| e76d49e | APipe Tester | 26 June 2015, 12:18:32 UTC | Updated `genome` tab completion. | 26 June 2015, 12:18:32 UTC |
| e0116f0 | Eddie Belter | 25 June 2015, 19:57:25 UTC | Merge pull request #832 from ebelter/ref-align RefAlign | 25 June 2015, 19:57:25 UTC |
| 34a3d5f | Eddie Belter | 25 June 2015, 19:43:46 UTC | Merge pull request #834 from ebelter/refseq-converter RefSeq Converter: add and use valid algorithms | 25 June 2015, 19:43:46 UTC |
| 60f27b6 | Eddie Belter | 25 June 2015, 19:25:23 UTC | Merge pull request #836 from ebelter/clin-seq CHANGELOG: bump clin-seq blessed build | 25 June 2015, 19:25:23 UTC |
| db74f0c | Eddie Belter | 24 June 2015, 19:59:23 UTC | CHANGELOG: bump clin-seq blessed build | 24 June 2015, 19:59:23 UTC |
| 348750b | Allison Penner Regier | 24 June 2015, 18:33:54 UTC | Merge pull request #829 from apregier/bedpe More tweaks to compare-bedpes | 24 June 2015, 18:33:54 UTC |
| 4fbb286 | Jason Walker | 24 June 2015, 16:46:41 UTC | Merge pull request #720 from jasonwalker80/clinseq_time_point ClinSeq caTissue Timepoint | 24 June 2015, 16:46:41 UTC |
| cdd96cc | Jason Walker | 24 June 2015, 15:51:11 UTC | Merged genome/genome master with PR720 | 24 June 2015, 15:51:11 UTC |
| 5e4c84d | apregier | 24 June 2015, 15:43:28 UTC | Error if we would overwrite a given metadata column | 24 June 2015, 15:43:28 UTC |
| 4021797 | apregier | 24 June 2015, 15:43:13 UTC | Fix doc punctuation | 24 June 2015, 15:43:13 UTC |
| 30e34c5 | APipe Tester | 24 June 2015, 12:20:45 UTC | Updated `genome` tab completion. | 24 June 2015, 12:20:45 UTC |
| ed5a3c0 | APipe Tester | 24 June 2015, 12:18:49 UTC | Updated class browser cache. | 24 June 2015, 12:18:49 UTC |
| c613e74 | Eddie Belter | 23 June 2015, 23:21:38 UTC | RefSeq Converter: remove uneeded use statement | 23 June 2015, 23:21:38 UTC |
| 09dff7b | Eddie Belter | 23 June 2015, 22:39:59 UTC | RefSeq Converter: use valid values from property instead of variable | 23 June 2015, 22:39:59 UTC |
| a171e36 | Eddie Belter | 23 June 2015, 22:10:24 UTC | RefSeq Converter: add and use valid algoritms variable | 23 June 2015, 22:10:24 UTC |
| 0ee62dc | Jason Walker | 23 June 2015, 20:43:39 UTC | Updated blessed build for apipe-test-clinseq-wer | 23 June 2015, 20:43:39 UTC |
| c163e7a | Eddie Belter | 23 June 2015, 19:41:37 UTC | Merge pull request #827 from ebelter/cqid Minor CQID updates | 23 June 2015, 19:41:37 UTC |
| 6739b6b | Eddie Belter | 23 June 2015, 19:38:06 UTC | RefAlign add die when getting default model name for lane qc adn no instdata is assigned add tests | 23 June 2015, 19:38:17 UTC |
| d86057e | Eddie Belter | 23 June 2015, 19:33:21 UTC | RefAlign: update accumulated alignments directory test | 23 June 2015, 19:33:21 UTC |
| a0159b8 | Eddie Belter | 23 June 2015, 18:07:23 UTC | CQID: update skipped status message | 23 June 2015, 18:07:23 UTC |
| 9dd5a47 | Adam Coffman | 23 June 2015, 15:58:35 UTC | Merge pull request #826 from acoffman/dynamic_resource_requirements_for_align_and_merge Dynamic resource requirements for AlignAndMerge (Speedseq) | 23 June 2015, 15:58:35 UTC |
| baa88c9 | Adam Coffman | 23 June 2015, 15:25:04 UTC | remove confusing reuse of "class" | 23 June 2015, 15:25:04 UTC |
| 5bf8129 | Adam Coffman | 23 June 2015, 15:22:45 UTC | define abstract subroutine with appropriate error | 23 June 2015, 15:22:45 UTC |
| 27275fb | Thomas B. Mooney | 23 June 2015, 13:32:01 UTC | Merge pull request #816 from tmooney/failed_model_ticket_status New command: failed-model-ticket-status | 23 June 2015, 13:32:01 UTC |
| 5135c9b | Eddie Belter | 22 June 2015, 22:03:06 UTC | Merge pull request #830 from ebelter/gmt-validation GMT Validation: status_message | 22 June 2015, 22:03:06 UTC |
| be959f8 | Eddie Belter | 22 June 2015, 21:33:23 UTC | GMT Validation: status_message | 22 June 2015, 21:33:23 UTC |
| 4b00282 | apregier | 18 June 2015, 20:07:15 UTC | Add count of unique gold calls | 22 June 2015, 20:41:10 UTC |
| 4905e17 | apregier | 18 June 2015, 16:36:15 UTC | Flatten stats hash into the general hash | 22 June 2015, 20:41:09 UTC |
| 6356f30 | apregier | 12 June 2015, 19:42:44 UTC | Make script more flexible to pass through arbitrary metadata | 22 June 2015, 20:41:08 UTC |
| 93c23bd | Eddie Belter | 19 June 2015, 22:03:52 UTC | Merge pull request #814 from ebelter/gm-dep-cron-ref-align Genotype Microarray Dependent Cron RefAlign | 19 June 2015, 22:03:52 UTC |
| 8f259d8 | Eddie Belter | 19 June 2015, 22:01:32 UTC | Merge pull request #820 from ebelter/rm-unused-solr-scripts Remove unsed solr scripts | 19 June 2015, 22:01:32 UTC |
| baace95 | Eddie Belter | 19 June 2015, 22:01:13 UTC | Merge pull request #825 from ebelter/instdata-command-update InstData Update Command | 19 June 2015, 22:01:13 UTC |
| 1ca5eb1 | Susanna Siebert | 19 June 2015, 16:02:23 UTC | Merge pull request #824 from susannasiebert/speedseq_lsf Update speedseq to not pass number threads along as an aligner_param | 19 June 2015, 16:02:23 UTC |
| 1da9b94 | Eddie Belter | 18 June 2015, 23:41:39 UTC | RefAlign: remove complete_build_directory, update accumulated alignment s dir' | 18 June 2015, 23:42:23 UTC |
| a1a63be | Eddie Belter | 18 June 2015, 23:40:22 UTC | RefAlign Test: remove unused function | 18 June 2015, 23:40:22 UTC |
| 40f4c4c | Eddie Belter | 18 June 2015, 23:40:08 UTC | RefAlign Test: remove test of last complete build | 18 June 2015, 23:40:08 UTC |
| 18658cc | Eddie Belter | 18 June 2015, 23:39:41 UTC | RefAlign Test: use the class, get model from test factory | 18 June 2015, 23:39:41 UTC |
| 58ce0c2 | Eddie Belter | 18 June 2015, 22:44:29 UTC | CQID: use bridge __display_name__ | 18 June 2015, 22:44:29 UTC |
| 3e817a2 | Eddie Belter | 18 June 2015, 22:44:02 UTC | AnP: add __display_name__ to bridge | 18 June 2015, 22:44:02 UTC |
| 86f5e81 | Eddie Belter | 18 June 2015, 22:33:19 UTC | CQID: pass anp instdata bridge to should_skip | 18 June 2015, 22:33:19 UTC |
| 0c78596 | Eddie Belter | 18 June 2015, 22:29:57 UTC | CQID: update skip message | 18 June 2015, 22:29:57 UTC |
| 826f089 | Eddie Belter | 18 June 2015, 22:27:32 UTC | CQID: state the AnP and instdata we are working on | 18 June 2015, 22:27:32 UTC |
| 13118de | Adam Coffman | 18 June 2015, 21:47:33 UTC | remove now unused lsf requirements | 18 June 2015, 21:47:33 UTC |
| b650a45 | Adam Coffman | 18 June 2015, 21:45:46 UTC | override subs in test - we dont have a real bam file to stat | 18 June 2015, 21:45:46 UTC |
| f5aa195 | Adam Coffman | 18 June 2015, 21:44:16 UTC | populate lsf resource requirements at workflow construction | 18 June 2015, 21:44:16 UTC |
| 853bfb7 | Adam Coffman | 18 June 2015, 21:43:35 UTC | add helper method to estimate gtmp usage for speedseq | 18 June 2015, 21:43:35 UTC |
| f291f8a | Anthony Brummett | 18 June 2015, 15:32:43 UTC | Merge pull request #823 from brummett/error-message Ensure the exception message shows up in the error message. | 18 June 2015, 15:32:43 UTC |
| 5776c72 | Eddie Belter | 17 June 2015, 21:24:56 UTC | InstData Update Command remove the only_if_null to allow values to be updated expand the exclude lsit of things that shold not be eaily modifyable | 17 June 2015, 21:24:56 UTC |
| a5282bc | Eddie Belter | 17 June 2015, 21:02:38 UTC | Merge pull request #817 from tmooney/assembly_validation_uses_new_shellcmd Assembly validation uses new shellcmd | 17 June 2015, 21:02:38 UTC |
| c0f90d2 | Adam Coffman | 17 June 2015, 20:10:06 UTC | convert name helpers to class methods | 17 June 2015, 20:10:06 UTC |
| ed57522 | Susanna Siebert | 17 June 2015, 19:27:47 UTC | Update tests to not pass along threads as an aligner param | 17 June 2015, 19:27:47 UTC |
| 0f4b508 | Susanna Siebert | 17 June 2015, 18:59:38 UTC | Get the number of threads to use for speedseq from the LSF environment variables | 17 June 2015, 18:59:38 UTC |
| 75d691c | Anthony Brummett | 17 June 2015, 16:36:47 UTC | Ensure the exception message shows up in the error message. Looks like rollback() was blanking $_, making the error message not helpful. | 17 June 2015, 16:37:40 UTC |
| 0ad03a8 | Eddie Belter | 16 June 2015, 22:51:12 UTC | Remove unsed solr scripts | 16 June 2015, 22:51:12 UTC |
| 800f793 | David Morton | 16 June 2015, 17:17:27 UTC | Merge pull request #810 from davidlmorton/ptero_build_view Ptero build view | 16 June 2015, 17:17:27 UTC |
| 79ce535 | Thomas B. Mooney | 16 June 2015, 17:11:50 UTC | Merge pull request #794 from tmooney/refactor_model_examination_in_model_summary Reduce Build Loading in ModelSummary | 16 June 2015, 17:11:50 UTC |
| de91d92 | Thomas Mooney | 15 June 2015, 17:25:21 UTC | Remove redundant print. | 16 June 2015, 15:47:57 UTC |
| 03b9611 | Thomas Mooney | 15 June 2015, 17:20:30 UTC | Use direct execution form of shellcmd to avoid shell characters in names | 16 June 2015, 15:47:57 UTC |
| 5aa4ff7 | Thomas Mooney | 15 June 2015, 15:57:11 UTC | Remove commented-out and cut code. | 16 June 2015, 15:47:57 UTC |
| 0d6de2f | Thomas Mooney | 15 June 2015, 15:49:19 UTC | Whitespace. | 16 June 2015, 15:47:57 UTC |
| b1cf904 | Thomas B. Mooney | 16 June 2015, 15:47:08 UTC | Merge pull request #813 from tmooney/no_newline_in_redirected_output Only print an extra newline if output was not redirected. | 16 June 2015, 15:47:08 UTC |
| 4378b98 | Thomas B. Mooney | 16 June 2015, 15:18:31 UTC | Merge pull request #806 from tmooney/small_rna_workflow_validation Remove Doubled-Up SmallRNA Workflow Links | 16 June 2015, 15:18:31 UTC |
| 541d94b | Thomas Mooney | 16 June 2015, 15:13:28 UTC | Avoid undef: Sort by created_at. (Unstartable builds aren't scheduled.) | 16 June 2015, 15:13:28 UTC |
| 75e6669 | Thomas Mooney | 04 June 2015, 18:23:57 UTC | Save the cookie jar directly in the UA. (That way they're ready for us even if we don't search.) | 16 June 2015, 15:12:34 UTC |
| 78bb2cf | Thomas Mooney | 03 June 2015, 21:52:58 UTC | Optionally include the ticket subjects in the output. | 16 June 2015, 15:12:33 UTC |
| cbef65a | Thomas Mooney | 03 June 2015, 21:32:04 UTC | Add "Nobody" as an example value for owner. | 16 June 2015, 15:12:33 UTC |
| e1456d0 | Thomas Mooney | 03 June 2015, 21:30:33 UTC | Extract common subroutines to a base class. | 16 June 2015, 15:12:33 UTC |
| fa84250 | Thomas Mooney | 03 June 2015, 21:20:30 UTC | Deduplicate ticket getting. | 16 June 2015, 15:12:33 UTC |
| bf54a3d | Thomas Mooney | 03 June 2015, 21:15:28 UTC | Deduplicate search for open tickets. | 16 June 2015, 15:12:33 UTC |
| 0c1656a | Thomas Mooney | 03 June 2015, 20:52:08 UTC | New command to summarize the status of models found in tickets. The command expects the tickets to contain the model IDs as formatted by the `genome model admin failed-model-tickets` command. | 16 June 2015, 15:12:32 UTC |
| c044c74 | Thomas Mooney | 03 June 2015, 20:51:24 UTC | Update help text to reflect the current behaviour. | 16 June 2015, 15:12:32 UTC |
| c560dfa | Thomas Mooney | 03 June 2015, 20:39:22 UTC | Remove unused includes. | 16 June 2015, 15:12:32 UTC |
| 494a9fc | Thomas B. Mooney | 16 June 2015, 15:09:28 UTC | Merge pull request #793 from tmooney/failed_model_tickets_gets_builds_directly Get failed/unstartable builds directly. | 16 June 2015, 15:09:28 UTC |
| 7ee2649 | APipe Tester | 16 June 2015, 12:19:43 UTC | Updated `genome` tab completion. | 16 June 2015, 12:19:43 UTC |
| 9b6fc21 | Susanna Siebert | 15 June 2015, 20:44:01 UTC | Merge pull request #811 from susannasiebert/speedseq_md5 Check that the md5 file exists after the merged speedseq alignment result gets created | 15 June 2015, 20:44:01 UTC |
| 9dfaea1 | Eddie Belter | 15 June 2015, 17:26:10 UTC | Merge pull request #812 from ebelter/gm-define Change property from variant_list_build to dbsnp_build in genotype model define command. | 15 June 2015, 17:26:10 UTC |
| 9775d31 | dmorton | 15 June 2015, 17:03:21 UTC | Make process a UR property instead of a method | 15 June 2015, 17:03:21 UTC |
| 7f6bce3 | Thomas Mooney | 15 June 2015, 15:10:25 UTC | Only print an extra newline if output was not redirected. This reverts commit ba557795fe0e72ca1d4a691230206d9e39e7e80e. | 15 June 2015, 15:17:36 UTC |
| 85569de | APipe Tester | 13 June 2015, 12:19:06 UTC | Updated `gmt` tab completion. | 13 June 2015, 12:19:06 UTC |
| 59a45aa | APipe Tester | 13 June 2015, 12:18:16 UTC | Updated `genome` tab completion. | 13 June 2015, 12:18:16 UTC |
| 12c10e8 | APipe Tester | 13 June 2015, 12:16:33 UTC | Updated class browser cache. | 13 June 2015, 12:16:33 UTC |
| 1e3e1d3 | Eddie Belter | 13 June 2015, 00:13:11 UTC | Genotype Microarry Dependent Cron RefAlign Allow getting of dependent cron ref align models w/o reference first, then filter by if the reference is compatible. | 13 June 2015, 00:13:11 UTC |
| 361d0ce | Eddie Belter | 12 June 2015, 22:50:46 UTC | Change property from variant_list_build to dbsnp_build in genotype model define command. | 12 June 2015, 23:10:26 UTC |
| da0fb0c | Allison Penner Regier | 12 June 2015, 19:23:40 UTC | Merge pull request #808 from apregier/bedpe EvaluateBedpe tweaks | 12 June 2015, 19:23:40 UTC |
| 5b20794 | Susanna Siebert | 12 June 2015, 15:13:22 UTC | Check that the md5 file exists after the merged alignment result gets created | 12 June 2015, 15:13:22 UTC |
| 623d1a4 | dmorton | 12 June 2015, 14:12:13 UTC | Allow 'genome model build view' to show PTero run workflows | 12 June 2015, 14:12:13 UTC |
| a100e82 | dmorton | 12 June 2015, 14:11:18 UTC | Extract method to get a process for a build | 12 June 2015, 14:11:18 UTC |
| 80a1f6d | Thomas B. Mooney | 11 June 2015, 22:01:25 UTC | Merge pull request #792 from tmooney/print_lock_resource_not_object_hash Print the resource in the debug message, not the object hash. | 11 June 2015, 22:01:25 UTC |
| e78597b | apregier | 11 June 2015, 20:28:56 UTC | Add tool to run a matrix of evaluate-bedpe experiments | 11 June 2015, 20:29:29 UTC |
| bbfad22 | apregier | 11 June 2015, 19:32:25 UTC | Only count unique sv calls | 11 June 2015, 20:29:27 UTC |
| 3e6151b | apregier | 11 June 2015, 18:57:04 UTC | Don't double count svs if they hit more than one gold sv | 11 June 2015, 20:29:27 UTC |
| c10e72b | apregier | 11 June 2015, 18:56:41 UTC | Add total calls stat | 11 June 2015, 20:29:25 UTC |
| 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 |
| 404856a | Thomas Mooney | 11 June 2015, 15:33:14 UTC | Remove strange string of #s. | 11 June 2015, 15:33:14 UTC |
| c6eb755 | Thomas Mooney | 11 June 2015, 15:33:02 UTC | Remove hard-coded log directory. | 11 June 2015, 15:33:02 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 |
| 77778eb | Thomas Mooney | 11 June 2015, 14:50:06 UTC | Remove extraneous links from/to "result" properties. | 11 June 2015, 14:50:40 UTC |
| e70fdaf | Thomas Mooney | 11 June 2015, 14:41:21 UTC | Whitespace. | 11 June 2015, 14:41:21 UTC |
