTC |
| fb64228 | Thomas B. Mooney | 20 June 2016, 21:34:25 UTC | Remove support for non-standard mus37wOSK reference. It could be imported as a ReferenceSequence if someone needs it! | 20 June 2016, 22:22:10 UTC |
| b05165e | Thomas B. Mooney | 20 June 2016, 21:32:31 UTC | Remove cut section with command line on it. | 20 June 2016, 22:22:09 UTC |
| f698477 | Thomas B. Mooney | 20 June 2016, 21:31:48 UTC | Remove example on sata135. | 20 June 2016, 22:22:09 UTC |
| 4d893a1 | Thomas B. Mooney | 20 June 2016, 21:30:20 UTC | Remove references to soon-to-be-retired volume, sata809. | 20 June 2016, 22:22:09 UTC |
| a4744ef | Thomas B. Mooney | 20 June 2016, 21:27:52 UTC | Remove example on deprecated volume. | 20 June 2016, 22:22:09 UTC |
| a3870c0 | Thomas B. Mooney | 20 June 2016, 21:25:29 UTC | Remove commented-out references to sata831. | 20 June 2016, 22:22:08 UTC |
| bec768d | Thomas B. Mooney | 20 June 2016, 21:20:07 UTC | Remove commented-out references to sata921. | 20 June 2016, 22:22:08 UTC |
| 32fc477 | Thomas B. Mooney | 20 June 2016, 21:00:14 UTC | Whitespace. | 20 June 2016, 22:22:03 UTC |
| 3990796 | Thomas B. Mooney | 20 June 2016, 20:59:25 UTC | Remove defaults on deprecated disk. | 20 June 2016, 22:21:16 UTC |
| bd1be4f | Thomas B. Mooney | 20 June 2016, 21:59:28 UTC | Remove old plotSV.pl script. It has references to both homedirs and a volume being retired. | 20 June 2016, 21:59:28 UTC |
| 5cca89a | Thomas B. Mooney | 20 June 2016, 21:54:15 UTC | Remove old `gmt capture process-models`. It depended on a tool removed in d08d6b84701442346ccfd9076c1be997c608732b in 2013, so it's unlikely it's still used :) | 20 June 2016, 21:54:15 UTC |
| c5c63b0 | Thomas B. Mooney | 20 June 2016, 21:50:47 UTC | Remove old CopyNumber tools that depend on volumes being retired. | 20 June 2016, 21:50:47 UTC |
| 303f1b6 | Thomas B. Mooney | 20 June 2016, 20:34:37 UTC | Put the true value at the end where it belongs. | 20 June 2016, 21:38:25 UTC |
| ed71992 | Thomas B. Mooney | 20 June 2016, 20:33:52 UTC | Whitespace. | 20 June 2016, 21:38:25 UTC |
| c02816a | Thomas B. Mooney | 20 June 2016, 20:32:58 UTC | Use dummy example paths. | 20 June 2016, 21:38:25 UTC |
| 950b12f | Thomas B. Mooney | 20 June 2016, 20:31:45 UTC | Remove commented out command-line example. | 20 June 2016, 21:38:25 UTC |
| 5f05d9b | Feiyu Du | 20 June 2016, 20:59:25 UTC | Double the memory usage | 20 June 2016, 20:59:25 UTC |
| 5a1ab23 | Thomas B. Mooney | 20 June 2016, 20:30:31 UTC | Remove example on deprecated volume. Examples should be in "example_values" anyway! | 20 June 2016, 20:30:31 UTC |
| d85dd24 | Thomas B. Mooney | 20 June 2016, 20:29:58 UTC | Whitespace. | 20 June 2016, 20:29:58 UTC |
| 8c08d2a | Thomas B. Mooney | 20 June 2016, 20:28:42 UTC | Remove unused default. (The parameter was already required.) | 20 June 2016, 20:28:42 UTC |
| 36f4b71 | Thomas B. Mooney | 20 June 2016, 19:40:58 UTC | Remove commented-out debug lines. | 20 June 2016, 19:40:58 UTC |
| 4fa90b8 | Thomas B. Mooney | 20 June 2016, 19:40:17 UTC | Whitespace. | 20 June 2016, 19:40:17 UTC |
| 6eb563a | Thomas B. Mooney | 20 June 2016, 15:53:59 UTC | Specify an LSF queue for VerifyBam. | 20 June 2016, 15:53:59 UTC |
| 453031e | Thomas B. Mooney | 20 June 2016, 15:53:24 UTC | Specify an LSF queue for Mutect jobs. | 20 June 2016, 15:53:24 UTC |
| 1c89495 | APipe Tester | 17 June 2016, 12:18:24 UTC | Updated `genome` tab completion. | 17 June 2016, 12:18:24 UTC |
| 9b94526 | Eddie Belter | 16 June 2016, 22:34:54 UTC | Trim By Pos: only add last keep set if there is something to keep | 16 June 2016, 22:34:54 UTC |
| f7e7576 | Eddie Belter | 16 June 2016, 22:33:11 UTC | Trim By Pos: clarify return from keep positions, removing the keep ALL indicator | 16 June 2016, 22:33:11 UTC |
| 9b6c456 | Eddie Belter | 16 June 2016, 22:22:05 UTC | Trim By Pos: add position file format doc | 16 June 2016, 22:22:05 UTC |
| c3b127c | Feiyu Du | 16 June 2016, 15:03:42 UTC | Merge pull request #1458 from dufeiyu/trio Make trio wrapper work on somatic cases | 16 June 2016, 15:03:42 UTC |
| 72a5757 | Thomas B. Mooney | 15 June 2016, 17:40:18 UTC | Use WorkflowBuilder to construct build workflow. | 15 June 2016, 17:40:18 UTC |
| c7461b5 | Thomas B. Mooney | 15 June 2016, 17:39:53 UTC | Update documentation to reflect that we use WorkflowBuilder. Not sure why the user cares either way, but there it is! | 15 June 2016, 17:39:53 UTC |
| c099efb | Eddie Belter | 14 June 2016, 22:38:46 UTC | Trim By Pos: execute | 14 June 2016, 22:38:46 UTC |
| fdc3802 | Eddie Belter | 14 June 2016, 22:17:36 UTC | Trim By Pos: update test data | 14 June 2016, 22:28:53 UTC |
| 7ba960a | APipe Tester | 14 June 2016, 12:20:51 UTC | Updated `gmt` tab completion. | 14 June 2016, 12:20:51 UTC |
| c6c18e7 | APipe Tester | 14 June 2016, 12:20:06 UTC | Updated `genome` tab completion. | 14 June 2016, 12:20:06 UTC |
