| 5096244 | Jason Walker | 27 May 2016, 20:04:17 UTC | Add a per-chromosome FASTA result. Add a Speedseq config file result that points at the per-chr FASTAs for each refseq build. | 27 May 2016, 20:04:17 UTC |
| 5bb8fcd | Jason Walker | 25 May 2016, 14:05:33 UTC | Merge pull request #1418 from jasonwalker80/ref_converter_chr2 Processed BED without chr substitution : Option #2 | 25 May 2016, 14:05:33 UTC |
| 76b52af | Susanna Kiwala | 25 May 2016, 14:00:53 UTC | Merge pull request #1423 from susannasiebert/clinseq_CreateMutationSpectrum Clinseq CreateMutationSpectrum uses Test Data | 25 May 2016, 14:00:53 UTC |
| bc65f6c | Thomas B. Mooney | 25 May 2016, 13:19:01 UTC | Merge pull request #1428 from tmooney/stop_using_server_dispatch Stop using "server_dispatch => 'inline'" feature. | 25 May 2016, 13:19:01 UTC |
| 4a0db5e | Thomas B. Mooney | 25 May 2016, 13:18:48 UTC | Merge pull request #1380 from tmooney/retire_phenotypecorrelation Remove "PhenotypeCorrelation" pipeline. | 25 May 2016, 13:18:48 UTC |
| d027ba1 | APipe Tester | 25 May 2016, 12:16:13 UTC | Updated `gmt` tab completion. | 25 May 2016, 12:16:13 UTC |
| 12b27d9 | APipe Tester | 25 May 2016, 12:15:29 UTC | Updated `genome` tab completion. | 25 May 2016, 12:15:29 UTC |
| 24d1d3a | Jason Walker | 24 May 2016, 19:07:00 UTC | Merge pull request #1417 from jasonwalker80/lsf_resource_review Review Variants LSF Resource | 24 May 2016, 19:07:00 UTC |
| d31b7b7 | Jason Walker | 24 May 2016, 17:49:39 UTC | Merge pull request #1410 from jasonwalker80/manta_sv_test_data New HCC1395 SV test data | 24 May 2016, 17:49:39 UTC |
| e90d8e7 | Jason Walker | 24 May 2016, 17:47:32 UTC | Merge pull request #1427 from jasonwalker80/speedseq_sv_verbose Add speedseq sv verbose argument. | 24 May 2016, 17:47:32 UTC |
| 844bc13 | Susanna Kiwala | 24 May 2016, 16:43:36 UTC | Get fasta path from reference directly instead of hard-coding it | 24 May 2016, 16:43:36 UTC |
| ce2e87f | APipe Tester | 24 May 2016, 12:17:01 UTC | Updated `gmt` tab completion. | 24 May 2016, 12:17:01 UTC |
| d3b4216 | APipe Tester | 24 May 2016, 12:16:19 UTC | Updated `genome` tab completion. | 24 May 2016, 12:16:19 UTC |
| 122b4f4 | APipe Tester | 24 May 2016, 12:14:45 UTC | Updated class browser cache. | 24 May 2016, 12:14:45 UTC |
| dee2536 | Thomas B. Mooney | 23 May 2016, 21:01:23 UTC | Stop using "server_dispatch => 'inline'" feature. The inline workflow_builder_backend takes care of most use cases. A future PR will remove this feature from Build entirely. | 23 May 2016, 21:01:23 UTC |
| a90ad3b | Jason Walker | 23 May 2016, 18:35:26 UTC | Update verbose doc. | 23 May 2016, 18:35:26 UTC |
| ca27b1c | Jason Walker | 23 May 2016, 14:44:06 UTC | Add speedseq sv verbose argument. | 23 May 2016, 14:44:06 UTC |
| 60e002e | Thomas B. Mooney | 23 May 2016, 14:17:18 UTC | Merge pull request #1386 from tmooney/dv2_polymutt_uses_workflowbuilder DV2 Polymutt uses WorkflowBuilder | 23 May 2016, 14:17:18 UTC |
| c0fe6d6 | sleongmgi | 23 May 2016, 14:11:58 UTC | Merge pull request #1425 from sleongmgi/sleong-lsb-sub-additional Add lsb sub additional etc spec | 23 May 2016, 14:11:58 UTC |
| d87b446 | Thomas B. Mooney | 23 May 2016, 14:00:11 UTC | Merge pull request #1399 from tmooney/smallrna_workflow_remove_extra_input_connections SmallRNA: Remove inputs that are already supplied via other steps. | 23 May 2016, 14:00:11 UTC |
| baca04c | Thomas B. Mooney | 23 May 2016, 13:59:54 UTC | Merge pull request #1388 from tmooney/parallel_blat_uses_workflowbuilder Remove Blat GMT Tree and Alignment Result | 23 May 2016, 13:59:54 UTC |
| 95a90c7 | Shin Leong | 19 May 2016, 16:50:05 UTC | set up the LSB_SUB_ADDITIONAL. | 19 May 2016, 16:50:05 UTC |
| de2caef | Shin Leong | 19 May 2016, 16:44:44 UTC | add lsb_sub_additonal spec to support docker. | 19 May 2016, 16:44:44 UTC |
| b0ea94c | APipe Tester | 19 May 2016, 12:18:03 UTC | Updated `genome` tab completion. | 19 May 2016, 12:18:03 UTC |
| ca95918 | APipe Tester | 19 May 2016, 12:16:34 UTC | Updated class browser cache. | 19 May 2016, 12:16:34 UTC |
| 8db4fc2 | Susanna Kiwala | 18 May 2016, 14:25:08 UTC | Merge pull request #1424 from susannasiebert/clinseq_ImportSnvsIndels Remove ClinSeq ImportSnvsIndels command | 18 May 2016, 14:25:08 UTC |
| b51e369 | Susanna Kiwala | 17 May 2016, 15:19:14 UTC | Remove ClinSeq ImportSnvsIndels command | 17 May 2016, 15:19:14 UTC |
| 5e45049 | Susanna Kiwala | 16 May 2016, 17:12:59 UTC | Merge pull request #1422 from susannasiebert/clinseq_summarizesvs ClinSeq SummarizeSvs uses test data for is test | 16 May 2016, 17:12:59 UTC |
| d873f70 | Susanna Kiwala | 13 May 2016, 17:41:09 UTC | ClinSeq CreateMutationSpectrum uses test data for its wgs test | 13 May 2016, 18:12:20 UTC |
| a46ed07 | Susanna Kiwala | 13 May 2016, 17:35:17 UTC | Remove stray breakpoints | 13 May 2016, 18:12:20 UTC |
| 9e0ee79 | Susanna Kiwala | 13 May 2016, 17:35:00 UTC | ClinSeq CreateMutationSpectrum uses test data for its exome test | 13 May 2016, 17:41:30 UTC |
| 64fa671 | Susanna Kiwala | 13 May 2016, 15:04:17 UTC | ClinSeq SummarizeSvs uses test data for is test | 13 May 2016, 17:18:01 UTC |
| a732aea | APipe Tester | 13 May 2016, 12:18:25 UTC | Updated `gmt` tab completion. | 13 May 2016, 12:18:25 UTC |
| d3b5c80 | APipe Tester | 13 May 2016, 12:17:39 UTC | Updated `genome` tab completion. | 13 May 2016, 12:17:39 UTC |
| 50e0186 | Thomas B. Mooney | 12 May 2016, 22:01:12 UTC | Merge pull request #1420 from tmooney/clinseq_modelsummary_test_uses_test_data ClinSeq ModelSummary test uses Test Data | 12 May 2016, 22:01:12 UTC |
| feafc43 | Thomas B. Mooney | 12 May 2016, 21:01:30 UTC | Switch result user/input creation to __define__. Some tests run UR::Context->commit(); which doesn't work if "real" objects have FKs to __defined__ ones. This makes sure all the descendents of our defined results are themselves __defined__ at cost of requiring knowledge of the implementation details of the results themselves. | 12 May 2016, 21:01:30 UTC |
| d264de8 | Thomas B. Mooney | 12 May 2016, 19:59:06 UTC | Pull package name into a variable. Use G:U:T to get the data_dir. | 12 May 2016, 19:59:06 UTC |
| 1665f2c | Thomas B. Mooney | 12 May 2016, 19:56:03 UTC | Switch test to use test data instead of a production model. | 12 May 2016, 19:56:03 UTC |
| e58023f | Thomas B. Mooney | 12 May 2016, 19:55:16 UTC | Add alignments to the RefAlign and RnaSeq builds in ClinSeq test data. | 12 May 2016, 19:55:16 UTC |
| b786fe3 | Thomas B. Mooney | 12 May 2016, 19:06:48 UTC | Remove "use" statement that precedes use_ok for same package. | 12 May 2016, 19:06:48 UTC |
| 11325d4 | Jason Walker | 12 May 2016, 18:46:24 UTC | Add option for stripping off the chr in processed_bed_file_content. | 12 May 2016, 18:46:24 UTC |
| 1125441 | Jason Walker | 12 May 2016, 18:19:40 UTC | Merge pull request #1414 from jasonwalker80/speedseq_params Add SpeedseqSv probability curves | 12 May 2016, 18:19:40 UTC |
| 96e7a19 | Jason Walker | 12 May 2016, 17:43:42 UTC | Add param to test the semi-colon separated parsing. | 12 May 2016, 17:43:42 UTC |
| a18ab4b | Susanna Kiwala | 12 May 2016, 16:55:52 UTC | Merge pull request #1413 from susannasiebert/interface_cleanup Use the subroutines in G::M::B::RunsDV2 instead of implementing our own | 12 May 2016, 16:55:52 UTC |
| a58277d | Jason Walker | 12 May 2016, 15:04:53 UTC | Make the review variants lsf resource configurable. | 12 May 2016, 15:04:53 UTC |
| 0667a17 | APipe Tester | 12 May 2016, 12:17:48 UTC | Updated `genome` tab completion. | 12 May 2016, 12:17:48 UTC |
| 754a16a | Susanna Kiwala | 11 May 2016, 20:13:21 UTC | Merge pull request #1415 from susannasiebert/blessed_build New ClinSeq blessed build | 11 May 2016, 20:13:21 UTC |
| 5684469 | Susanna Kiwala | 11 May 2016, 19:39:48 UTC | New ClinSeq blessed build | 11 May 2016, 19:39:48 UTC |
| 28d3c86 | Jason Walker | 11 May 2016, 19:39:16 UTC | remove inadvertent breakpoint | 11 May 2016, 19:39:16 UTC |
| 0130011 | Jason Walker | 11 May 2016, 19:17:28 UTC | Add support for -P param to speedseq sv. cleanup the variable and method names resolving tool parameters. | 11 May 2016, 19:17:28 UTC |
| a44e669 | Susanna Kiwala | 11 May 2016, 18:40:42 UTC | Clean up the snvs_annotated_variants_vcf_file since the annotated file is SomVar specific | 11 May 2016, 18:40:42 UTC |
| d106aeb | Susanna Kiwala | 11 May 2016, 18:06:44 UTC | Use the subroutines in G::M::B::RunsDV2 instead of implementing our own | 11 May 2016, 18:06:44 UTC |
| 0270bce | Jason Walker | 11 May 2016, 17:15:23 UTC | Merge pull request #1412 from jasonwalker80/vep_for_dog VEP for dog genome. | 11 May 2016, 17:15:23 UTC |
| cfafeba | Jason Walker | 11 May 2016, 16:41:09 UTC | Add dog reference as a valid value. | 11 May 2016, 16:41:09 UTC |
| b776c8e | Thomas B. Mooney | 11 May 2016, 15:09:09 UTC | Merge pull request #1406 from tmooney/remove_clinseq_originalscripts Remove ClinSeq OriginalScripts Directory | 11 May 2016, 15:09:09 UTC |
| 528608d | Jason Walker | 11 May 2016, 14:57:49 UTC | Add new HCC1395 test data that actually produces a DEL call with Manta. | 11 May 2016, 14:57:49 UTC |
| 2706cc6 | APipe Tester | 11 May 2016, 12:18:54 UTC | Updated `gmt` tab completion. | 11 May 2016, 12:18:54 UTC |
| 2648fd1 | APipe Tester | 11 May 2016, 12:18:11 UTC | Updated `genome` tab completion. | 11 May 2016, 12:18:11 UTC |
| 8a9b0a7 | APipe Tester | 11 May 2016, 12:16:37 UTC | Updated class browser cache. | 11 May 2016, 12:16:37 UTC |
| 549aab9 | Thomas B. Mooney | 10 May 2016, 21:39:44 UTC | Remove ClinSeq-specific parts of Command::Tester (This should probably be removed completely in a new PR!) | 10 May 2016, 21:39:44 UTC |
| a8ab88a | Thomas B. Mooney | 10 May 2016, 21:37:56 UTC | Remove old ClinSeq "OriginalScripts" directory. | 10 May 2016, 21:37:56 UTC |
| 8c20844 | Thomas B. Mooney | 10 May 2016, 21:00:08 UTC | Remove Utility::PSL that was used by old Blat tools. | 10 May 2016, 21:14:15 UTC |
| a730fda | Thomas B. Mooney | 10 May 2016, 20:59:41 UTC | Remove old Blat commands. | 10 May 2016, 21:14:15 UTC |
| 76632e9 | Thomas Mooney | 27 April 2016, 22:55:50 UTC | Convert "blat subjects" workflow to WorkflowBuilder. | 10 May 2016, 21:13:46 UTC |
| 7a5b3d7 | Thomas Mooney | 27 April 2016, 22:52:53 UTC | Remove commented-out code. | 10 May 2016, 21:13:46 UTC |
| a93f6ad | Thomas Mooney | 27 April 2016, 22:51:50 UTC | Remove lies and use Genome::Sys for the temp directory. | 10 May 2016, 21:13:45 UTC |
| d927593 | Thomas Mooney | 27 April 2016, 22:51:03 UTC | Remove strange .pl | 10 May 2016, 21:13:45 UTC |
| c19e90b | Thomas Mooney | 27 April 2016, 21:38:29 UTC | Use Genome::Sys->create_temp_directory for test location. That way we get all the benefits of using the built-in LSF tmpdir when this is bsubbed. | 10 May 2016, 21:13:45 UTC |
| 5420c13 | Thomas Mooney | 27 April 2016, 21:37:53 UTC | Convert to WorkflowBuilder. | 10 May 2016, 21:13:45 UTC |
| 8882b2f | Susanna Kiwala | 10 May 2016, 20:16:08 UTC | Merge pull request #1392 from susannasiebert/clinseq_somatic_interface Allow ClinSeq to also use Somatic Validation models as inputs | 10 May 2016, 20:16:08 UTC |
| 562e20d | Thomas B. Mooney | 10 May 2016, 20:10:40 UTC | Merge pull request #1405 from tmooney/copynumber_cnview_tests_use_test_cnv_data CopyNumber CnView: Use test CNV data. | 10 May 2016, 20:10:40 UTC |
| e467d39 | Thomas B. Mooney | 10 May 2016, 20:10:30 UTC | Merge pull request #1404 from tmooney/remove_somvar_compare_variants Remove SomticVariation Compare Variants. | 10 May 2016, 20:10:30 UTC |
| b60bbf0 | Thomas B. Mooney | 10 May 2016, 20:10:21 UTC | Merge pull request #1403 from tmooney/clinseq_summarizesnvs_test_uses_test_data ClinSeq SummarizeCnvs uses test data for its test. | 10 May 2016, 20:10:21 UTC |
| 88472ac | Thomas B. Mooney | 10 May 2016, 20:10:12 UTC | Merge pull request #1402 from tmooney/converge_summarizesnvindelreport_uses_test_data ClinSeq's SummarizeSnvIndel Converge Test Uses Test Data | 10 May 2016, 20:10:12 UTC |
| e0a15a1 | Thomas B. Mooney | 10 May 2016, 20:10:02 UTC | Merge pull request #1401 from tmooney/cufflinksde_converge_uses_test_data ClinSeq's Cufflinks Converge uses Test Data | 10 May 2016, 20:10:02 UTC |
| 9b2af1e | Eddie Belter | 10 May 2016, 18:25:51 UTC | Merge pull request #1398 from ebelter/split-by-scaffold SX: Split sequences by ns | 10 May 2016, 18:25:51 UTC |
| 8623ddb | Thomas B. Mooney | 10 May 2016, 18:22:22 UTC | Update test description--not from the DB anymore! | 10 May 2016, 18:22:22 UTC |
| 01d6152 | Thomas B. Mooney | 10 May 2016, 18:19:46 UTC | Use test CNV data. | 10 May 2016, 18:19:46 UTC |
| 4bf4581 | Thomas B. Mooney | 10 May 2016, 17:51:52 UTC | Remove SomticVariation Compare Variants. | 10 May 2016, 17:51:52 UTC |
| 17748a9 | Thomas B. Mooney | 10 May 2016, 17:40:12 UTC | ClinSeq SummarizeCnvs uses test data for its test. | 10 May 2016, 17:40:12 UTC |
| 9702ef6 | Thomas B. Mooney | 10 May 2016, 15:58:33 UTC | Update test to use test data instead of production data. | 10 May 2016, 15:58:33 UTC |
| 307e1cf | Thomas B. Mooney | 10 May 2016, 15:25:52 UTC | Sort so we get a consistent output result. | 10 May 2016, 15:25:52 UTC |
| 2f72c03 | Thomas B. Mooney | 10 May 2016, 15:25:26 UTC | Use fake builds for the test instead of relying on database data. | 10 May 2016, 15:25:26 UTC |
| 2594bc1 | Thomas B. Mooney | 10 May 2016, 13:15:24 UTC | Update expected test data. (Now with better directory naming!) | 10 May 2016, 15:15:30 UTC |
| d00f0ca | Thomas B. Mooney | 10 May 2016, 13:13:36 UTC | Extract a variable for the package name. | 10 May 2016, 13:13:36 UTC |
| 85f51a4 | Thomas B. Mooney | 10 May 2016, 13:10:54 UTC | Stop using the command we're about to "use_ok". | 10 May 2016, 13:10:54 UTC |
| 3848f82 | Eddie Belter | 09 May 2016, 20:39:33 UTC | Split qualities too | 09 May 2016, 20:39:33 UTC |
| 7559c15 | Eddie Belter | 09 May 2016, 20:39:18 UTC | Split qualities too | 09 May 2016, 20:39:18 UTC |
| 1a94725 | Eddie Belter | 09 May 2016, 20:13:58 UTC | Use subtest | 09 May 2016, 20:13:58 UTC |
| 7e78577 | Eddie Belter | 09 May 2016, 20:04:02 UTC | Use iterator style split function | 09 May 2016, 20:04:02 UTC |
| 4fd9a41 | APipe Tester | 09 May 2016, 20:01:04 UTC | Updated `gmt` tab completion. | 09 May 2016, 20:01:04 UTC |
| e850ab2 | APipe Tester | 09 May 2016, 19:58:39 UTC | Updated `genome` tab completion. | 09 May 2016, 19:58:39 UTC |
| 8609ce5 | APipe Tester | 09 May 2016, 19:52:58 UTC | Updated class browser cache. | 09 May 2016, 19:52:58 UTC |
| 7ba5aba | Thomas B. Mooney | 09 May 2016, 18:20:06 UTC | Merge pull request #1384 from tmooney/workflowbuilder_supports_nested_xml WorkflowBuilder supports references to other XML files | 09 May 2016, 18:20:06 UTC |
| 6fd1351 | Eddie Belter | 09 May 2016, 17:01:57 UTC | Use create temp dir | 09 May 2016, 17:01:57 UTC |
| 171b573 | Eddie Belter | 09 May 2016, 16:50:53 UTC | Split By Ns: immediately write split seqs | 09 May 2016, 16:50:53 UTC |
| 88c682b | Susanna Kiwala | 09 May 2016, 16:42:04 UTC | Update test db | 09 May 2016, 16:42:04 UTC |
| 098408f | Susanna Kiwala | 09 May 2016, 16:38:23 UTC | Fix a few more spots where we used to get properties via the model instead of the build | 09 May 2016, 16:38:23 UTC |
| 2b71455 | Susanna Kiwala | 09 May 2016, 16:37:58 UTC | Use fatal_message instead of die error_message | 09 May 2016, 16:37:58 UTC |
| aa86614 | Thomas B. Mooney | 09 May 2016, 13:47:18 UTC | Remove inputs that are really supplied via other steps. | 09 May 2016, 13:47:18 UTC |
