| 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 |
| 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 |
| 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 |
| 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 |
| e6c2eec | Thomas Mooney | 11 June 2015, 13:02:25 UTC | Link the outputs of the steps to unique outputs of the workflow model. | 11 June 2015, 14:24:14 UTC |
| 3fb5077 | Thomas Mooney | 11 June 2015, 14:23:42 UTC | Remove redundant output declaration. | 11 June 2015, 14:24:13 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 |
| b4a65a1 | Thomas Mooney | 10 June 2015, 22:54:05 UTC | Whitespace. | 10 June 2015, 22:54:05 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 |
