| 7c41446 | Eddie Belter | 27 July 2015, 18:35:12 UTC | AR BLAT: rm unneeded comments and commented out code | 27 July 2015, 18:35:12 UTC |
| 2b4c96a | Eddie Belter | 27 July 2015, 18:30:55 UTC | RM Iferguso: remove from under allocated email | 27 July 2015, 18:30:55 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 0a28189 | Thomas Mooney | 14 July 2015, 18:10:28 UTC | Check for the full target path's existence before beginning work. This will trigger the automounter if necessary and save iterating through all the components of the path if it already exists. | 14 July 2015, 18:14:30 UTC |
| 56f4411 | Thomas Mooney | 14 July 2015, 14:00:47 UTC | Add "Deprecated" as a non-current status (hot on the heels of #861). | 14 July 2015, 15:58:13 UTC |
| a077d29 | Jason Walker | 14 July 2015, 15:57:42 UTC | Merge pull request #861 from jasonwalker80/deprecate_anp Command to Deprecate Analysis Projects | 14 July 2015, 15:57:42 UTC |
| 1e43362 | Jason Walker | 14 July 2015, 13:55:31 UTC | Correct typo in test description | 14 July 2015, 13:55:31 UTC |
| b308489 | dmorton | 14 July 2015, 03:27:48 UTC | Fix comment | 14 July 2015, 03:28:58 UTC |
| a938c7a | Thomas B. Mooney | 13 July 2015, 22:42:45 UTC | Merge pull request #807 from tmooney/only_schedule_current_dependent_refaligns Only schedule current dependent reference alignments. | 13 July 2015, 22:42:45 UTC |
| 34d0696 | Thomas B. Mooney | 13 July 2015, 22:41:19 UTC | Merge pull request #815 from tmooney/remove_bespoke_locking_for_sr_users Remove other locking now that SR::User is ObjectWithLockedConstruction. | 13 July 2015, 22:41:19 UTC |
| d5adb85 | Jason Walker | 13 July 2015, 15:51:48 UTC | Use Base command and single input project. Add valid_statuses for deprecate and improve test coverage for deprecated status. | 13 July 2015, 15:51:48 UTC |
| 0d6696f | Thomas Mooney | 27 May 2015, 18:09:23 UTC | A G:InstrumentData is not a G:SoftwareResult. This code was specious and has never accomplished anything, so remove it. | 13 July 2015, 15:18:51 UTC |
| 595ee00 | Thomas Mooney | 27 May 2015, 18:06:37 UTC | Implemented the requested test. | 13 July 2015, 15:18:51 UTC |
| bbcef24 | Thomas Mooney | 27 May 2015, 17:58:30 UTC | Use the reallocate method provided by Stageable. | 13 July 2015, 15:18:51 UTC |
| 45ad348 | Thomas Mooney | 27 May 2015, 17:45:40 UTC | Remove ancient FIXME. We check defined right below it! | 13 July 2015, 15:18:50 UTC |
| dabb3de | Thomas Mooney | 27 May 2015, 17:45:07 UTC | Don't worry about fixing a situation that we don't care to support. | 13 July 2015, 15:18:50 UTC |
| be14ea7 | Thomas B. Mooney | 13 July 2015, 14:24:05 UTC | Merge pull request #847 from tmooney/cleanup_per_lane_tophat Minor Cleanup of PerLaneTophat module | 13 July 2015, 14:24:05 UTC |
| 8fe968d | Thomas B. Mooney | 13 July 2015, 14:23:38 UTC | Merge pull request #854 from tmooney/fix_process_pindel_reads_error_message List the path we checked in error message. | 13 July 2015, 14:23:38 UTC |
| d7e5e4b | David Morton | 13 July 2015, 00:24:01 UTC | Merge pull request #818 from davidlmorton/ptero_wrapper_logging Ensure reason for error is written to the log file | 13 July 2015, 00:24:01 UTC |
| 5a34f0b | dmorton | 11 July 2015, 07:15:46 UTC | Save $_ to named variable | 11 July 2015, 07:15:46 UTC |
| c597b42 | dmorton | 11 July 2015, 06:46:32 UTC | Rewrite Genome::Utility::Inputs to support more It now supports: - Mixed element types in ARRAYs - Nested ARRAYs - Non-object HASHREFs Error handling around object decoding has been improved. | 11 July 2015, 07:06:50 UTC |
| 9f706f5 | Eddie Belter | 10 July 2015, 17:43:19 UTC | Merge pull request #860 from ebelter/dv2-alloc-error DV2: correct error message and use built in sprintf | 10 July 2015, 17:43:19 UTC |
