| cc17600 | Anthony Brummett | 10 June 2015, 20:01:48 UTC | Merge pull request #805 from brummett/more-test-info Print out diag info when the test fails | 10 June 2015, 20:01:48 UTC |
| 1e9afe5 | Anthony Brummett | 10 June 2015, 19:41:19 UTC | Print out diag info when the test fails This test is consistently failing in Jenkins, but I can't reproduce it myself. | 10 June 2015, 19:41:19 UTC |
| 81a6fe1 | Anthony Brummett | 09 June 2015, 20:13:54 UTC | Merge pull request #804 from brummett/dindel Get dindel working again | 09 June 2015, 20:13:54 UTC |
| 0721201 | Anthony Brummett | 09 June 2015, 18:51:28 UTC | Don't mkdir or unlink Since we're using the packaged version | 09 June 2015, 18:51:28 UTC |
| 1ff55ea | Anthony Brummett | 09 June 2015, 18:51:09 UTC | remove breakpoint | 09 June 2015, 18:51:09 UTC |
| e4cbeea | Anthony Brummett | 09 June 2015, 16:21:59 UTC | Get dindel working again The volume it used to live on was removed. This makes it use the packaged version. | 09 June 2015, 16:21:59 UTC |
| ea704d6 | Susanna Siebert | 09 June 2015, 13:05:33 UTC | Merge pull request #796 from susannasiebert/speedseq_improvements AlignAndMerge only creates per-lane alignment objects without revivification | 09 June 2015, 13:05:33 UTC |
| b6a4000 | Susanna Siebert | 08 June 2015, 20:29:45 UTC | Merge pull request #801 from susannasiebert/speedseq_path Update speedseq test version to our frozen version | 08 June 2015, 20:29:45 UTC |
| 304a10e | Thomas B. Mooney | 08 June 2015, 17:33:15 UTC | Merge pull request #798 from tmooney/remove_duplicate_lsf_resource Remove second lsf_resource property in AnnotateAndUploadVariants | 08 June 2015, 17:33:15 UTC |
| 5e5b7ab | Avinash Ramu | 05 June 2015, 23:30:58 UTC | Merge pull request #776 from kkrysiak/add_LOH_clinseq Add loh tool to clinseq pipeline | 05 June 2015, 23:30:58 UTC |
| b9da0fc | Susanna Siebert | 05 June 2015, 16:56:40 UTC | Update speedseq test version to our frozen version | 05 June 2015, 16:56:40 UTC |
| 789de8e | APipe Tester | 05 June 2015, 15:12:27 UTC | Updated `genome` tab completion. | 05 June 2015, 15:12:27 UTC |
| 2d10371 | Thomas B. Mooney | 04 June 2015, 20:04:17 UTC | Merge pull request #797 from tmooney/somatic_variation_create_report_sets_tmp_request Set a default tmp space request for SomaticVariation's CreateReport step | 04 June 2015, 20:04:17 UTC |
| 8ae0792 | Susanna Siebert | 04 June 2015, 14:13:22 UTC | Pass package as a parameter into the get_bam_lock subroutine | 04 June 2015, 14:13:22 UTC |
| 4eb43ef | Susanna Siebert | 04 June 2015, 13:20:48 UTC | Remove duplicated call to _prepare_output_directory | 04 June 2015, 13:20:48 UTC |
| 7bc4b44 | Susanna Siebert | 04 June 2015, 13:19:49 UTC | Remove unnecessary error checking | 04 June 2015, 13:19:49 UTC |
| 507157c | Susanna Siebert | 04 June 2015, 13:16:20 UTC | Move debug messages into their respective subroutines | 04 June 2015, 13:16:20 UTC |
| ad3d4d6 | Thomas Mooney | 03 June 2015, 17:55:30 UTC | Remove second lsf_resource property. Defining the request once ought to be enough! | 03 June 2015, 17:55:30 UTC |
| 4072512 | Thomas Mooney | 03 June 2015, 17:48:25 UTC | Set a default tmp space request. | 03 June 2015, 17:48:25 UTC |
| 2e92b94 | Allison Penner Regier | 03 June 2015, 14:24:31 UTC | Merge pull request #795 from apregier/statistic_fix Fix wrongly labeled statistic | 03 June 2015, 14:24:31 UTC |
| bc5fd00 | Susanna Siebert | 01 June 2015, 21:55:40 UTC | Run post-processing during first revivification of the per-lane bam | 03 June 2015, 13:16:39 UTC |
| 78429b6 | Susanna Siebert | 01 June 2015, 21:54:51 UTC | Create the object only; don't do any post-processing | 03 June 2015, 13:16:39 UTC |
| de8fe80 | Susanna Siebert | 01 June 2015, 21:52:17 UTC | Don't create md5 and index files | 03 June 2015, 13:16:39 UTC |
| 2e7d4cc | Susanna Siebert | 01 June 2015, 21:49:18 UTC | Fix error message | 03 June 2015, 13:16:34 UTC |
| 422fcb3 | Susanna Siebert | 01 June 2015, 21:49:04 UTC | Factor disk allocation creation into its own subroutine | 03 June 2015, 13:16:34 UTC |
| cf169f2 | Susanna Siebert | 01 June 2015, 21:47:59 UTC | Factor steps after initial object creation into their own subroutine | 03 June 2015, 13:16:34 UTC |
| 37f7164 | APipe Tester | 03 June 2015, 12:19:31 UTC | Updated `genome` tab completion. | 03 June 2015, 12:19:31 UTC |
| 42028b3 | APipe Tester | 03 June 2015, 12:17:32 UTC | Updated class browser cache. | 03 June 2015, 12:17:32 UTC |
| 3748bc8 | apregier | 02 June 2015, 22:22:21 UTC | Wrong statistic!!! | 02 June 2015, 22:22:21 UTC |
| 6d71707 | apregier | 02 June 2015, 22:00:49 UTC | CHANGELOG: New required param for vep Both `genome db ensembl vep` and `genome db ensembl run vep` now require the parameter --reference-version Valid values are GRCh37, GRCh38, and GRCm38 | 02 June 2015, 22:00:49 UTC |
| 843dd02 | Nathaniel Nutter | 02 June 2015, 20:45:51 UTC | Merge pull request #790 from nnutter/master make search queue deduplication use less memory | 02 June 2015, 20:45:51 UTC |
| 9b61ede | Allison Penner Regier | 02 June 2015, 20:22:32 UTC | Merge pull request #785 from apregier/vep Support new versions of vep cache | 02 June 2015, 20:22:32 UTC |
| ce5923e | Susanna Siebert | 02 June 2015, 19:52:41 UTC | Merge pull request #791 from susannasiebert/speedseq_bugfix QC bugfix | 02 June 2015, 19:52:41 UTC |
| d8c13f2 | apregier | 02 June 2015, 16:34:37 UTC | Merge remote-tracking branch 'origin/master' into fix Conflicts: bin/genome-env Needed to add my test-db changes on top of Susi's | 02 June 2015, 16:34:37 UTC |
| b8ad96c | Susanna Siebert | 02 June 2015, 16:28:10 UTC | Explicitly set chart_output param for picard CollectGcBiasMetrics qc tool | 02 June 2015, 16:28:10 UTC |
| cbed367 | Susanna Siebert | 02 June 2015, 16:27:28 UTC | Use temp file for unused output instead of writing to /dev/null | 02 June 2015, 16:27:28 UTC |
| 98899d1 | Susanna Siebert | 02 June 2015, 16:26:44 UTC | Rename qc output_file to qc_metrics_file | 02 June 2015, 16:26:44 UTC |
| 39b0f15 | apregier | 02 June 2015, 16:05:36 UTC | Remove unneeded legacy stuff | 02 June 2015, 16:05:36 UTC |
| 23ee3e9 | Nathaniel Nutter | 02 June 2015, 15:49:50 UTC | no need to keep first member | 02 June 2015, 15:49:50 UTC |
| edebd28 | Nathaniel Nutter | 02 June 2015, 15:35:48 UTC | Merge pull request #777 from nnutter/default_from add `default_from` to config | 02 June 2015, 15:35:48 UTC |
| bd7becb | Thomas B. Mooney | 02 June 2015, 14:53:43 UTC | Merge pull request #765 from tmooney/model_summary_uses_determine_error ModelSummary uses DetermineError to decide build progress | 02 June 2015, 14:53:43 UTC |
| 2a8bb0c | Thomas B. Mooney | 02 June 2015, 14:51:21 UTC | Merge pull request #745 from tmooney/direct_cmds_in_shellcmd Allow specifying the command as a list in Genome::Sys->shellcmd | 02 June 2015, 14:51:21 UTC |
| 7c8f578 | Susanna Siebert | 02 June 2015, 14:29:00 UTC | Merge pull request #774 from susannasiebert/speedseq_clean Speedseq alignment strategy, software results, and qc | 02 June 2015, 14:29:00 UTC |
| 5317127 | APipe Tester | 02 June 2015, 12:21:34 UTC | Updated `gmt` tab completion. | 02 June 2015, 12:21:34 UTC |
| 63e8805 | APipe Tester | 02 June 2015, 12:20:41 UTC | Updated `genome` tab completion. | 02 June 2015, 12:20:41 UTC |
| e9d100b | APipe Tester | 02 June 2015, 12:18:39 UTC | Updated class browser cache. | 02 June 2015, 12:18:39 UTC |
| 0ad38c1 | dmorton | 02 June 2015, 03:24:37 UTC | Account for default values that evaluate to false | 02 June 2015, 03:24:37 UTC |
| 6b53b53 | Malachi Griffith | 02 June 2015, 00:26:28 UTC | Merge pull request #788 from malachig/master minor update to clinseq to handle some edge cases | 02 June 2015, 00:26:28 UTC |
| 7627825 | Nathaniel Nutter | 01 June 2015, 23:30:09 UTC | remove rogue paren | 01 June 2015, 23:30:09 UTC |
| d151f14 | Nathaniel Nutter | 01 June 2015, 23:29:49 UTC | change loop_sleep default to one second | 01 June 2015, 23:29:49 UTC |
| 7a5ff5a | Nathaniel Nutter | 01 June 2015, 23:26:30 UTC | chomp and add newlines to messages I think I inadvertantly changed this behavior when consolidating Genome::Role::Logger and Genome::Logger. | 01 June 2015, 23:26:30 UTC |
| 2b32947 | Nathaniel Nutter | 01 June 2015, 23:15:28 UTC | validate inputs to `dedup_set` | 01 June 2015, 23:15:28 UTC |
| 909f87f | Nathaniel Nutter | 01 June 2015, 23:04:21 UTC | deduplicate the queue as it's processed instead of all upfront | 01 June 2015, 23:04:21 UTC |
| 9c7e763 | Nathaniel Nutter | 01 June 2015, 23:03:31 UTC | extract function: dedup_set | 01 June 2015, 23:03:31 UTC |
| 3e8ea4c | Nathaniel Nutter | 01 June 2015, 22:34:20 UTC | add some logging | 01 June 2015, 22:34:20 UTC |
| 006e796 | Nathaniel Nutter | 01 June 2015, 21:47:12 UTC | refactor and improve search queue deduplication This refactors and improves the search queue deduplication to use less memory: - remove duplicate deduplication code in `deduplicate` sub-command - move deduplication code to `Genome::Search::Queue` - change deduplication code to iterate over `subject_class`-`subject_id` pairings with pruning enabled to consume less memory | 01 June 2015, 21:47:12 UTC |
| 9201e80 | Nathaniel Nutter | 01 June 2015, 21:46:33 UTC | convert to use subtests | 01 June 2015, 21:46:33 UTC |
| 7023d19 | Nathaniel Nutter | 01 June 2015, 21:37:42 UTC | use Sub::Override to avoid warnings, etc. | 01 June 2015, 21:37:42 UTC |
| 4608a0c | David Morton | 01 June 2015, 21:12:47 UTC | Merge pull request #789 from davidlmorton/fix_builds_use_process Fix builds use process | 01 June 2015, 21:12:47 UTC |
| 5038e05 | Malachi Griffith | 01 June 2015, 20:29:35 UTC | clin-seq: change --force option to more descriptive --allow-multiple-individuals | 01 June 2015, 20:29:35 UTC |
| ff967d3 | dmorton | 01 June 2015, 20:04:48 UTC | Allow default_value to satisfy a required input in WorkflowBuilder | 01 June 2015, 20:04:48 UTC |
| 7f927a7 | dmorton | 01 June 2015, 20:04:05 UTC | Mark input as optional The model-test does not specify this input. | 01 June 2015, 20:04:05 UTC |
| 2cd0a15 | dmorton | 01 June 2015, 20:02:36 UTC | Don't call _initialize_workflow twice ReferenceAlignment and Clinseq models have implemented side-effects within this method or methods it calls. | 01 June 2015, 20:02:36 UTC |
| ff5d5d2 | APipe Tester | 01 June 2015, 19:35:15 UTC | updated jenkins submodule to 1d450cd | 01 June 2015, 19:35:15 UTC |
| 67b9b9a | Susanna Siebert | 01 June 2015, 18:23:23 UTC | Test instrument data needs to be paired-end | 01 June 2015, 18:23:23 UTC |
| 156ced0 | Eddie Belter | 01 June 2015, 16:55:05 UTC | Merge pull request #786 from ebelter/utility-inputs Utility::inputs can encode/decode non UR objects | 01 June 2015, 16:55:05 UTC |
| d1a030d | Susanna Siebert | 01 June 2015, 16:25:28 UTC | Need to overwrite accepts_bam_input to return 1 so the bam doesn't get converted to fastq | 01 June 2015, 16:25:28 UTC |
| dcf3d4f | Chris Miller | 01 June 2015, 15:40:50 UTC | Merge pull request #787 from chrisamiller/master allowing 4-column bed files to be output from VCF conversion | 01 June 2015, 15:40:50 UTC |
| dad2f4f | Thomas B. Mooney | 01 June 2015, 13:20:28 UTC | Merge pull request #779 from tmooney/log_dispatch_renamed_in_genome_logger Call renamed accessor in search index command. | 01 June 2015, 13:20:28 UTC |
| 22d5037 | Malachi Griffith | 29 May 2015, 21:48:37 UTC | minor update to clinseq to handle some edge cases | 29 May 2015, 21:48:37 UTC |
| 2b2168a | Chris Miller | 29 May 2015, 21:27:34 UTC | removing explicitly blank quality columns. This allows for outputting 4-col bed files, using the options in Convert.pm | 29 May 2015, 21:27:34 UTC |
| 22f8aea | Chris Miller | 29 May 2015, 21:25:46 UTC | adding option to omit the quality/depth columns | 29 May 2015, 21:25:46 UTC |
| a1ab96d | Eddie Belter | 29 May 2015, 20:54:03 UTC | Utility::inputs can encode/decode non UR objects | 29 May 2015, 20:54:03 UTC |
| 31127e0 | Nathaniel Nutter | 29 May 2015, 19:44:09 UTC | Merge pull request #778 from nnutter/lsf allow calculated_default to be used for special lsf properties | 29 May 2015, 19:44:09 UTC |
| df43f83 | Nathaniel Nutter | 29 May 2015, 19:44:03 UTC | Merge pull request #781 from nnutter/logger don't need to use Genome here | 29 May 2015, 19:44:03 UTC |
| 95447e1 | Nathaniel Nutter | 29 May 2015, 19:43:46 UTC | Merge pull request #782 from nnutter/sam misc cleanup in `gmt sam` | 29 May 2015, 19:43:46 UTC |
| 7eed81b | Nathaniel Nutter | 29 May 2015, 19:43:38 UTC | Merge pull request #783 from nnutter/less-perms remove execute permissions from several types of files | 29 May 2015, 19:43:38 UTC |
| e7fa9ea | Susanna Siebert | 29 May 2015, 18:05:08 UTC | Add more LSF resource options | 29 May 2015, 19:21:31 UTC |
| ba413ca | apregier | 29 May 2015, 17:11:46 UTC | Update testdb snapshot This includes vep caches with reference_version set | 29 May 2015, 17:28:54 UTC |
| 29f06c0 | apregier | 29 May 2015, 17:07:25 UTC | Add reference version to vep cache New versions of the vep cache are available for both GRCh37 ad GRCh38, and we need to be sure to get the correct one. | 29 May 2015, 17:28:42 UTC |
| 02c2c00 | apregier | 29 May 2015, 17:02:49 UTC | Update method to get ensembl api | 29 May 2015, 17:28:29 UTC |
| edf37a3 | David Morton | 29 May 2015, 17:25:11 UTC | Merge pull request #784 from davidlmorton/workflowbuilder_fixes Workflowbuilder fixes | 29 May 2015, 17:25:11 UTC |
| 63878d1 | Susanna Siebert | 29 May 2015, 16:53:13 UTC | Increase LSF memory | 29 May 2015, 16:53:13 UTC |
| 2dae80e | Susanna Siebert | 29 May 2015, 16:52:57 UTC | Parse speedseq aligner params and pass along to the gmt | 29 May 2015, 16:52:57 UTC |
| 50c98e7 | Susanna Siebert | 29 May 2015, 13:47:17 UTC | Code cleanup of G::Test::Data | 29 May 2015, 13:47:17 UTC |
| 4fe28e6 | Susanna Siebert | 29 May 2015, 13:47:01 UTC | Code cleanup of G::ID::AR::ReliesOnBwa | 29 May 2015, 13:47:01 UTC |
| 35e2943 | Susanna Siebert | 29 May 2015, 13:46:40 UTC | Make G::ID::AR::Bwasw a G::ID::AR::ReliesOnBwa | 29 May 2015, 13:46:40 UTC |
| 072cc83 | dmorton | 28 May 2015, 23:01:10 UTC | Add support for Events to WorkflowBuilder | 28 May 2015, 23:01:10 UTC |
| dbdc090 | dmorton | 28 May 2015, 22:32:28 UTC | Get operationtype attributes from the xml These attributes: - lsf_project - lsf_queue - lsf_resource were only being found (if they existed) on the Command class itself. Therefore when you read in a workflow, and it had specified any of these values, they were ignored. The hash EXPECTED_ATTRIBUTES was changed to a method so we could move the functionality for finding these attributes in the xml up into the base class. | 28 May 2015, 22:32:28 UTC |
| d3a75d2 | Nathaniel Nutter | 28 May 2015, 21:46:28 UTC | remove execute permissions from several types of files Permissions were removed with the following commands: ``` $ find * -name '*.pm' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.png' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.psd' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.js' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.css' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.html' -perm /a+x -exec chmod a-x {} \; $ chmod a-x java/edu/wustl/genome/samtools/GCSamToFastq.java $ find * -name '*.Rnw' -perm /a+x -exec chmod a-x {} \; ``` | 28 May 2015, 21:46:28 UTC |
| 8a3dce3 | Nathaniel Nutter | 28 May 2015, 20:16:37 UTC | default is displayed by UR so no need to add it to doc string | 28 May 2015, 20:16:37 UTC |
| 8120b17 | Nathaniel Nutter | 28 May 2015, 20:16:20 UTC | remove out-of-date comment | 28 May 2015, 20:16:20 UTC |
| ba82d33 | Nathaniel Nutter | 28 May 2015, 20:15:12 UTC | whitespace | 28 May 2015, 20:15:12 UTC |
| 3ff2ba9 | Nathaniel Nutter | 28 May 2015, 20:07:26 UTC | don't need to use Genome here I'm trying to avoid just blindly using Genome which can trigger accidental circular dependencies if packages such as this are used by any of the packages that are loading during `use Genome`. | 28 May 2015, 20:07:26 UTC |
| 46c7e2c | Susanna Siebert | 28 May 2015, 19:48:32 UTC | Create 'role' for aligners that rely on bwa | 28 May 2015, 19:58:40 UTC |
| 7a5c022 | Thomas Mooney | 28 May 2015, 19:24:05 UTC | log_dispatch was renamed delegate_logger. | 28 May 2015, 19:24:05 UTC |
| df14787 | Nathaniel Nutter | 28 May 2015, 19:21:07 UTC | only make class/package in memory | 28 May 2015, 19:21:07 UTC |
| b998b0d | Susanna Siebert | 28 May 2015, 18:59:59 UTC | Create bam header path in staging directory during initial AR::Speedseq creation | 28 May 2015, 18:59:59 UTC |
| f29ca99 | Nathaniel Nutter | 28 May 2015, 15:52:25 UTC | allow calculated_default to be used for special lsf properties | 28 May 2015, 16:41:26 UTC |
| 8eee452 | Nathaniel Nutter | 28 May 2015, 15:37:53 UTC | add `default_from` to config | 28 May 2015, 15:41:21 UTC |
