| e2d860c | Eddie Belter | 14 April 2015, 18:00:45 UTC | Merge pull request #659 from ebelter/instdata3 InstData Import: move setting original_data_path and do not set if exists | 14 April 2015, 18:00:45 UTC |
| 916dedf | Nathaniel Nutter | 14 April 2015, 17:18:22 UTC | Merge pull request #651 from nnutter/carp Genome::Carp | 14 April 2015, 17:18:22 UTC |
| 6c7741c | Allison Penner Regier | 14 April 2015, 17:18:13 UTC | Merge pull request #656 from tmooney/listing_results_in_void_context Include the LQ results in the array so they get linked to the build | 14 April 2015, 17:18:13 UTC |
| 93afdb1 | Nathaniel Nutter | 14 April 2015, 17:17:09 UTC | Merge pull request #653 from nnutter/cnv reserve 8 GB memory for ClinSeq's MicroarrayCnv | 14 April 2015, 17:17:09 UTC |
| 4086ece | Adam Coffman | 14 April 2015, 16:51:57 UTC | Merge pull request #525 from gschang/master New Genome::Model::Tools::Analysis::Coverage::CoveragePlot added | 14 April 2015, 16:51:57 UTC |
| 6b45bb6 | Eddie Belter | 13 April 2015, 23:08:40 UTC | InstData Import: move setting original_data_path and do not set if exists | 13 April 2015, 23:08:40 UTC |
| 8e8e92c | Thomas Mooney | 13 April 2015, 21:57:06 UTC | Get all the results. | 13 April 2015, 21:57:06 UTC |
| d758002 | Nathaniel Nutter | 13 April 2015, 20:11:48 UTC | rename test | 13 April 2015, 20:13:40 UTC |
| d9e7cf6 | Nathaniel Nutter | 13 April 2015, 20:09:35 UTC | add test to make sure methods are correctly mimicked | 13 April 2015, 20:13:38 UTC |
| aed98ff | Nathaniel Nutter | 13 April 2015, 20:08:19 UTC | fix CarpLevel at zero to mimic die/warn when it has been set by caller | 13 April 2015, 20:08:19 UTC |
| 16e558f | Nathaniel Nutter | 13 April 2015, 20:07:59 UTC | deduplicate dief/warnf | 13 April 2015, 20:07:59 UTC |
| d34b266 | Nathaniel Nutter | 13 April 2015, 20:07:21 UTC | increment CarpLevel instead of fixing at one | 13 April 2015, 20:07:21 UTC |
| 751399a | Nathaniel Nutter | 13 April 2015, 16:14:11 UTC | reserve 8 GB memory for ClinSeq's MicroarrayCnv The MRS1 were failing due to reaching the default memory limit of 4 GB. As a quick fix I increased memory to 16 GB and the models were run but only consumed about 6.5 GB so for this change I've limited the reservation to 8 GB. See [RT#105133][1] for additional context. [1]: https://rt.gsc.wustl.edu/Ticket/Display.html?id=105133 | 13 April 2015, 16:14:11 UTC |
| 4734a77 | Nathaniel Nutter | 13 April 2015, 16:01:08 UTC | Merge pull request #650 from nnutter/genome-env can't show MODULE_PATH when it's empty | 13 April 2015, 16:01:08 UTC |
| 929ec81 | Eddie Belter | 11 April 2015, 00:05:43 UTC | Merge pull request #649 from ebelter/instdata-import InstData Import: remove support for direct interaction with cghub | 11 April 2015, 00:05:43 UTC |
| 0a63296 | Nathaniel Nutter | 06 April 2015, 17:37:51 UTC | add Genome::Carp | 10 April 2015, 20:17:43 UTC |
| 1f0d563 | Nathaniel Nutter | 10 April 2015, 18:19:11 UTC | can't show MODULE_PATH when it's empty | 10 April 2015, 20:16:34 UTC |
| 0b046de | Eddie Belter | 10 April 2015, 18:07:53 UTC | InstData Import: remove support for direct interaction with cghub | 10 April 2015, 18:07:53 UTC |
| 7003fd3 | Allison Penner Regier | 10 April 2015, 15:04:10 UTC | Merge pull request #647 from apregier/limit_get_merged_results Limit merged results to ones that match all params | 10 April 2015, 15:04:10 UTC |
| 4365b2b | Ian Ferguson | 09 April 2015, 21:36:12 UTC | Merge pull request #622 from iferguson90/check-illumina-directory Update GMT::Picard::CheckIlluminaDirectory | 09 April 2015, 21:36:12 UTC |
| 679cb7d | Gabriel Sanderson | 09 April 2015, 19:04:14 UTC | Merge pull request #613 from gsanders/bam_accessor Refactor revivified_alignment_bam_file_paths to handle its own tempdir. | 09 April 2015, 19:04:14 UTC |
| 6e626b2 | apregier | 09 April 2015, 18:09:18 UTC | Evaluate with a boolexpr instead of limiting the query This speeds things up enormously | 09 April 2015, 18:09:18 UTC |
| 3ec02f6 | apregier | 09 April 2015, 17:34:34 UTC | Actually get the params | 09 April 2015, 17:34:34 UTC |
| 44c9fad | apregier | 09 April 2015, 13:52:37 UTC | Limit merged results to ones that match all params | 09 April 2015, 13:52:37 UTC |
| 1bbf72f | APipe Tester | 09 April 2015, 12:17:18 UTC | Updated `genome` tab completion. | 09 April 2015, 12:17:18 UTC |
| 67cfa97 | APipe Tester | 09 April 2015, 12:15:27 UTC | Updated class browser cache. | 09 April 2015, 12:15:27 UTC |
| 40839c9 | Nathaniel Nutter | 09 April 2015, 06:44:42 UTC | Merge pull request #644 from nnutter/lock-pair fix lock directory being created with incorrect permissions | 09 April 2015, 06:44:42 UTC |
| 1772638 | Eddie Belter | 08 April 2015, 21:41:04 UTC | Merge pull request #642 from ebelter/instdata InstData Import: sort then sanitize; add attrs to skip for reimport | 08 April 2015, 21:41:04 UTC |
| 1f10e6e | Nathaniel Nutter | 08 April 2015, 21:37:40 UTC | remove unnecessary re-stringification | 08 April 2015, 21:37:40 UTC |
| fad8623 | Gabriel Sanderson | 08 April 2015, 20:58:27 UTC | Compilation error. | 08 April 2015, 20:58:27 UTC |
| 2d89b97 | Nathaniel Nutter | 08 April 2015, 20:41:44 UTC | make it more explicit that we're adding group permissions | 08 April 2015, 20:44:50 UTC |
| 2bc0220 | Nathaniel Nutter | 08 April 2015, 20:37:01 UTC | fix lock directory being created with incorrect permissions We need to use `create_directory` so that `/var/lock/genome` gets created with the `info` group as the owner. Previous code resulted in default `gid` being used, ``` blade15-1-13:~ $ ls -dlh /var/lock/genome drwxrwxr-x 2 mxie visitor 40 2015-04-08 15:14 /var/lock/genome ``` | 08 April 2015, 20:43:40 UTC |
| ef6e2b5 | Gabriel Sanderson | 08 April 2015, 20:31:02 UTC | More code and test cleanup after refactoring revivified_alignment_bam_file_path | 08 April 2015, 20:31:02 UTC |
| af7dbc0 | Gabriel Sanderson | 08 April 2015, 19:15:04 UTC | Correct revivified_alignment_bam_file_path params. | 08 April 2015, 19:15:04 UTC |
| a39ec73 | Eddie Belter | 08 April 2015, 17:57:35 UTC | Merge pull request #630 from ebelter/de-novo-assembly De Novo Assembly: add number of threads to lsf resource when processing instrument data. | 08 April 2015, 17:57:35 UTC |
| 91f00fe | Eddie Belter | 08 April 2015, 17:57:22 UTC | InstData Import: use can on command class to determine method | 08 April 2015, 17:57:22 UTC |
| 5f00725 | David Morton | 08 April 2015, 16:47:01 UTC | Merge pull request #629 from davidlmorton/more-ptero-integration-latest PTero can run workflows | 08 April 2015, 16:47:01 UTC |
| bf4e73d | Feiyu Du | 08 April 2015, 15:25:31 UTC | Merge pull request #641 from dufeiyu/include_qc_failed Include QC failed reads when recreating per lane bam from merged bam | 08 April 2015, 15:25:31 UTC |
| 39c6346 | Allison Penner Regier | 08 April 2015, 15:02:51 UTC | Merge pull request #639 from apregier/exclude_yaml_from_trio_process_diffs Exclude yaml from trio process diffs | 08 April 2015, 15:02:51 UTC |
| 9ea9cfc | APipe Tester | 08 April 2015, 12:17:13 UTC | Updated `genome` tab completion. | 08 April 2015, 12:17:13 UTC |
| 31193c8 | Feiyu Du | 08 April 2015, 03:37:25 UTC | fix indentation | 08 April 2015, 03:37:25 UTC |
| b1d5fe5 | Dave Larson | 08 April 2015, 03:15:01 UTC | Merge pull request #637 from genome/graph_domainless remove skipping of transcripts with no domains. | 08 April 2015, 03:15:01 UTC |
| 043bcb9 | mkiwala | 07 April 2015, 22:57:23 UTC | Merge pull request #634 from mkiwala/clipoverlap-md5 Clipoverlap md5 | 07 April 2015, 22:57:23 UTC |
| 20c7bc5 | Eddie Belter | 07 April 2015, 22:01:10 UTC | InstData Import: sort then sanitize | 07 April 2015, 22:01:10 UTC |
| d5541c8 | Eddie Belter | 07 April 2015, 21:57:48 UTC | InstData: update attributes to skip for reimport | 07 April 2015, 21:57:48 UTC |
| 05ac5b5 | Thomas B. Mooney | 07 April 2015, 21:31:51 UTC | Merge pull request #636 from tmooney/pass_bedtools_version_to_merge Pass bedtools version to merge | 07 April 2015, 21:31:51 UTC |
| aa79935 | Feiyu Du | 07 April 2015, 21:13:12 UTC | Include QC failed reads when recreating per lane bam from merged bam | 07 April 2015, 21:13:12 UTC |
| 81bc39e | dmorton | 07 April 2015, 18:40:06 UTC | Add status message before waiting for workflow. | 07 April 2015, 19:59:14 UTC |
| 0018e88 | dmorton | 07 April 2015, 18:41:43 UTC | rename _output_names to _output_properties | 07 April 2015, 19:58:34 UTC |
| 2ac9f4b | dmorton | 07 April 2015, 19:01:02 UTC | Notice when UR::Context->commit doesn't return true | 07 April 2015, 19:58:28 UTC |
| 67da44e | dmorton | 07 April 2015, 19:02:31 UTC | Remove event-based workflow compatibility | 07 April 2015, 19:58:22 UTC |
| 6dabc18 | dmorton | 07 April 2015, 19:03:46 UTC | Fix typo in die message | 07 April 2015, 19:58:14 UTC |
| ff6671d | Thomas B. Mooney | 07 April 2015, 18:44:58 UTC | Merge pull request #617 from tmooney/ignore_non_used_results_in_somvar_tier_variants When Tiering in SomVar only Consider Results we "Use" | 07 April 2015, 18:44:58 UTC |
| 1f179b8 | apregier | 07 April 2015, 16:40:58 UTC | Skip diffing yaml files They contain result ids and allocation paths that are process specific | 07 April 2015, 16:40:58 UTC |
| c5c9b50 | apregier | 07 April 2015, 16:39:57 UTC | Simplify passing the params | 07 April 2015, 16:39:57 UTC |
| 7306613 | Thomas B. Mooney | 07 April 2015, 13:28:00 UTC | Merge pull request #638 from tmooney/spaces_in_picard_arguments Allow spaces in comments again. | 07 April 2015, 13:28:00 UTC |
| d552b4e | Thomas Mooney | 07 April 2015, 13:03:42 UTC | Allow spaces in comments again. This commit was produced in Saint Louis, Missouri, USA. | 07 April 2015, 13:03:42 UTC |
| 0322963 | Gabriel Sanderson | 06 April 2015, 22:09:34 UTC | Rename paths->path, since only a single bam is returned. | 06 April 2015, 22:09:34 UTC |
| 7139fe5 | Gabriel Sanderson | 06 April 2015, 22:07:02 UTC | Delete temp allocation during pre-commit instead of commit. | 06 April 2015, 22:07:02 UTC |
| 36becf7 | Eddie Belter | 06 April 2015, 21:32:35 UTC | DeNovo Assembly: add threads to op type instead of using resolve resource | 06 April 2015, 21:36:17 UTC |
| 75ded63 | Dave Larson | 06 April 2015, 21:03:00 UTC | remove skipping of transcripts with no domains. | 06 April 2015, 21:03:00 UTC |
| f87e418 | Thomas Mooney | 06 April 2015, 20:45:08 UTC | Wire up the new bedtools_version property. | 06 April 2015, 20:45:08 UTC |
| 6d90a02 | Thomas Mooney | 06 April 2015, 20:21:52 UTC | Add optional bedtools_version. Now we can find per-lane alignments that had one set! | 06 April 2015, 20:21:52 UTC |
| f905399 | APipe Tester | 06 April 2015, 18:49:43 UTC | updated jenkins submodule to 08335ed | 06 April 2015, 19:59:01 UTC |
| de99f2e | Michael J. Kiwala | 06 April 2015, 19:52:06 UTC | Test that an existing .md5 would not be overwritten | 06 April 2015, 19:52:06 UTC |
| 3951448 | Michael J. Kiwala | 06 April 2015, 19:51:40 UTC | Use Genome::Sys::write_file() instead of File::Slurp | 06 April 2015, 19:51:40 UTC |
| 0730304 | Susanna Siebert | 06 April 2015, 19:37:43 UTC | Merge pull request #627 from susannasiebert/variant_reporting_vep Change ON_TARGET merge strategy to uniq-concat | 06 April 2015, 19:37:43 UTC |
| 9342665 | Thomas B. Mooney | 06 April 2015, 19:29:18 UTC | Merge pull request #620 from tmooney/deduplicate_picard_histogram Deduplicate histogram and metrics processing subroutines. | 06 April 2015, 19:29:18 UTC |
| fa44ef7 | Thomas B. Mooney | 06 April 2015, 19:28:38 UTC | Merge pull request #615 from tmooney/remove_check_for_errors_without_eval Remove useless use of $@ not with eval... | 06 April 2015, 19:28:38 UTC |
| d3ba968 | Michael J. Kiwala | 06 April 2015, 18:19:59 UTC | Fix whitespace | 06 April 2015, 18:20:37 UTC |
| 0ff86b0 | Michael J. Kiwala | 06 April 2015, 18:19:20 UTC | Add create_md5sum() to G:M:T:BamUtil::ClipOverlap | 06 April 2015, 18:20:37 UTC |
| 76bb598 | Dave Larson | 06 April 2015, 17:22:38 UTC | Merge pull request #633 from tmooney/build_requested_cleverness Fix BQM's ability to decide what column to use for "build_requested". | 06 April 2015, 17:22:38 UTC |
| 44775d5 | Thomas B. Mooney | 06 April 2015, 15:32:25 UTC | Merge pull request #614 from tmooney/pass_the_vcf_sample_name_to_picard Picard needs to know the name in the VCF. | 06 April 2015, 15:32:25 UTC |
| 58dad41 | Thomas Mooney | 06 April 2015, 15:08:32 UTC | Fix broken indirection. | 06 April 2015, 15:08:32 UTC |
| c911f7f | Nathaniel Nutter | 06 April 2015, 14:51:44 UTC | Merge pull request #625 from nnutter/tgisan migrate off of `tgisan` and `unknown` scopes | 06 April 2015, 14:51:44 UTC |
| cf16851 | Nathaniel Nutter | 06 April 2015, 14:49:28 UTC | Merge pull request #632 from nnutter/master fix typo during LockProxy conversion | 06 April 2015, 14:49:28 UTC |
| 2abfdfc | Nathaniel Nutter | 04 April 2015, 19:15:29 UTC | fix typo during LockProxy conversion | 04 April 2015, 19:15:29 UTC |
| ee32b2e | APipe Tester | 04 April 2015, 12:17:46 UTC | Updated `gmt` tab completion. | 04 April 2015, 12:17:46 UTC |
| 2d46aa1 | APipe Tester | 04 April 2015, 12:16:54 UTC | Updated `genome` tab completion. | 04 April 2015, 12:16:54 UTC |
| dd24fa0 | Eddie Belter | 03 April 2015, 23:11:34 UTC | Merge pull request #631 from ebelter/sync Sync: fix lock parameter | 03 April 2015, 23:11:34 UTC |
| 580cd05 | dmorton | 03 April 2015, 22:58:43 UTC | Update json test data | 03 April 2015, 22:58:43 UTC |
| b1714d7 | Eddie Belter | 03 April 2015, 22:56:23 UTC | Sync: fix lock parameter | 03 April 2015, 22:56:23 UTC |
| 647c068 | Nathaniel Nutter | 03 April 2015, 04:46:26 UTC | start migration off of `unknown` scope | 03 April 2015, 21:19:52 UTC |
| ddb9be4 | Nathaniel Nutter | 03 April 2015, 00:42:33 UTC | start migration off of `tgisan` | 03 April 2015, 21:19:51 UTC |
| 9f0daa4 | Nathaniel Nutter | 02 April 2015, 22:18:01 UTC | add `host` scope for locking | 03 April 2015, 21:19:50 UTC |
| 705205b | Nathaniel Nutter | 02 April 2015, 21:59:21 UTC | add "namespace" support for NessyBackend | 03 April 2015, 21:19:50 UTC |
| b83be9d | Nathaniel Nutter | 03 April 2015, 21:18:43 UTC | Merge pull request #624 from nnutter/genome-env break circular dependency between Genome, Genome::Env, and Genome::Site::TGI | 03 April 2015, 21:18:43 UTC |
| d4d365e | Nathaniel Nutter | 03 April 2015, 21:18:23 UTC | Merge pull request #626 from nnutter/lock_resource minimize use of Genome::Sys::Lock API | 03 April 2015, 21:18:23 UTC |
| 910ffe0 | Nathaniel Nutter | 03 April 2015, 21:17:48 UTC | Merge pull request #619 from nnutter/RT-104979 only build workflows should go in build workflow queue | 03 April 2015, 21:17:48 UTC |
| 0a0c2f5 | Eddie Belter | 03 April 2015, 21:11:23 UTC | DeNovo Assembly: add resolve_resource_requirements to add thread count to lsf resource (work flow only) | 03 April 2015, 21:11:23 UTC |
| b92dccb | Eddie Belter | 03 April 2015, 20:28:51 UTC | DeNovo: move prepare instdata from command to build directory | 03 April 2015, 20:59:23 UTC |
| d56a8b0 | Gue Su Chang | 03 April 2015, 20:47:52 UTC | Minor upgrade 3 in Genome::Model::Tools::Analysis::Coverage::MergeReadcounts | 03 April 2015, 20:47:52 UTC |
| 42b25d6 | Eddie Belter | 03 April 2015, 20:25:56 UTC | SX Validate: make the validate module have create, is_valid and number_of_threads_required | 03 April 2015, 20:25:56 UTC |
| 70c644c | Nathaniel Nutter | 03 April 2015, 17:23:05 UTC | convert genome-webserver scripts to LockProxy | 03 April 2015, 19:22:07 UTC |
| be97dae | Nathaniel Nutter | 03 April 2015, 17:18:04 UTC | remove legacy locking methods | 03 April 2015, 19:22:06 UTC |
| 8c63895 | Nathaniel Nutter | 03 April 2015, 17:15:24 UTC | use LockProxy in LockMigrationProxy.t | 03 April 2015, 19:22:04 UTC |
| 79397a2 | Avinash Ramu | 03 April 2015, 19:18:03 UTC | Merge pull request #621 from gatoravi/clinseq_bedtools_path Figure out bedtools path better | 03 April 2015, 19:18:03 UTC |
| 8064564 | Eddie Belter | 03 April 2015, 18:57:44 UTC | Merge pull request #612 from ebelter/cghub-metadata-create-from-xml GMT CG Hub: metadata can be created from XML and file | 03 April 2015, 18:57:44 UTC |
| 9e9ad10 | Eddie Belter | 03 April 2015, 18:57:37 UTC | Merge pull request #616 from ebelter/cghub-query-with-rest-api CG Hub: query uses rest API | 03 April 2015, 18:57:37 UTC |
| bd10318 | Susanna Siebert | 03 April 2015, 17:28:52 UTC | change ON_TARGET merge strategy to uniq-concat | 03 April 2015, 17:28:52 UTC |
