| a653e09 | Thomas B. Mooney | 28 July 2015, 17:39:15 UTC | Merge pull request #879 from tmooney/disconnect_dbh_before_long_waiting_things Disconnect Database Handles before potentially long-running actions | 28 July 2015, 17:39:15 UTC |
| c3125a1 | Thomas B. Mooney | 28 July 2015, 14:46:06 UTC | Merge pull request #865 from tmooney/deduplicate_reference_indices Deduplicate Aligner and Annotation Index Classes | 28 July 2015, 14:46:06 UTC |
| 838ccdb | Jason Walker | 28 July 2015, 14:13:13 UTC | Merge pull request #851 from jasonwalker80/library_duplication_rates Library Duplication Rates from Reference Alignment builds | 28 July 2015, 14:13:13 UTC |
| ed245d3 | APipe Tester | 27 July 2015, 18:27:24 UTC | updated jenkins submodule to 6a39f4b | 27 July 2015, 19:22:27 UTC |
| 940b82b | Eddie Belter | 27 July 2015, 18:54:59 UTC | Merge pull request #878 from ebelter/model-rm-trigger-downstream-models Model: remove unused _trigger_downstream_builds | 27 July 2015, 18:54:59 UTC |
| 513b692 | Avinash Ramu | 27 July 2015, 15:02:51 UTC | Merge pull request #849 from gatoravi/loh_plot_update Remove unwanted points from LOH plot | 27 July 2015, 15:02:51 UTC |
| 3d18bdc | Thomas Mooney | 27 July 2015, 14:21:09 UTC | IDs could be non-numeric these days. | 27 July 2015, 14:21:09 UTC |
| ba5f374 | Thomas B. Mooney | 27 July 2015, 14:19:17 UTC | Merge pull request #877 from tmooney/fix_microarray_dependent_model_check Fix Microarray dependent model check | 27 July 2015, 14:19:17 UTC |
| ac7459a | Thomas Mooney | 27 July 2015, 14:15:18 UTC | Also disconnect before waiting on PTero workflow. | 27 July 2015, 14:15:18 UTC |
| 2b27910 | Thomas B. Mooney | 27 July 2015, 14:11:09 UTC | Merge pull request #885 from tmooney/workflowbuilder_streamgraph_uses_shellcmd Use shellcmd instead of IPC::Run. | 27 July 2015, 14:11:09 UTC |
| 2c006d8 | APipe Tester | 26 July 2015, 18:51:41 UTC | updated ur submodule to b40400c | 26 July 2015, 18:51:41 UTC |
| 6fa7a43 | APipe Tester | 25 July 2015, 12:17:43 UTC | Updated `genome` tab completion. | 25 July 2015, 12:17:43 UTC |
| aa66c27 | APipe Tester | 25 July 2015, 12:15:43 UTC | Updated class browser cache. | 25 July 2015, 12:15:43 UTC |
| c017835 | David Morton | 25 July 2015, 03:58:49 UTC | Merge pull request #888 from davidlmorton/control_flow PTero: Control flow feature | 25 July 2015, 03:58:49 UTC |
| 59250e1 | dmorton | 24 July 2015, 22:12:16 UTC | Update test data for libptero-perl 0.1.7+ The json representation of a workflow changed with respect to how the links section is encoded. | 24 July 2015, 22:12:16 UTC |
| 533cddb | dmorton | 24 July 2015, 22:06:02 UTC | Update how we build PTero workflows for sdk 0.1.7+ libptero-perl 0.1.7 changed the api related to defining links so that more than one data-flow could be defined between a pair of tasks. | 24 July 2015, 22:06:02 UTC |
| f385e25 | dmorton | 24 July 2015, 22:03:22 UTC | Add test that can be run for Genome::Processes This isn't an automated perl-test but it is a Process that you can run manually. It was useful for making sure Genome::Processes can be run with both legacy workflow as well as PTero without testing using a variant-report or something computationally expensive/complex. | 24 July 2015, 22:05:56 UTC |
| 99ed1cc | Thomas Mooney | 23 July 2015, 21:45:01 UTC | Use shellcmd instead of IPC::Run | 23 July 2015, 21:45:01 UTC |
| 80e97c0 | Eddie Belter | 23 July 2015, 19:48:57 UTC | Merge pull request #875 from ebelter/model-define Model define.t simplification | 23 July 2015, 19:48:57 UTC |
| 9fa15e8 | David Morton | 23 July 2015, 19:36:34 UTC | Merge pull request #883 from davidlmorton/ptero_sdk_1_6_update Update test-data for Ptero sdk version 0.1.6 | 23 July 2015, 19:36:34 UTC |
| ef18dbd | dmorton | 23 July 2015, 19:34:49 UTC | Update test-data for Ptero sdk version 0.1.6 This version introduced the 'dataFlow' syntax to the link definitions. | 23 July 2015, 19:34:49 UTC |
| b94f072 | Thomas Mooney | 23 July 2015, 13:42:40 UTC | Disconnect dbh before launching readcounts workflow. | 23 July 2015, 13:42:40 UTC |
| 2c81ebe | Thomas Mooney | 22 July 2015, 21:00:39 UTC | Disconnect DBH before submitting workflow. This won't return until it's done. | 22 July 2015, 21:00:39 UTC |
| 7576d58 | Thomas Mooney | 22 July 2015, 21:00:06 UTC | Disconnect from DB before locking. We might be waiting hours or days... | 22 July 2015, 21:00:06 UTC |
| 6cf073a | Thomas B. Mooney | 22 July 2015, 20:07:13 UTC | Merge pull request #874 from tmooney/send_to_pap_wf_errors_are_errors Use error_message for SendToPap's Workflow Errors | 22 July 2015, 20:07:13 UTC |
| 26913ed | Eddie Belter | 22 July 2015, 19:15:36 UTC | Build: rm _trigger_downstream_builds call | 22 July 2015, 19:15:36 UTC |
| 98b4c76 | Thomas Mooney | 22 July 2015, 15:32:57 UTC | Model IDs aren't numeric. | 22 July 2015, 15:32:57 UTC |
| 2352e7a | Thomas Mooney | 22 July 2015, 15:32:38 UTC | Fix precedence in dependent model logic. | 22 July 2015, 15:32:38 UTC |
| d6c983f | Eddie Belter | 21 July 2015, 22:45:20 UTC | Model: remove unused _trigger_downstream_builds | 21 July 2015, 22:45:20 UTC |
| f317fec | Eddie Belter | 21 July 2015, 22:42:42 UTC | Model Define: use sub tests | 21 July 2015, 22:42:42 UTC |
| 8103702 | Eddie Belter | 21 July 2015, 22:37:26 UTC | Model Define: simplify accessor tests | 21 July 2015, 22:37:26 UTC |
| 5a887a0 | Eddie Belter | 21 July 2015, 22:24:28 UTC | Model Define: rm skipped tests | 21 July 2015, 22:24:28 UTC |
| 1675d1c | Eddie Belter | 21 July 2015, 22:06:23 UTC | Model Define: rm unsed variables | 21 July 2015, 22:07:06 UTC |
| e662f08 | Eddie Belter | 21 July 2015, 22:03:52 UTC | Model Define: merge tests | 21 July 2015, 22:03:52 UTC |
| 7456189 | Eddie Belter | 21 July 2015, 22:03:47 UTC | Model Define: merge tests | 21 July 2015, 22:03:47 UTC |
| 12db73e | Eddie Belter | 21 July 2015, 21:54:52 UTC | Model Define: test processing profile directly | 21 July 2015, 21:54:52 UTC |
| 0d21a8a | Eddie Belter | 21 July 2015, 21:52:03 UTC | Model Define: use define class instead of deriving it | 21 July 2015, 21:52:03 UTC |
| ecb246a | Eddie Belter | 21 July 2015, 21:49:38 UTC | Model Define: use test factory for reseq | 21 July 2015, 21:49:38 UTC |
| bf0b04b | Eddie Belter | 21 July 2015, 21:42:36 UTC | Model Define: no more convergence models | 21 July 2015, 21:42:36 UTC |
| de6cb80 | Eddie Belter | 21 July 2015, 21:41:57 UTC | Model Define: pass model group objects | 21 July 2015, 21:41:57 UTC |
| 28e8555 | Eddie Belter | 21 July 2015, 21:36:18 UTC | Model Define: rm unneeded test creating model w/ diff refseq | 21 July 2015, 21:37:10 UTC |
| 190d76e | Eddie Belter | 21 July 2015, 21:33:12 UTC | Model Define: rm test_model_from_params and call successful_create_model directly | 21 July 2015, 21:33:21 UTC |
| f1631bc | Eddie Belter | 21 July 2015, 21:26:36 UTC | Model Define: rm unused failure testing | 21 July 2015, 21:26:44 UTC |
| 0d10384 | Eddie Belter | 21 July 2015, 21:23:34 UTC | Model Define: rm tmpdir | 21 July 2015, 21:23:34 UTC |
| 90e79b2 | Eddie Belter | 21 July 2015, 21:21:59 UTC | Model Define: do not test processing profile param accessors | 21 July 2015, 21:22:40 UTC |
| 004915a | Eddie Belter | 21 July 2015, 21:21:30 UTC | Model Define: add plan | 21 July 2015, 21:21:30 UTC |
| 750ebe8 | Eddie Belter | 21 July 2015, 21:19:32 UTC | Model Define: use test factory for sample | 21 July 2015, 21:19:52 UTC |
| 25fee4d | Eddie Belter | 21 July 2015, 21:17:41 UTC | Model Define: use test factory for processing profile | 21 July 2015, 21:17:41 UTC |
| 4d45c10 | Eddie Belter | 21 July 2015, 21:10:37 UTC | Model Define: rm used modules | 21 July 2015, 21:10:37 UTC |
| c2e1002 | Eddie Belter | 21 July 2015, 20:59:17 UTC | Model Define: rm skipped test and unused sub | 21 July 2015, 21:06:21 UTC |
| 05ce10a | Eddie Belter | 21 July 2015, 20:58:29 UTC | Model Define: rm unused sub in test | 21 July 2015, 20:58:29 UTC |
| b651bc0 | Thomas Mooney | 21 July 2015, 20:53:46 UTC | Use error_message to print info about errors. | 21 July 2015, 20:53:46 UTC |
| 4389fd1 | Thomas Mooney | 21 July 2015, 20:52:31 UTC | Remove useless $Id$ | 21 July 2015, 20:52:31 UTC |
| da33e4f | Thomas Mooney | 21 July 2015, 20:52:13 UTC | Whitespace. | 21 July 2015, 20:52:13 UTC |
| e74c950 | Thomas B. Mooney | 21 July 2015, 15:57:45 UTC | Merge pull request #867 from jasonwalker80/inactive_config_item_status Inactive analysis project config profile item status | 21 July 2015, 15:57:45 UTC |
| 11133d7 | Thomas B. Mooney | 21 July 2015, 15:57:27 UTC | Merge pull request #870 from tmooney/eliminate_hardcoded_disk_groups Replace hard-coded disk groups with calls to config. | 21 July 2015, 15:57:27 UTC |
| 472899c | Anthony Brummett | 20 July 2015, 21:10:09 UTC | Merge pull request #871 from brummett/aggr It'll now work with aggrs containing any number of digits. | 20 July 2015, 21:10:09 UTC |
| 8477e42 | Anthony Brummett | 20 July 2015, 20:30:24 UTC | It'll now work with aggrs containing any number of digits. The regex was failing to match /vol/aggr3/ which only contained one digit | 20 July 2015, 20:30:24 UTC |
| d0fb1ab | Thomas B. Mooney | 20 July 2015, 19:04:38 UTC | Merge pull request #868 from tmooney/APIPE-2810 Add test case that we get Tag back when validation fails. | 20 July 2015, 19:04:38 UTC |
| 949f90a | Thomas Mooney | 20 July 2015, 18:13:51 UTC | Replace hard-coded disk groups with calls to config. | 20 July 2015, 18:13:51 UTC |
| 46baccc | Thomas B. Mooney | 20 July 2015, 17:35:37 UTC | Merge pull request #809 from tmooney/make_path_tests_for_directory Also test for directory existence before trying to create it. | 20 July 2015, 17:35:37 UTC |
| 71b2d01 | APipe Tester | 18 July 2015, 12:18:36 UTC | Updated `genome` tab completion. | 18 July 2015, 12:18:36 UTC |
| 05846cc | APipe Tester | 18 July 2015, 12:16:48 UTC | Updated class browser cache. | 18 July 2015, 12:16:48 UTC |
| 6dfd34a | Eddie Belter | 17 July 2015, 19:59:42 UTC | Merge pull request #853 from ebelter/refcov-metrics RefCov Metrics | 17 July 2015, 19:59:42 UTC |
| af67d87 | Eddie Belter | 17 July 2015, 19:52:55 UTC | RefCov Metrics Cmd: update help mock results when no results | 17 July 2015, 19:52:59 UTC |
| e6a7eb9 | Eddie Belter | 17 July 2015, 17:37:57 UTC | Merge pull request #866 from ebelter/gm Genotype Microarray InstData: allow update when calling genotype_file accessor | 17 July 2015, 17:37:57 UTC |
| 24eda7e | Susanna Siebert | 17 July 2015, 13:40:11 UTC | Merge pull request #839 from susannasiebert/qc_framework_metrics Add additional qc metrics | 17 July 2015, 13:40:11 UTC |
| df3f4c4 | APipe Tester | 17 July 2015, 12:19:40 UTC | Updated `genome` tab completion. | 17 July 2015, 12:19:40 UTC |
| c867b54 | APipe Tester | 17 July 2015, 12:17:59 UTC | Updated class browser cache. | 17 July 2015, 12:17:59 UTC |
| 27bf04d | David Morton | 17 July 2015, 03:04:51 UTC | Merge pull request #862 from davidlmorton/encode_decode Rewrite Genome::Utility::Inputs to support more | 17 July 2015, 03:04:51 UTC |
| c0510ad | Susanna Siebert | 16 July 2015, 20:20:49 UTC | Add QC metrisc for number of reads that are properly paired | 16 July 2015, 20:20:49 UTC |
| 7169401 | Jim Eldred | 16 July 2015, 16:18:51 UTC | Merge pull request #859 from brummett/project-purge-command Project purge command | 16 July 2015, 16:18:51 UTC |
| 703c762 | Thomas Mooney | 15 July 2015, 19:46:52 UTC | Add test case that we get Tag back when validation fails. | 15 July 2015, 19:47:52 UTC |
| 519ba70 | Anthony Brummett | 15 July 2015, 19:10:31 UTC | extract preparing SQL to a method and only do it once | 15 July 2015, 19:10:31 UTC |
| 2e8a795 | Anthony Brummett | 15 July 2015, 19:09:59 UTC | only expunge if --dry-run is off! | 15 July 2015, 19:09:59 UTC |
| ab82f5f | Eddie Belter | 15 July 2015, 18:06:56 UTC | RefCov Metrics: move creating mock objects into functions | 15 July 2015, 18:06:56 UTC |
| 8c7a0e7 | Eddie Belter | 15 July 2015, 18:04:09 UTC | RefCov Metrics: fix bugs in setting row ids | 15 July 2015, 18:04:09 UTC |
| 9936625 | Anthony Brummett | 15 July 2015, 17:40:06 UTC | Unify messages printed while expunging In dry-run mode, it prints out "Would remove", while in regular mode prints "Removing" | 15 July 2015, 17:40:06 UTC |
| 5f531ed | Anthony Brummett | 15 July 2015, 17:30:54 UTC | Extract method to do the expunging, and throw exception if commit() fails | 15 July 2015, 17:30:54 UTC |
| 8f2f4a4 | Thomas B. Mooney | 15 July 2015, 17:30:11 UTC | Merge pull request #864 from tmooney/add_deprecated_to_non_current_statuses Add "Deprecated" as a non-current status | 15 July 2015, 17:30:11 UTC |
| 4fb354d | Jason Walker | 15 July 2015, 15:40:29 UTC | Merge pull request #1 from tmooney/inactive_config_item_status Changes to Support new "Inactive" status | 15 July 2015, 15:40:29 UTC |
| 054781d | Thomas Mooney | 15 July 2015, 14:57:55 UTC | Add a colour for "inactive" status in view. | 15 July 2015, 14:57:55 UTC |
| 42ba4b6 | Thomas Mooney | 15 July 2015, 14:54:29 UTC | Only manually add models to inactive configs. | 15 July 2015, 14:56:01 UTC |
| cd94c9f | Thomas Mooney | 15 July 2015, 14:53:07 UTC | Inactive configs are still "current". | 15 July 2015, 14:53:07 UTC |
| f09622a | Thomas Mooney | 15 July 2015, 14:50:42 UTC | Only include "active" configurations when preparing Profile for CQID. | 15 July 2015, 14:50:42 UTC |
| 28fa619 | APipe Tester | 15 July 2015, 14:24:54 UTC | Updated `genome` tab completion. | 15 July 2015, 14:24:54 UTC |
| 81e123a | APipe Tester | 15 July 2015, 14:21:51 UTC | Updated class browser cache. | 15 July 2015, 14:21:51 UTC |
| 5ea590c | Jason Walker | 15 July 2015, 14:19:33 UTC | Add inactive status for analysis project config profile items. The inactive status is used for the store-only option when adding config. | 15 July 2015, 14:19:33 UTC |
| 161b974 | Eddie Belter | 14 July 2015, 22:45:06 UTC | RefCov Metric Command allow different types of models add row identifiers update the way headers are uniq'd | 14 July 2015, 22:45:06 UTC |
| affa987 | Eddie Belter | 14 July 2015, 21:25:55 UTC | Genotype Microarray InstData: allow update when calling genotype_file accessor | 14 July 2015, 21:25:55 UTC |
| 8d328b9 | Thomas B. Mooney | 14 July 2015, 19:58:20 UTC | Merge pull request #863 from tmooney/instrument_data_fixme Cleanup in Genome/InstrumentData | 14 July 2015, 19:58:20 UTC |
| 93676f9 | Thomas Mooney | 14 July 2015, 19:51:02 UTC | Reformat class definition (whitespace). | 14 July 2015, 19:55:29 UTC |
| 5c23f93 | Thomas Mooney | 14 July 2015, 19:44:16 UTC | Pull up resolution of the reference fasta. | 14 July 2015, 19:55:29 UTC |
| 080c121 | Thomas Mooney | 14 July 2015, 19:36:47 UTC | Extract promotion logic to base class. | 14 July 2015, 19:36:47 UTC |
| 62d599b | Thomas Mooney | 14 July 2015, 19:26:53 UTC | Pull up create() to base class. | 14 July 2015, 19:26:53 UTC |
| 1eabaad | Thomas Mooney | 14 July 2015, 19:24:22 UTC | Rename index preparation methods to common _prepare_index | 14 July 2015, 19:24:22 UTC |
| 72b5a5f | Thomas Mooney | 14 July 2015, 19:18:59 UTC | Remove redundant debug_message. The same information is printed in the very next message. | 14 July 2015, 19:18:59 UTC |
| ce1178f | Thomas Mooney | 14 July 2015, 19:14:51 UTC | Pull up get_or_create and dependent subroutines. AnnotationIndex no longer overrides get(). | 14 July 2015, 19:18:52 UTC |
| aadedac | Thomas Mooney | 14 July 2015, 19:11:11 UTC | Remove unused code. | 14 July 2015, 19:11:11 UTC |
| 605382b | Thomas Mooney | 14 July 2015, 19:09:50 UTC | Rename check_dependencies to generate_dependenices_as_needed. This name was updated in AlignerIndex previously. | 14 July 2015, 19:09:50 UTC |
