| ca7f6d0 | Eddie Belter | 03 June 2016, 20:42:40 UTC | Merge pull request #1447 from ebelter/sx-split-by-ns SX Split By Ns UPDATE | 03 June 2016, 20:42:40 UTC |
| 770835d | APipe Tester | 03 June 2016, 12:17:53 UTC | Updated `genome` tab completion. | 03 June 2016, 12:17:53 UTC |
| fe449ee | Thomas B. Mooney | 02 June 2016, 22:36:08 UTC | Merge pull request #1446 from tmooney/annotate_variants_has_lsf_resource Add a config variable for the LSF resource for annotation. | 02 June 2016, 22:36:08 UTC |
| 4336e4e | Thomas B. Mooney | 02 June 2016, 22:32:46 UTC | Merge pull request #1445 from tmooney/more_smallrna_workflow_fixes Remove more redundant workflow links from SmallRNAWorkflow. | 02 June 2016, 22:32:46 UTC |
| bbb6125 | Eddie Belter | 02 June 2016, 20:51:45 UTC | SX Split BY Ns: return gap info if requested | 02 June 2016, 20:56:23 UTC |
| a113a6b | Eddie Belter | 02 June 2016, 20:40:59 UTC | SX Split by Ns: accomodate string of Ns over regex max of 32767 | 02 June 2016, 20:40:59 UTC |
| 218835a | APipe Tester | 02 June 2016, 12:18:27 UTC | Updated `gmt` tab completion. | 02 June 2016, 12:18:27 UTC |
| 769f71c | APipe Tester | 02 June 2016, 12:17:43 UTC | Updated `genome` tab completion. | 02 June 2016, 12:17:43 UTC |
| 88ae8ce | APipe Tester | 02 June 2016, 12:16:12 UTC | Updated class browser cache. | 02 June 2016, 12:16:12 UTC |
| f7438e4 | Eddie Belter | 02 June 2016, 00:00:40 UTC | Split By Ns: convert to use iterator | 02 June 2016, 00:00:54 UTC |
| 90a8062 | Thomas B. Mooney | 01 June 2016, 20:15:55 UTC | Merge pull request #1429 from tmooney/remove_relationship_sequencing_qc Remove "sequencing-qc" tool and its corresponding result. | 01 June 2016, 20:15:55 UTC |
| a5848eb | Thomas B. Mooney | 01 June 2016, 20:04:40 UTC | Add a config variable for the LSF resource for annotation. | 01 June 2016, 20:04:40 UTC |
| d031872 | Thomas B. Mooney | 01 June 2016, 18:58:19 UTC | Merge pull request #1444 from tmooney/update_annotation_builds_for_some_tests Update annotation builds to some that exist. | 01 June 2016, 18:58:19 UTC |
| ae44b0c | Thomas B. Mooney | 01 June 2016, 18:18:35 UTC | Remove more redundant workflow links from SmallRNAWorkflow. | 01 June 2016, 18:18:35 UTC |
| d382d38 | APipe Tester | 01 June 2016, 12:15:11 UTC | Updated `genome` tab completion. | 01 June 2016, 12:15:11 UTC |
| 0a7cb78 | APipe Tester | 01 June 2016, 12:13:40 UTC | Updated class browser cache. | 01 June 2016, 12:13:40 UTC |
| a7eaa4f | Thomas B. Mooney | 31 May 2016, 22:58:19 UTC | Merge pull request #1379 from tmooney/remove_importedassembly Remove old "ImportedAssembly" pipeline. | 31 May 2016, 22:58:19 UTC |
| d8e4283 | Thomas B. Mooney | 31 May 2016, 21:39:26 UTC | Use test data instead of production data. | 31 May 2016, 21:39:26 UTC |
| 15f0f93 | Thomas B. Mooney | 31 May 2016, 17:43:42 UTC | Update annotation builds to some that exist. | 31 May 2016, 17:43:42 UTC |
| cca794b | Jason Walker | 31 May 2016, 16:14:54 UTC | Merge pull request #1443 from jasonwalker80/speedseq_sv_config Speedseq sv config file | 31 May 2016, 16:14:54 UTC |
| 2f1c279 | Thomas B. Mooney | 31 May 2016, 13:13:53 UTC | Merge pull request #1439 from tmooney/add_blessed_ssg_build Add a blessed SSG test build. | 31 May 2016, 13:13:53 UTC |
| 322b76d | Thomas B. Mooney | 31 May 2016, 13:13:30 UTC | Merge pull request #1431 from tmooney/ccsvcf_tests_use_inline_workflow CCSVCF tests use "inline" WorkflowBuilder backend instead of NO_LSF variable. | 31 May 2016, 13:13:30 UTC |
| 7979069 | Thomas B. Mooney | 31 May 2016, 13:13:20 UTC | Merge pull request #1432 from tmooney/build_start_test_doesnt_care_about_no_lsf_variable Don't worry about the value of NO_LSF variable in Build Start test. | 31 May 2016, 13:13:20 UTC |
| c017403 | Thomas B. Mooney | 31 May 2016, 13:13:06 UTC | Merge pull request #1430 from tmooney/dont_set_no_lsf_in_polymutt Don't set NO_LSF now that this doesn't run a workflow. | 31 May 2016, 13:13:06 UTC |
| 807a3f1 | Thomas B. Mooney | 31 May 2016, 13:12:47 UTC | Merge pull request #1426 from tmooney/annotation_data_no_longer_on_genome_disk Path for BER has moved. | 31 May 2016, 13:12:47 UTC |
| fcd2b23 | Thomas B. Mooney | 31 May 2016, 13:12:34 UTC | Merge pull request #1348 from tmooney/determine_error_handles_ptero DetermineError Handles PTero Builds | 31 May 2016, 13:12:34 UTC |
| 148d84c | Thomas B. Mooney | 31 May 2016, 13:12:21 UTC | Merge pull request #1416 from tmooney/better_intermediate_result_handling Better Intermediate Result Deletion | 31 May 2016, 13:12:21 UTC |
| cc41dc4 | Jason Walker | 27 May 2016, 20:15:59 UTC | Update the expected speedseq sv test files. | 27 May 2016, 20:15:59 UTC |
| 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 |
| 273e29c | Allison Penner Regier | 27 May 2016, 15:31:57 UTC | Merge pull request #1441 from apregier/speedseq_fix Only pass through boolean tool argument if true | 27 May 2016, 15:31:57 UTC |
| e6070cf | APipe Tester | 27 May 2016, 12:18:58 UTC | Updated `gmt` tab completion. | 27 May 2016, 12:18:58 UTC |
| 70c038c | APipe Tester | 27 May 2016, 12:18:17 UTC | Updated `genome` tab completion. | 27 May 2016, 12:18:17 UTC |
| 633f95c | APipe Tester | 27 May 2016, 12:16:46 UTC | Updated class browser cache. | 27 May 2016, 12:16:46 UTC |
| 92cefc0 | Thomas B. Mooney | 26 May 2016, 22:19:27 UTC | Merge pull request #1436 from tmooney/remove_germline_burden_analysis Remove old workflow for Burden Analysis. | 26 May 2016, 22:19:27 UTC |
| 14060e1 | Thomas B. Mooney | 26 May 2016, 22:19:16 UTC | Merge pull request #1438 from tmooney/remove_bmr_submit_commands Remove BMR Submit commands. | 26 May 2016, 22:19:16 UTC |
| 8f93377 | Thomas B. Mooney | 26 May 2016, 22:19:04 UTC | Merge pull request #1437 from tmooney/remove_runvarscanvalidation_command Remove command to manually run `gmt varscan validation` on a build. | 26 May 2016, 22:19:04 UTC |
| 6d50e7e | apregier | 26 May 2016, 20:39:15 UTC | Consolidate type logic | 26 May 2016, 20:39:15 UTC |
| a0715c6 | Thomas B. Mooney | 26 May 2016, 20:27:12 UTC | Merge pull request #1434 from tmooney/stop_using_workflow_in_safevcfmerge Remove unused includes in SafeVcfMerge. | 26 May 2016, 20:27:12 UTC |
| ecdf7bd | apregier | 26 May 2016, 20:02:26 UTC | Only pass through boolean tool argument if true Otherwise just pass an empty string | 26 May 2016, 20:02:26 UTC |
| 0864225 | Thomas B. Mooney | 26 May 2016, 19:09:11 UTC | Merge pull request #1440 from tmooney/lsb_sub_additional_needs_to_happen_sooner LSB_SUB_ADDITIONAL needs to be set sooner. | 26 May 2016, 19:09:11 UTC |
| dfd766d | Thomas B. Mooney | 26 May 2016, 16:44:19 UTC | This will always be defined (default is ""), so test if it's true. | 26 May 2016, 16:44:19 UTC |
| a64ab36 | Thomas B. Mooney | 26 May 2016, 15:49:54 UTC | Set LSB_SUB_ADDITIONAL when constructing the execute job for PTero. | 26 May 2016, 16:09:41 UTC |
| c370085 | Thomas B. Mooney | 26 May 2016, 15:27:41 UTC | Revert "set up the LSB_SUB_ADDITIONAL." This reverts commit 95a90c7af9450cc85cf7fbe0f6b500020e4aafd3. This is too late for this variable to be set, as this is the command that is bsubbed rather than the thing doing the submission. | 26 May 2016, 15:27:41 UTC |
| 29cdec9 | Thomas B. Mooney | 26 May 2016, 13:56:32 UTC | Add a blessed SSG build for testing. | 26 May 2016, 13:56:32 UTC |
| 00a6f2e | APipe Tester | 26 May 2016, 12:18:46 UTC | Updated `gmt` tab completion. | 26 May 2016, 12:18:46 UTC |
| aaf2e79 | APipe Tester | 26 May 2016, 12:18:00 UTC | Updated `genome` tab completion. | 26 May 2016, 12:18:00 UTC |
| ae0b3f1 | APipe Tester | 26 May 2016, 12:16:27 UTC | Updated class browser cache. | 26 May 2016, 12:16:27 UTC |
| 9d1abe8 | Thomas B. Mooney | 25 May 2016, 21:58:51 UTC | Remove BMR Submit commands. These are wrappers that `bsub` other commands. | 25 May 2016, 21:58:51 UTC |
| 339b20e | Thomas B. Mooney | 25 May 2016, 21:33:12 UTC | Remove command to manually run varscan validation on a build. Validation is available as a DV2 tool for use in builds. | 25 May 2016, 21:33:12 UTC |
| 3b44d94 | Thomas B. Mooney | 25 May 2016, 21:20:07 UTC | Remove old workflow for Burden Analysis. This had two versions: one using Workflow and one using a bare `bsub`. We're trying to eliminate both things in the codebase, so this PR proposes removing the tools rather than writing a third, WorkflowBuilder-based version. | 25 May 2016, 21:20:07 UTC |
| 7ed7b22 | Thomas B. Mooney | 25 May 2016, 20:25:35 UTC | Remove unused includes. These should have been removed as part of #1358. | 25 May 2016, 20:25:35 UTC |
| a6fc179 | Thomas B. Mooney | 25 May 2016, 17:47:05 UTC | Don't worry about the value of NO_LSF variable. | 25 May 2016, 17:47:05 UTC |
| 3de0dd2 | Thomas B. Mooney | 25 May 2016, 17:42:11 UTC | Use "inline" workflowbuild backend instead of NO_LSF variable. | 25 May 2016, 17:42:11 UTC |
| 3a49574 | Thomas B. Mooney | 25 May 2016, 17:32:13 UTC | Don't set NO_LSF now that this doesn't run a workflow. | 25 May 2016, 17:32:13 UTC |
| 227c12a | Thomas B. Mooney | 25 May 2016, 17:28:13 UTC | Remove "sequencing-qc" tool and its corresponding result. This is another old tool that uses old Workflow. Removal is offered here as an alternative to updating it to WorkflowBuilder. | 25 May 2016, 17:28:13 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 |
| 35f28c4 | Thomas B. Mooney | 23 May 2016, 15:19:23 UTC | Path for BER has moved. These modules are slated for eventual removal... but the contents of /gscmnt/gc9002/ are slated for earlier removal than that. | 23 May 2016, 15:19:23 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 |
