| 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 |
| 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 |
| 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 |
| 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 |
| d794e97 | Thomas B. Mooney | 09 May 2016, 13:35:44 UTC | Merge pull request #1387 from tmooney/remove_weird_move_alignment_directory_command Remove obsolete "MoveAlignmentDirectory" command. | 09 May 2016, 13:35:44 UTC |
| e4ecbd2 | Thomas B. Mooney | 09 May 2016, 13:35:14 UTC | Merge pull request #1383 from tmooney/genotypemicroarray_test_doesnt_use_workflowsimple Remove unused include in GenotypeMicroarray.t | 09 May 2016, 13:35:14 UTC |
| 47e0157 | Thomas B. Mooney | 09 May 2016, 13:35:00 UTC | Merge pull request #1382 from tmooney/remove_blastx_parallel Remove "parallel" blastx tool. | 09 May 2016, 13:35:00 UTC |
| a79e2b7 | Thomas B. Mooney | 09 May 2016, 13:34:19 UTC | Merge pull request #1360 from tmooney/remove_parallel_annotator Remove Parallel Annotator. | 09 May 2016, 13:34:19 UTC |
| 645534f | Thomas B. Mooney | 09 May 2016, 13:34:04 UTC | Merge pull request #1359 from tmooney/remove_parallel_refcov Remove old "parallel ref-cov". | 09 May 2016, 13:34:04 UTC |
| a6bfaf0 | Thomas B. Mooney | 09 May 2016, 13:33:43 UTC | Merge pull request #1358 from tmooney/safe_vcf_merge_uses_workflowbuilder Use WorkflowBuilder to make SafeVCFMerge workflow. | 09 May 2016, 13:33:43 UTC |
| 00c4fc6 | Thomas B. Mooney | 09 May 2016, 13:33:23 UTC | Merge pull request #1395 from tmooney/vep_typos_fo_potput Fix some typos in documentation of Ensembl annotation runner. | 09 May 2016, 13:33:23 UTC |
| 5a0821b | Susanna Kiwala | 06 May 2016, 18:36:29 UTC | Run AnnotateSnvsVcf step as part of ClinSeq workflow | 06 May 2016, 18:36:29 UTC |
| 9c002ce | Susanna Kiwala | 06 May 2016, 15:02:26 UTC | Have AnnotateSnvsVcf take a somatic build as an input, not the vcf | 06 May 2016, 15:24:46 UTC |
| 6688d36 | Susanna Kiwala | 06 May 2016, 14:47:00 UTC | Revert "Rename class" This reverts commit 13d3b4b2e6bbb3397b4ed89a0d8d8724817fdd62. | 06 May 2016, 14:47:00 UTC |
| 74d7019 | Susanna Kiwala | 06 May 2016, 14:21:14 UTC | Merge branch 'master' of https://github.com/genome/genome into clinseq_somatic_interface | 06 May 2016, 14:21:14 UTC |
| 554e42d | Susanna Kiwala | 06 May 2016, 14:20:32 UTC | Merge pull request #1397 from susannasiebert/vcf_annotate_sr A new ClinSeq command and software result for annotating snvs vcf file | 06 May 2016, 14:20:32 UTC |
| b446a14 | Eddie Belter | 05 May 2016, 21:47:01 UTC | Split by this many or more ns | 05 May 2016, 21:47:01 UTC |
| b731655 | Eddie Belter | 05 May 2016, 21:24:12 UTC | Split sequences by ns | 05 May 2016, 21:24:12 UTC |
| 13d3b4b | Susanna Kiwala | 05 May 2016, 19:49:27 UTC | Rename class | 05 May 2016, 19:49:27 UTC |
| e0974dd | Thomas B. Mooney | 05 May 2016, 19:42:15 UTC | Merge pull request #1334 from tmooney/instrumentdata_import_uses_workflowbuilder_inline Use the new execute_inline for DAG instead of relying on Workflow. | 05 May 2016, 19:42:15 UTC |
| 8b1eb8c | Thomas B. Mooney | 05 May 2016, 19:41:52 UTC | Merge pull request #1324 from tmooney/sata420_isnt_real Remove references to sata420. | 05 May 2016, 19:41:52 UTC |
| 05c3504 | Thomas B. Mooney | 05 May 2016, 19:41:35 UTC | Merge pull request #1317 from tmooney/ptero_execution_info A Command to Get Information about a PTero Execution. | 05 May 2016, 19:41:35 UTC |
| 009140b | Jason Walker | 05 May 2016, 19:37:19 UTC | Merge pull request #1389 from jasonwalker80/manta_dv2 Manta DV2 Detector | 05 May 2016, 19:37:19 UTC |
| b8403e1 | Thomas B. Mooney | 05 May 2016, 19:21:26 UTC | Merge pull request #1300 from tmooney/ssg_can_symlink_results SingleSampleGenotype Can Be Checked Out; Uses Said Checkout for Diffs | 05 May 2016, 19:21:26 UTC |
| fe5f271 | Susanna Kiwala | 05 May 2016, 18:49:01 UTC | Make info_fields optional | 05 May 2016, 18:49:01 UTC |
| 3703f97 | Susanna Kiwala | 05 May 2016, 18:17:42 UTC | Name the output file the same as the input file annotate is an overloaded term | 05 May 2016, 18:17:42 UTC |
| 4a753da | Susanna Kiwala | 05 May 2016, 15:11:14 UTC | ClinSeq command and software result for annotating snvs vcf file | 05 May 2016, 15:11:14 UTC |
| ccf71f5 | Susanna Kiwala | 05 May 2016, 15:10:38 UTC | Fix bug in the use_bgzip option in the joinx vcf-annotate wrapper | 05 May 2016, 15:10:38 UTC |
| 7665def | sleongmgi | 04 May 2016, 18:05:35 UTC | Merge pull request #1396 from sleongmgi/sleong-add-message-to-test put an message because it might cause error if it is only one test. | 04 May 2016, 18:05:35 UTC |
| a2c3751 | Shin Leong | 04 May 2016, 17:55:02 UTC | remove the comment and add the intention to the old comment. | 04 May 2016, 17:55:02 UTC |
| 0abb090 | Shin Leong | 04 May 2016, 17:20:54 UTC | put an message because it might cause error if it is only one test. | 04 May 2016, 17:20:54 UTC |
| 51b108f | Jason Walker | 04 May 2016, 15:03:32 UTC | Use Path::Class to resolve relative path rather than regex. | 04 May 2016, 15:03:32 UTC |
| 6cd45bf | Thomas B. Mooney | 03 May 2016, 21:41:56 UTC | s/fo/of/ and s/potput/output/. | 03 May 2016, 21:41:56 UTC |
| f7b69e7 | Susanna Kiwala | 03 May 2016, 18:16:40 UTC | Update test db | 03 May 2016, 18:16:40 UTC |
| fcb067d | Susanna Kiwala | 03 May 2016, 17:17:09 UTC | Rework how microarray builds are retrieved from ClinSeq builds | 03 May 2016, 17:47:15 UTC |
| 48cdfce | Susanna Kiwala | 03 May 2016, 16:47:00 UTC | Use fatal_message | 03 May 2016, 17:47:15 UTC |
| 8bd2611 | Susanna Kiwala | 03 May 2016, 16:46:16 UTC | Use SomaticInterface | 03 May 2016, 17:47:14 UTC |
| 0734d88 | Susanna Kiwala | 03 May 2016, 16:46:00 UTC | Fix typos | 03 May 2016, 17:47:14 UTC |
| 92dddf4 | Susanna Kiwala | 03 May 2016, 16:45:39 UTC | Fix logic to determine individual | 03 May 2016, 17:47:14 UTC |
| 8432277 | Susanna Kiwala | 03 May 2016, 16:44:53 UTC | clean up _input_models and input_builds subroutines | 03 May 2016, 17:47:13 UTC |
| 8311ba2 | Susanna Kiwala | 03 May 2016, 16:43:42 UTC | use File::Spec->join | 03 May 2016, 17:47:13 UTC |
| dcb72a7 | Thomas B. Mooney | 03 May 2016, 13:58:47 UTC | Merge pull request #1393 from tmooney/quiet_ssg_listoutputfiles_single_use_warning Quiet variable use warning in SSG ListOutputFiles test. | 03 May 2016, 13:58:47 UTC |
| aacd306 | sleongmgi | 03 May 2016, 13:58:33 UTC | Merge pull request #1394 from sleongmgi/sleong-redirect-standard-out-to-dev-null Redirect the standard output and error to the /dev/null. | 03 May 2016, 13:58:33 UTC |
| a0e3287 | Shin Leong | 03 May 2016, 12:32:18 UTC | Redirect the standard output and error to the /dev/null. Otherwise, the standard output will interfere with the TAP output. | 03 May 2016, 12:32:18 UTC |
| 6e8e57f | Jason Walker | 02 May 2016, 21:36:05 UTC | Move the substitution into the if condition since it returns true if there is a match. | 02 May 2016, 21:36:05 UTC |
| 542ecfe | Jason Walker | 02 May 2016, 19:09:52 UTC | spelling correction | 02 May 2016, 19:09:52 UTC |
| d381467 | Jason Walker | 02 May 2016, 18:42:08 UTC | Update all directory accessors to use output_directory instead of _temp_staging_directory since the Dispatcher never uses a staging directory at all. | 02 May 2016, 18:42:08 UTC |
| 41328ba | Jason Walker | 02 May 2016, 15:31:29 UTC | Convert all _temp_staging_directory paths and symlinks to use File::Spec->join | 02 May 2016, 15:31:29 UTC |
| 98c9e8f | Thomas B. Mooney | 02 May 2016, 13:30:05 UTC | Quiet warning for global var used only once by using a lexical twice. | 02 May 2016, 13:30:05 UTC |
| 455b4f0 | Jason Walker | 29 April 2016, 19:58:59 UTC | Use shellwords rather than split on whitespace. | 29 April 2016, 19:58:59 UTC |
| e180181 | Jason Walker | 29 April 2016, 19:45:02 UTC | Use _temp_staging_directory rather than output_directory since they are the same as set in create_temp_directories. Only return a relative path if it is indeed under the _temp_staging_directory, otherwise return undef. | 29 April 2016, 19:45:02 UTC |
| 02b7d51 | Jason Walker | 29 April 2016, 18:46:28 UTC | Update the RAM to account for ~2GB per Manta workflow slot. | 29 April 2016, 18:46:28 UTC |
| 25a6e4b | Jason Walker | 29 April 2016, 17:02:12 UTC | in class definition, set the config_file as a param rather than input. | 29 April 2016, 17:02:12 UTC |
| 2d59c96 | Jason Walker | 29 April 2016, 17:01:21 UTC | Derefrencing hash ref until a different solution is found for parsing params. | 29 April 2016, 17:01:21 UTC |
| 7f3d911 | Jason Walker | 29 April 2016, 16:46:44 UTC | Missing full path files are not fatal for snv and indel. | 29 April 2016, 16:46:44 UTC |
| c90881d | Susanna Kiwala | 28 April 2016, 15:58:48 UTC | Fix missing workflow inputs | 29 April 2016, 15:01:27 UTC |
| 8633e90 | Jason Walker | 02 March 2016, 19:27:26 UTC | Required changes for exome CNV to complete Cnmops | 29 April 2016, 15:01:27 UTC |
| 7511998 | Susanna Kiwala | 25 April 2016, 18:18:18 UTC | Update test db | 29 April 2016, 15:01:26 UTC |
| 3b62ec4 | Susanna Kiwala | 25 April 2016, 18:08:41 UTC | Allow SomaticValidation builds as inputs to the ClinSeq pipeline | 29 April 2016, 15:01:26 UTC |
| e4bcee0 | Susanna Kiwala | 25 April 2016, 14:30:41 UTC | Implement a ran_copycat subroutine for somatic builds | 29 April 2016, 15:01:26 UTC |
| 845621c | Susanna Kiwala | 25 April 2016, 14:28:24 UTC | Implement a has_microarray_build subroutine for somatic builds | 29 April 2016, 15:01:26 UTC |
| 39edda0 | Susanna Kiwala | 25 April 2016, 14:27:34 UTC | Implement a `individual` subroutine for somatic builds | 29 April 2016, 15:01:26 UTC |
| d152396 | Susanna Kiwala | 22 April 2016, 19:19:19 UTC | Minor refactor of CreateMutationSpectrum | 29 April 2016, 15:01:26 UTC |
| b125cb7 | Susanna Kiwala | 21 April 2016, 17:16:10 UTC | Refactor GetVariantSources | 29 April 2016, 15:01:25 UTC |
