| 5395bf9 | Thomas B. Mooney | 11 June 2015, 20:12:26 UTC | Merge pull request #601 from tmooney/set_users_in_result_users Lock all SR User construction to enforce uniqueness. | 11 June 2015, 20:12:26 UTC |
| a1c4b26 | David Morton | 11 June 2015, 17:44:43 UTC | Merge pull request #803 from davidlmorton/ptero_process_view Ptero process view | 11 June 2015, 17:44:43 UTC |
| 30f43d3 | Susanna Siebert | 11 June 2015, 15:49:13 UTC | Merge pull request #802 from susannasiebert/speedseq_improvements2 Have speedseq per-lane alignment header only include matching instrument data's RG | 11 June 2015, 15:49:13 UTC |
| bbd9e3f | mkiwala | 11 June 2015, 15:19:19 UTC | Merge pull request #800 from mkiwala/ptero-wrapper-teardown_logging-alt _teardown_logging when re-throwing exceptions | 11 June 2015, 15:19:19 UTC |
| b2bbed5 | Susanna Siebert | 11 June 2015, 13:52:20 UTC | Factor scratch sam header creation into its own subroutine | 11 June 2015, 13:52:20 UTC |
| 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 |
| 23c7cd4 | dmorton | 09 June 2015, 22:27:29 UTC | Order parallel-by steps by 'color' | 09 June 2015, 22:27:29 UTC |
| 3f7d4cb | dmorton | 09 June 2015, 22:22:11 UTC | Use $handle->print instead of print $handle | 09 June 2015, 22:22:11 UTC |
| a742c49 | dmorton | 09 June 2015, 22:20:55 UTC | Don't display Stdout Log It is almost identical to Stderr Log and is almost always empty. | 09 June 2015, 22:20:55 UTC |
| f7c3b78 | dmorton | 09 June 2015, 19:18:11 UTC | Ensure failed steps aren't displayed like 'unstarted' ones. | 09 June 2015, 21:24:56 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 |
| 64ccad2 | dmorton | 09 June 2015, 18:38:03 UTC | fix test to pass object to get_ptero_builder_for_process It used to take a process_id, now we define a TestProcess and pass that instead. | 09 June 2015, 18:38:03 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 |
| ba3bb22 | Michael J. Kiwala | 09 June 2015, 15:57:21 UTC | Keep calls to _teardown_logging and _setup_logging in same function Keeping the call to _teardown_logging() in the same function as _setup_logging() is ideal to me. Here I'm using an extra layer of try-catch to achieve this ideal. Alternatively, return codes could have been used to achieve this same ideal. | 09 June 2015, 15:57:21 UTC |
| 06b0870 | dmorton | 09 June 2015, 14:43:27 UTC | Do not clobber _status_color This was causing legacy workflows to fail to colorize statuses. | 09 June 2015, 14:43:27 UTC |
| 6003e04 | dmorton | 09 June 2015, 03:01:31 UTC | Add support for viewing workflows run by PTero | 09 June 2015, 14:27:39 UTC |
| 1377c03 | Susanna Siebert | 09 June 2015, 13:20:21 UTC | Update speedseq test data | 09 June 2015, 13:20:21 UTC |
| 1c522c0 | Susanna Siebert | 08 June 2015, 20:18:42 UTC | Fix if clause logic | 09 June 2015, 13:07:05 UTC |
| 07f3457 | Susanna Siebert | 08 June 2015, 20:17:21 UTC | Better error message | 09 June 2015, 13:07:05 UTC |
| c3261e5 | Susanna Siebert | 08 June 2015, 20:15:25 UTC | Revert "If more than one metric key is found, try to resolve by library name" This reverts commit f31542b3e118e8cecda05e0137abe95d8e8cb2b1. | 09 June 2015, 13:07:05 UTC |
| 09c10fb | Susanna Siebert | 08 June 2015, 20:14:51 UTC | Test speedseq AlignAndMerge with two instrument data | 09 June 2015, 13:07:05 UTC |
| 91fab38 | Susanna Siebert | 08 June 2015, 20:12:50 UTC | Create bam header with the instrument data's @RG only | 09 June 2015, 13:07:04 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 |
| c12becd | dmorton | 05 June 2015, 19:11:32 UTC | Processes submitted to PTero specify name | 05 June 2015, 19:11:32 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 |
| d2f0e0f | Michael J. Kiwala | 05 June 2015, 05:00:26 UTC | _teardown_logging when re-throwing exceptions | 05 June 2015, 05:00:26 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 |
