| c21ced3 | APipe Tester | 24 December 2015, 20:11:21 UTC | updated ur submodule to 6ae9457 | 24 December 2015, 20:11:21 UTC |
| 820ea71 | Thomas B. Mooney | 24 December 2015, 17:20:42 UTC | Merge pull request #1125 from tmooney/stageable_simple_recalls_with_subclass Let UR re-call with the correct subclass if StageableSimple called abstractly. | 24 December 2015, 17:20:42 UTC |
| abe871e | Thomas B. Mooney | 24 December 2015, 16:55:02 UTC | Merge pull request #1152 from tmooney/eliminate_duplicate_subroutine_declaration_in_file_comparer Don't import "compare" since we're defining our own. | 24 December 2015, 16:55:02 UTC |
| 328035e | Thomas Mooney | 08 December 2015, 20:32:10 UTC | Don't import "compare" since we're defining our own. | 24 December 2015, 14:31:07 UTC |
| ff99ea5 | APipe Tester | 24 December 2015, 13:16:50 UTC | Updated `genome` tab completion. | 24 December 2015, 13:16:50 UTC |
| 095f77d | APipe Tester | 24 December 2015, 13:15:13 UTC | Updated class browser cache. | 24 December 2015, 13:15:13 UTC |
| 9ce8222 | Eddie Belter | 23 December 2015, 21:07:29 UTC | Merge pull request #1170 from ebelter/sync-users Sync Sys/LDAP Users: Add --max-changes-allowed option to run with more than 10 changes | 23 December 2015, 21:07:29 UTC |
| f612fd5 | Thomas B. Mooney | 23 December 2015, 14:19:42 UTC | Merge pull request #1139 from tmooney/list_build_queue_limits_running_builds Add running build limit in "list-build-queue" | 23 December 2015, 14:19:42 UTC |
| 772a227 | APipe Tester | 23 December 2015, 13:16:28 UTC | Updated `genome` tab completion. | 23 December 2015, 13:16:28 UTC |
| f386190 | Eddie Belter | 22 December 2015, 21:15:50 UTC | Add explicit exit | 22 December 2015, 21:15:59 UTC |
| 7342bd5 | Eddie Belter | 22 December 2015, 21:12:00 UTC | spell check | 22 December 2015, 21:12:00 UTC |
| 77ad6db | Dave Larson | 22 December 2015, 21:07:07 UTC | Merge pull request #1167 from ernfrid/update_cle_prime2 Only load those converters that don't have test_name set | 22 December 2015, 21:07:07 UTC |
| 1c77c8e | Eddie Belter | 22 December 2015, 21:04:38 UTC | Merge pull request #1162 from ebelter/anp-reprocess-instdata AnP Reprocess | 22 December 2015, 21:04:38 UTC |
| 012b46f | Eddie Belter | 22 December 2015, 21:04:02 UTC | Sync Sys:LDAP Users: always display creates/deletes for reference; moved to method | 22 December 2015, 21:04:02 UTC |
| 215b9be | Eddie Belter | 22 December 2015, 20:49:50 UTC | Sync Users: rename force to max_changes_allowed; update messages | 22 December 2015, 20:49:50 UTC |
| ac998be | Eddie Belter | 22 December 2015, 20:37:26 UTC | Update no changes status message | 22 December 2015, 20:37:26 UTC |
| 5f06ba6 | Eddie Belter | 22 December 2015, 20:35:46 UTC | Use scalar arrayref to get counts, add changes message | 22 December 2015, 20:35:46 UTC |
| fdba152 | Eddie Belter | 22 December 2015, 20:31:24 UTC | Changes returns creates adn deletes arrayrefs | 22 December 2015, 20:31:24 UTC |
| f3bd52c | Eddie Belter | 22 December 2015, 20:30:51 UTC | Update test to expect arrayrefs aas returns for changes | 22 December 2015, 20:30:51 UTC |
| 5877771 | Eddie Belter | 22 December 2015, 01:10:19 UTC | Use status message instead of print | 22 December 2015, 20:09:57 UTC |
| 478a588 | Eddie Belter | 22 December 2015, 01:08:33 UTC | Sync Sys/LDAP Users: Add --force option to run with more than 10 changes | 22 December 2015, 20:09:50 UTC |
| 728e1e4 | APipe Tester | 22 December 2015, 13:16:37 UTC | Updated `genome` tab completion. | 22 December 2015, 13:16:37 UTC |
| 5729310 | APipe Tester | 22 December 2015, 13:15:02 UTC | Updated class browser cache. | 22 December 2015, 13:15:02 UTC |
| e7cad37 | David Morton | 22 December 2015, 01:03:30 UTC | Merge pull request #1163 from davidlmorton/lock_exit Asynchronous Shortcutting when using PTero | 22 December 2015, 01:03:30 UTC |
| 8dd349d | Thomas B. Mooney | 21 December 2015, 21:51:00 UTC | Merge pull request #1165 from tmooney/remove_simplealignment_model_type Remove "SimpleAlignment" model type. | 21 December 2015, 21:51:00 UTC |
| 0c032bb | David Morton | 21 December 2015, 20:20:12 UTC | Make env variable match name of config option | 21 December 2015, 20:20:12 UTC |
| 794c539 | Dave Larson | 21 December 2015, 16:02:53 UTC | only load those converters that don't have test_name set | 21 December 2015, 16:02:53 UTC |
| 93b831c | Thomas Mooney | 17 December 2015, 23:39:02 UTC | Remove "SimpleAlignment" pipeline. | 21 December 2015, 14:21:29 UTC |
| 160c7b7 | David Morton | 21 December 2015, 00:22:13 UTC | Update PTero test data We added "retry_settings" that get reflected in the JSON. | 21 December 2015, 00:22:13 UTC |
| 79398dc | APipe Tester | 18 December 2015, 13:18:07 UTC | Updated `genome` tab completion. | 18 December 2015, 13:18:07 UTC |
| fbd4135 | APipe Tester | 18 December 2015, 13:16:31 UTC | Updated class browser cache. | 18 December 2015, 13:16:31 UTC |
| a3a63cf | Eddie Belter | 18 December 2015, 00:29:09 UTC | Merge pull request #1114 from ebelter/biosamtools GMT Bio Sam AlignmentSummary updates | 18 December 2015, 00:29:09 UTC |
| 09d832e | Eddie Belter | 17 December 2015, 23:30:08 UTC | Merge pull request #1160 from ebelter/import-do-not-unarchive InstData Import: do not unarchive fastqs | 17 December 2015, 23:30:08 UTC |
| e625dd4 | Eddie Belter | 17 December 2015, 23:27:04 UTC | AnP Reprocess: do not use dot syntax for direct properties | 17 December 2015, 23:27:04 UTC |
| d352d8f | David Morton | 17 December 2015, 20:26:53 UTC | Make asynchronous shortcutting more targeted and robust 1) can be toggled separately from specifying the exit_code 2) can specify other aspects such as intervals and number of attempts 3) only affects software-result locking 4) only affects PTero jobs submitted to the shell-command service (shortcut attempts) 5) should work with all locking backends (not just the file-based backend) | 17 December 2015, 21:28:07 UTC |
| de84225 | Thomas B. Mooney | 17 December 2015, 20:52:56 UTC | Merge pull request #1154 from tmooney/remove_comparison_model_type Remove Genome::Model::Comparison. | 17 December 2015, 20:52:56 UTC |
| b30c7f1 | Thomas B. Mooney | 17 December 2015, 20:09:20 UTC | Merge pull request #1155 from tmooney/stash_our_trash_beautify_bluffington Remove trash folder support. Delete purged data immediately. | 17 December 2015, 20:09:20 UTC |
| 07a3147 | Adam Coffman | 17 December 2015, 16:30:00 UTC | Merge pull request #1158 from acoffman/use_display_name_for_anps Use display_name for printing AnalysisProject when Unarchiving | 17 December 2015, 16:30:00 UTC |
| a6e86cf | Thomas B. Mooney | 17 December 2015, 14:01:41 UTC | Merge pull request #1161 from tmooney/varscan_high_confidence_filter_uses_default_dv2_worker_queue Remove LSF queue overrides in Varscan "high confidence" filters. | 17 December 2015, 14:01:41 UTC |
| 049a4b0 | Eddie Belter | 16 December 2015, 21:33:07 UTC | AnP Reprocess: use instdata ids to get bridges | 16 December 2015, 21:33:07 UTC |
| 175859f | Eddie Belter | 16 December 2015, 21:30:37 UTC | AnP Reprocess: test reprocess 2 instdata | 16 December 2015, 21:30:37 UTC |
| 058f10a | David Morton | 16 December 2015, 20:39:01 UTC | Ensure logs are not overwritten With asynchronous shortcutting, we want to see logs from each attempt, not just the last one. | 16 December 2015, 20:39:01 UTC |
| bc67d63 | David Morton | 16 December 2015, 20:37:32 UTC | Allow Asynchronous Shortcutting when using PTero | 16 December 2015, 20:37:32 UTC |
| 21abda8 | Eddie Belter | 16 December 2015, 20:24:38 UTC | AnP Reprocess: organize subtests | 16 December 2015, 20:24:38 UTC |
| a5394ab | Eddie Belter | 16 December 2015, 20:21:40 UTC | AnP Reprocess: allow only select instdata to be reprocessed | 16 December 2015, 20:21:40 UTC |
| cc43600 | Eddie Belter | 16 December 2015, 20:21:05 UTC | AnP Reprocess: add subtest to reprocess only select instdata | 16 December 2015, 20:21:05 UTC |
| 5f834b7 | Thomas Mooney | 15 December 2015, 14:56:24 UTC | Remove LSF queue overrides in Varscan "high confidence" filters. They'll now use the default in DV2/Filter.pm | 15 December 2015, 14:56:24 UTC |
| bec97f9 | Eddie Belter | 15 December 2015, 00:31:27 UTC | InstData Import: do not unarchive fastqs | 15 December 2015, 00:31:27 UTC |
| dd08871 | Adam Coffman | 11 December 2015, 21:08:28 UTC | pass display_name to status_message instead of the object | 14 December 2015, 22:11:54 UTC |
| 2d2f91c | Feiyu Du | 11 December 2015, 20:54:30 UTC | Merge pull request #1157 from dufeiyu/tcga TCGA Priorities: make sample get_tcga_names return all possible tcga names | 11 December 2015, 20:54:30 UTC |
| de58326 | Feiyu Du | 11 December 2015, 18:53:27 UTC | make sample get_tcga_names return all possible tcga names | 11 December 2015, 18:53:27 UTC |
| b9e5612 | Susanna Kiwala | 11 December 2015, 16:25:14 UTC | Merge pull request #1156 from ernfrid/update_blessed_process Update CLE Test | 11 December 2015, 16:25:14 UTC |
| c2d121a | Dave Larson | 11 December 2015, 15:07:16 UTC | Update blessed process for CLE test | 11 December 2015, 15:07:16 UTC |
| 5d9ffdf | Thomas Mooney | 10 December 2015, 21:29:20 UTC | Remove trash disk group from valid groups. Once old snapshots have this change we can remove the value from the per-machine configuration files. | 10 December 2015, 21:29:20 UTC |
| 473bcaf | Thomas Mooney | 10 December 2015, 20:49:26 UTC | Update docs. | 10 December 2015, 20:49:26 UTC |
| a965e49 | Thomas Mooney | 10 December 2015, 20:39:18 UTC | Remove trash folder support. Delete purged data immediately. | 10 December 2015, 20:39:18 UTC |
| 817757c | Thomas Mooney | 10 December 2015, 16:39:33 UTC | Make maximum number of running builds a parameter. This still hardcodes a multiplier for apipe-builder, though. | 10 December 2015, 16:39:33 UTC |
| fe055c4 | Thomas Mooney | 10 December 2015, 16:13:35 UTC | Remove Genome::Model::Comparison. It was never fully implemented. | 10 December 2015, 16:14:26 UTC |
| e455b44 | APipe Tester | 10 December 2015, 13:17:18 UTC | Updated `gmt` tab completion. | 10 December 2015, 13:17:18 UTC |
| 1d991fe | APipe Tester | 10 December 2015, 13:16:34 UTC | Updated `genome` tab completion. | 10 December 2015, 13:16:34 UTC |
| a720830 | APipe Tester | 10 December 2015, 13:15:00 UTC | Updated class browser cache. | 10 December 2015, 13:15:00 UTC |
| 08b7a20 | Eddie Belter | 09 December 2015, 21:08:13 UTC | Merge pull request #1153 from ernfrid/blessed_process_update update blessed process to account for new N-caller and VAF fixes | 09 December 2015, 21:08:13 UTC |
| a3beeff | Dave Larson | 09 December 2015, 19:24:47 UTC | update blessed process to account for new N-caller and VAF fixes | 09 December 2015, 19:24:47 UTC |
| 44ce7eb | Feiyu Du | 09 December 2015, 18:33:21 UTC | Merge pull request #1149 from dufeiyu/tcga TCGA Priorities: Add dump_vcfs option to create sdrf file only | 09 December 2015, 18:33:21 UTC |
| 86ff863 | Thomas B. Mooney | 09 December 2015, 18:26:04 UTC | Merge pull request #1148 from tmooney/somatic_validation_subject_mapping_exporter SomaticValidation SubjectMapping Exporter | 09 December 2015, 18:26:04 UTC |
| 3981829 | Anthony Brummett | 09 December 2015, 14:26:45 UTC | Merge pull request #1066 from brummett/model-create-delete Model create delete | 09 December 2015, 14:26:45 UTC |
| 6dd2e61 | Feiyu Du | 08 December 2015, 19:45:20 UTC | print vcf manifest only if dump_vcfs is true | 08 December 2015, 19:45:20 UTC |
| 179a670 | Dave Larson | 08 December 2015, 19:41:12 UTC | Merge pull request #1096 from ernfrid/readcount_annotation_fix Readcount annotation fix | 08 December 2015, 19:41:12 UTC |
| e08bbac | Dave Larson | 08 December 2015, 19:27:24 UTC | Merge pull request #1098 from ernfrid/igv_session_labeling Attempt to fix Trio Reporting IGV labels | 08 December 2015, 19:27:24 UTC |
| 6a111cd | Dave Larson | 08 December 2015, 19:27:12 UTC | Merge pull request #1080 from apregier/ncallers-fix Ncallers fix | 08 December 2015, 19:27:12 UTC |
| e1b44e8 | Feiyu Du | 08 December 2015, 19:17:51 UTC | more changes requested by Mike | 08 December 2015, 19:17:51 UTC |
| 65adb3d | Feiyu Du | 08 December 2015, 16:33:44 UTC | add dump_vcfs option to create sdrf file only | 08 December 2015, 16:33:44 UTC |
| 7c6f95a | Thomas Mooney | 08 December 2015, 16:03:14 UTC | Use a common test for both importing and exporting somval mappings. | 08 December 2015, 16:03:14 UTC |
| e2147c9 | Thomas Mooney | 08 December 2015, 16:00:58 UTC | Don't print warnings for missing values. | 08 December 2015, 16:00:58 UTC |
| 0b58923 | Thomas Mooney | 08 December 2015, 15:57:40 UTC | New command to export subject mappings back out. (This will only work for somatic-validation subject mappings previously created with the import command. Any others will produce a bad file.) | 08 December 2015, 15:57:40 UTC |
| c45c580 | Thomas Mooney | 08 December 2015, 15:13:07 UTC | Remove unused "use Genome::Command::Crud". | 08 December 2015, 15:13:07 UTC |
| ce86c75 | APipe Tester | 07 December 2015, 22:56:31 UTC | updated ur submodule to 1eb3c02 | 07 December 2015, 22:56:31 UTC |
| 9d99a0e | Chris Miller | 07 December 2015, 22:43:28 UTC | Merge pull request #1138 from chrisamiller/cn updating path to bam-window cmd in help | 07 December 2015, 22:43:28 UTC |
| 0cd0ed1 | Adam Coffman | 07 December 2015, 20:58:47 UTC | Merge pull request #1147 from acoffman/alias_metric_name Make name/value accessors consistent for differing metric types. | 07 December 2015, 20:58:47 UTC |
| 8c1247c | Adam Coffman | 04 December 2015, 22:18:05 UTC | alias metric name and value for a consistent interface | 07 December 2015, 16:41:44 UTC |
| c66de64 | Thomas B. Mooney | 07 December 2015, 16:32:23 UTC | Merge pull request #1143 from tmooney/remove_disk_allocations_from_test_db_remembers_testdb RemoveDiskAllocationsFromTestDb remembers which TestDB was used. | 07 December 2015, 16:32:23 UTC |
| 4443f2b | Thomas B. Mooney | 07 December 2015, 15:01:46 UTC | Merge pull request #1145 from tmooney/analysis_project_view_includes_status Include status in `genome analysis-project view` output | 07 December 2015, 15:01:46 UTC |
| d68906e | APipe Tester | 04 December 2015, 22:25:36 UTC | updated ur submodule to 3f3ca68 | 04 December 2015, 22:25:36 UTC |
| eb1c0f6 | Feiyu Du | 04 December 2015, 20:10:01 UTC | Merge pull request #1146 from dufeiyu/tcga TCGA Priorities: Put lookup hash by bam base name in cache | 04 December 2015, 20:10:01 UTC |
| 187baeb | Feiyu Du | 04 December 2015, 19:03:24 UTC | Put lookup hash by bam base name in cache | 04 December 2015, 19:03:24 UTC |
| a5da876 | Dave Larson | 04 December 2015, 18:58:02 UTC | revert calculated vaf changes. These don't count properly for SNVs when bam-readcount isn't run in insertion-centric mode. bam-readcount needs to be fixed. | 04 December 2015, 18:58:02 UTC |
| 8d5e553 | Feiyu Du | 04 December 2015, 16:52:07 UTC | Merge pull request #1144 from dufeiyu/tcga TCGA Priorities: Add alternative way to get cghub id | 04 December 2015, 16:52:07 UTC |
| eabac6a | Feiyu Du | 03 December 2015, 22:07:01 UTC | use scalar variable | 03 December 2015, 22:07:01 UTC |
| fcca81f | Thomas Mooney | 03 December 2015, 22:05:00 UTC | Include status in Analysis Project view. | 03 December 2015, 22:05:00 UTC |
| 2d74b02 | Feiyu Du | 03 December 2015, 21:49:24 UTC | change the order | 03 December 2015, 21:49:24 UTC |
| 3cfbcc9 | Feiyu Du | 03 December 2015, 21:22:00 UTC | name_in_vcf is the right way to get TCGA names | 03 December 2015, 21:22:00 UTC |
| 00f66c6 | Feiyu Du | 03 December 2015, 21:06:50 UTC | add an alternative way by using bam base to search | 03 December 2015, 21:06:50 UTC |
| 1ba62d1 | Eddie Belter | 03 December 2015, 18:15:29 UTC | Merge pull request #1140 from ebelter/anp-release-status AnP: Add status message to release command | 03 December 2015, 18:15:29 UTC |
| 4646361 | APipe Tester | 03 December 2015, 13:16:46 UTC | Updated `genome` tab completion. | 03 December 2015, 13:16:46 UTC |
| fa706f3 | APipe Tester | 03 December 2015, 13:15:11 UTC | Updated class browser cache. | 03 December 2015, 13:15:11 UTC |
| 0153e30 | Thomas Mooney | 02 December 2015, 21:53:40 UTC | Localize before deleting values. | 02 December 2015, 21:53:40 UTC |
| 63d7f03 | Eddie Belter | 02 December 2015, 19:19:59 UTC | AnP: release cmd test spell check | 02 December 2015, 19:19:59 UTC |
| 5095ed3 | Eddie Belter | 02 December 2015, 18:55:11 UTC | AnP: clean up adn update release test | 02 December 2015, 18:57:18 UTC |
| a599536 | Eddie Belter | 02 December 2015, 18:54:55 UTC | AnP: add status message to release command | 02 December 2015, 18:54:55 UTC |
| dee1ceb | Thomas Mooney | 02 December 2015, 18:31:47 UTC | Whitespace. | 02 December 2015, 18:31:47 UTC |
