| d6c983f | Eddie Belter | 21 July 2015, 22:45:20 UTC | Model: remove unused _trigger_downstream_builds | 21 July 2015, 22:45:20 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 |
| b71a042 | Susanna Siebert | 10 July 2015, 15:43:56 UTC | Update the calculation of reads_mapped_in_interchromosomal_pairs_percentage | 10 July 2015, 16:53:37 UTC |
| 9ea66a8 | APipe Tester | 09 July 2015, 20:47:31 UTC | updated ur submodule to ac1d211 | 09 July 2015, 20:47:31 UTC |
| fe66fb1 | Jason Walker | 09 July 2015, 18:38:39 UTC | Remove Deprecated from the lists of ALLOWED statuses to operate on for Hold and Release commands. | 09 July 2015, 18:38:39 UTC |
| cf64654 | Jason Walker | 09 July 2015, 16:54:54 UTC | Updated help_detail. | 09 July 2015, 16:54:54 UTC |
| 51d4454 | Susanna Siebert | 09 July 2015, 15:54:29 UTC | Merge pull request #857 from susannasiebert/qc_framework_verify_bam_id_merged Allow QC framework to work on merged alignment results | 09 July 2015, 15:54:29 UTC |
| 5cfc51f | Jason Walker | 09 July 2015, 15:51:52 UTC | New analysis project status Depcrecated and a new Deprecate command. Support for Deprecated status added to existing status update commands. | 09 July 2015, 15:51:52 UTC |
| 8d4cb66 | Susanna Siebert | 09 July 2015, 14:57:20 UTC | Even better error message | 09 July 2015, 14:57:20 UTC |
| 9f22972 | APipe Tester | 09 July 2015, 12:19:23 UTC | Updated `genome` tab completion. | 09 July 2015, 12:19:23 UTC |
| aa9c079 | APipe Tester | 09 July 2015, 12:17:43 UTC | Updated class browser cache. | 09 July 2015, 12:17:43 UTC |
| 00721d8 | Eddie Belter | 08 July 2015, 23:41:54 UTC | RefCov Metrics accept ref-align or som-val models go through builds results to find coverage stats add test for no results found | 08 July 2015, 23:41:54 UTC |
| e3c12f3 | Thomas B. Mooney | 08 July 2015, 22:40:25 UTC | Merge pull request #856 from tmooney/gp_eukaryotic_split_fasta_is_many GP Eukaryotic: Make fasta_files is_many in SplitFasta | 08 July 2015, 22:40:25 UTC |
| 4cb8b00 | Thomas B. Mooney | 08 July 2015, 22:40:14 UTC | Merge pull request #855 from tmooney/add_block_operation_to_workflowbuilder WorkflowBuilder class for Block operations. | 08 July 2015, 22:40:14 UTC |
| c57fa8a | Thomas Mooney | 08 July 2015, 20:51:33 UTC | Require the module we're about to use. | 08 July 2015, 20:51:33 UTC |
| dfbf8b4 | Eddie Belter | 08 July 2015, 19:51:22 UTC | DV2 Alloc Error: class instead of self | 08 July 2015, 19:51:22 UTC |
| f5bf38d | Eddie Belter | 08 July 2015, 19:49:34 UTC | DV2: call error_message instead of using variable | 08 July 2015, 19:49:34 UTC |
| 0ccb5e6 | Anthony Brummett | 08 July 2015, 19:40:41 UTC | Ensure we'll unlock if the SQL dies Make sure there's no way to die between locking the analysis project and creating the guard. | 08 July 2015, 19:40:41 UTC |
| cf6e2a9 | Anthony Brummett | 08 July 2015, 19:31:13 UTC | Don't need the commit observer The Scope Guard object is performing the same job. Additionally, we want to keep the analysis project locked until we're done with the whole thing, not just after each software result when the commit() happens. | 08 July 2015, 19:31:13 UTC |
| 94e6e8e | Anthony Brummett | 08 July 2015, 19:19:10 UTC | Lock while handling each analysis project It also prints a report about the total space freed at the end of each anp | 08 July 2015, 19:19:10 UTC |
| 1737cbf | Anthony Brummett | 08 July 2015, 19:17:54 UTC | return only the columns we're interested in | 08 July 2015, 19:17:54 UTC |
| ae473c7 | Anthony Brummett | 08 July 2015, 18:53:01 UTC | use error_message() and status_message() | 08 July 2015, 18:53:01 UTC |
| 82a723b | Anthony Brummett | 08 July 2015, 18:49:07 UTC | extract method to determine if the anp was modified more than the specified number of days | 08 July 2015, 18:49:07 UTC |
| 0b70b31 | Anthony Brummett | 08 July 2015, 18:43:11 UTC | extract method for purging one anp | 08 July 2015, 18:43:11 UTC |
| f62efa8 | Anthony Brummett | 08 July 2015, 18:37:45 UTC | add dry-run option for running without deleting anything | 08 July 2015, 18:37:45 UTC |
| 29d49f5 | Anthony Brummett | 08 July 2015, 18:27:39 UTC | Convert to be a Command::V2 module | 08 July 2015, 18:27:39 UTC |
| aba19b6 | Anthony Brummett | 08 July 2015, 18:14:31 UTC | initial commit from Jason's script | 08 July 2015, 18:14:31 UTC |
| b44e8cf | dmorton | 16 June 2015, 18:53:54 UTC | Allow for Block type operations in WorkflowBuilder Conflicts: lib/perl/Genome/WorkflowBuilder/Block.pm | 08 July 2015, 17:56:46 UTC |
| 74d0a30 | Susanna Siebert | 30 June 2015, 18:20:24 UTC | Add test for running qc on merged alignment result | 08 July 2015, 14:15:53 UTC |
| 51e305f | Susanna Siebert | 30 June 2015, 18:20:04 UTC | Make is_capture subroutine work for merged alignment results | 08 July 2015, 13:34:18 UTC |
| 7c9d2d2 | Susanna Siebert | 30 June 2015, 18:19:38 UTC | Better error message | 08 July 2015, 13:34:17 UTC |
| 2b2a306 | APipe Tester | 08 July 2015, 12:23:42 UTC | Updated `gmt` tab completion. | 08 July 2015, 12:23:42 UTC |
| 8ae155d | APipe Tester | 08 July 2015, 12:22:43 UTC | Updated `genome` tab completion. | 08 July 2015, 12:22:43 UTC |
| 49b709a | Thomas Mooney | 07 July 2015, 21:34:39 UTC | Make fasta_files is_many. WorkflowBuilder cares about the difference between an ARRAY and an is_many property as the input to a parallelBy workflow. The name must be changed to split_fasta_files, because otherwise UR creates a singular "fasta_file" accessor that overwrites the input property. | 07 July 2015, 23:00:03 UTC |
| ffd5d0d | Thomas Mooney | 07 July 2015, 20:39:39 UTC | WorkflowBuilder class for Block operations. | 07 July 2015, 22:01:42 UTC |
| 1a2e07d | Thomas B. Mooney | 07 July 2015, 21:43:19 UTC | Merge pull request #850 from tmooney/configurable_dv2_dispatcher_lsf_resource Extract DV2 dispatcher resource requirements to a configuration variable. | 07 July 2015, 21:43:19 UTC |
| 9abe84e | Thomas B. Mooney | 07 July 2015, 21:43:07 UTC | Merge pull request #852 from tmooney/design_set_reference_doesnt_matter Don't worry about design_set reference in SomaticValidation | 07 July 2015, 21:43:07 UTC |
| faaf36c | Thomas Mooney | 07 July 2015, 19:42:32 UTC | Consistently use "default" instead of "default_value". | 07 July 2015, 19:42:32 UTC |
| dcee00b | Thomas B. Mooney | 07 July 2015, 19:40:39 UTC | Merge pull request #848 from tmooney/ligers_and_tigons_and_bears_oh_my Typofix: aliger => aligner | 07 July 2015, 19:40:39 UTC |
| 328fc8f | Eddie Belter | 07 July 2015, 19:03:39 UTC | DV2: correct error message and use built in sprintf | 07 July 2015, 19:03:39 UTC |
| 1ed3e51 | Thomas Mooney | 07 July 2015, 14:37:55 UTC | Whitespace. | 07 July 2015, 14:37:55 UTC |
| 42adcb0 | Thomas Mooney | 07 July 2015, 14:37:12 UTC | Print the path we actually tried to find! | 07 July 2015, 14:37:12 UTC |
| d7a7946 | Eddie Belter | 06 July 2015, 21:00:23 UTC | RefCov Metrics remove unneeded print use metric key with coverage and wingspan warn if no results found for a model | 06 July 2015, 21:02:51 UTC |
| 99a8e3c | Eddie Belter | 06 July 2015, 21:00:04 UTC | RefCov Metrics: class definition update | 06 July 2015, 21:00:04 UTC |
| 0ae1d63 | Eddie Belter | 06 July 2015, 20:59:19 UTC | RefCov Metrics: add output check | 06 July 2015, 20:59:19 UTC |
