| 521fa00 | Thomas B. Mooney | 09 March 2016, 16:56:44 UTC | Merge pull request #1302 from tmooney/bamqc_works_on_non_laneqc_builds BamQC should only check instrument data for the result it will run on. | 09 March 2016, 16:56:44 UTC |
| 3aa60bc | Thomas Mooney | 09 March 2016, 13:51:43 UTC | BamQC should only check instrument data for the result it will run on. | 09 March 2016, 13:51:43 UTC |
| f5f801a | APipe Tester | 09 March 2016, 13:16:49 UTC | Updated `genome` tab completion. | 09 March 2016, 13:16:49 UTC |
| 3cf1098 | APipe Tester | 09 March 2016, 13:15:13 UTC | Updated class browser cache. | 09 March 2016, 13:15:13 UTC |
| 6d80cbd | Thomas B. Mooney | 08 March 2016, 21:27:57 UTC | Merge pull request #1299 from tmooney/one_bam_to_rule_them_all ReferenceAlignment makes one BAM regardless of mixed sample assignment. | 08 March 2016, 21:27:57 UTC |
| c518931 | Thomas B. Mooney | 08 March 2016, 19:48:15 UTC | Merge pull request #1296 from tmooney/base_of_ssg_command_tree Add a base for the SSG command tree. | 08 March 2016, 19:48:15 UTC |
| db6aeba | Thomas Mooney | 08 March 2016, 13:57:26 UTC | ReferenceAlignment makes one BAM regardless of mixed sample assignment. | 08 March 2016, 13:57:26 UTC |
| 84575d4 | APipe Tester | 08 March 2016, 13:16:36 UTC | Updated `genome` tab completion. | 08 March 2016, 13:16:36 UTC |
| 7dc29ee | APipe Tester | 08 March 2016, 13:14:59 UTC | Updated class browser cache. | 08 March 2016, 13:14:59 UTC |
| c77894f | Thomas B. Mooney | 07 March 2016, 23:58:27 UTC | Merge pull request #1297 from tmooney/add_scheduled_as_build_status Add Scheduled as valid build status. | 07 March 2016, 23:58:27 UTC |
| 8ec12ca | Thomas Mooney | 07 March 2016, 23:12:13 UTC | Add Scheduled as valid build status. | 07 March 2016, 23:12:13 UTC |
| 0d9ca0c | Thomas Mooney | 07 March 2016, 19:54:56 UTC | Add a base for the SSG command tree. This should fix tab-completion and the commands showing up in `genome model --help`. | 07 March 2016, 19:56:09 UTC |
| d2f08f7 | Anthony Brummett | 07 March 2016, 16:11:45 UTC | Merge pull request #1283 from brummett/build-volume-command2 Build volume lister command | 07 March 2016, 16:11:45 UTC |
| 32599e2 | Jason Walker | 07 March 2016, 15:03:45 UTC | Merge pull request #1285 from jasonwalker80/qc_build_metric_report Qc build metric report | 07 March 2016, 15:03:45 UTC |
| 478c87b | Jason Walker | 07 March 2016, 14:13:20 UTC | Merge pull request #1293 from jasonwalker80/somatic_subject_subroutines Common somatic interface to the tumor/normal samples. | 07 March 2016, 14:13:20 UTC |
| f3fae09 | Jason Walker | 04 March 2016, 21:50:00 UTC | Common somatic interface to the tumor/normal samples. | 04 March 2016, 21:50:00 UTC |
| 71d2957 | Eddie Belter | 04 March 2016, 20:37:31 UTC | Merge pull request #1269 from ebelter/anp-replace-model-uses-profile AnP Replace Model Uses Config Profile | 04 March 2016, 20:37:31 UTC |
| eb660fa | Jason Walker | 04 March 2016, 19:02:31 UTC | For exome, use the metric headers in a loop since the hash key is the same but uppercase. | 04 March 2016, 19:02:31 UTC |
| 14f9f4d | APipe Tester | 04 March 2016, 13:15:58 UTC | Updated `genome` tab completion. | 04 March 2016, 13:15:58 UTC |
| b61cda8 | APipe Tester | 04 March 2016, 13:14:18 UTC | Updated class browser cache. | 04 March 2016, 13:14:18 UTC |
| 3410fc2 | Thomas B. Mooney | 03 March 2016, 14:07:11 UTC | Merge pull request #1280 from tmooney/remove_remnants_of_old_druggablegene Remove Remnants of old Perl-based DruggableGene. | 03 March 2016, 14:07:11 UTC |
| 5a3d52f | APipe Tester | 03 March 2016, 13:17:22 UTC | Updated `gmt` tab completion. | 03 March 2016, 13:17:22 UTC |
| 2374259 | APipe Tester | 03 March 2016, 13:16:39 UTC | Updated `genome` tab completion. | 03 March 2016, 13:16:39 UTC |
| c5dba6f | APipe Tester | 03 March 2016, 13:15:06 UTC | Updated class browser cache. | 03 March 2016, 13:15:06 UTC |
| be853cb | Thomas B. Mooney | 02 March 2016, 20:10:33 UTC | Merge pull request #1275 from tmooney/remove_liftovermultiplecolumns_gmt Remove "LiftOverMultipleColumns" GMT. | 02 March 2016, 20:10:33 UTC |
| a3e6442 | Thomas B. Mooney | 02 March 2016, 17:43:06 UTC | Merge pull request #1245 from tmooney/remove_refalign_pp_subclasses_part_two Complete the removal of RefAlign PP subclasses. | 02 March 2016, 17:43:06 UTC |
| 4d5bc61 | Thomas B. Mooney | 02 March 2016, 15:53:43 UTC | Merge pull request #1270 from tmooney/refalign_doesnt_use_stages ReferenceAlignment No Longer Uses a Staged ProcessingProfile. | 02 March 2016, 15:53:43 UTC |
| 0e105eb | APipe Tester | 01 March 2016, 13:17:22 UTC | Updated `gmt` tab completion. | 01 March 2016, 13:17:22 UTC |
| da8c1d5 | APipe Tester | 01 March 2016, 13:16:40 UTC | Updated `genome` tab completion. | 01 March 2016, 13:16:40 UTC |
| 9421777 | APipe Tester | 01 March 2016, 13:15:10 UTC | Updated class browser cache. | 01 March 2016, 13:15:10 UTC |
| a33737c | Anthony Brummett | 29 February 2016, 20:54:09 UTC | avoid "redefined" warnings | 29 February 2016, 20:54:09 UTC |
| 867eab9 | Jason Walker | 29 February 2016, 20:37:49 UTC | Expect a single element array instead of scalar for verifyBamId results. | 29 February 2016, 20:37:49 UTC |
| 7abbfc2 | Jason Walker | 29 February 2016, 18:48:28 UTC | Remove VerifyBamId dedup logic since results from builds are now unique. | 29 February 2016, 18:48:28 UTC |
| 1467af5 | Susanna Kiwala | 29 February 2016, 18:13:20 UTC | Merge pull request #1284 from susannasiebert/epitope_prediction_bugfix Epitope length needs to be of Integer data type instead of Text | 29 February 2016, 18:13:20 UTC |
| b8cade6 | Jason Walker | 29 February 2016, 17:54:05 UTC | Add QC config test factory. | 29 February 2016, 17:54:05 UTC |
| aa86f95 | Jason Walker | 29 February 2016, 17:43:32 UTC | Add PF_READS. Resolve the qc config type rather than defining a profile as user input. | 29 February 2016, 17:43:32 UTC |
| a333a65 | Thomas B. Mooney | 29 February 2016, 14:08:14 UTC | Merge pull request #1278 from tmooney/alignmentresult_uses_alignmentsummary_gmt AlignmentResult uses the AlignmentSummary GMT. | 29 February 2016, 14:08:14 UTC |
| 6b70f20 | Thomas B. Mooney | 29 February 2016, 14:07:57 UTC | Merge pull request #1271 from tmooney/remove_seefive_gmts Remove disused "SeeFive" GMT tree. | 29 February 2016, 14:07:57 UTC |
| e28906e | Thomas B. Mooney | 29 February 2016, 14:07:48 UTC | Merge pull request #1272 from tmooney/remove_completegenomics_gmts Remove disused "CompleteGenomics" GMTs. | 29 February 2016, 14:07:48 UTC |
| 5fb69cc | Thomas B. Mooney | 29 February 2016, 14:07:35 UTC | Merge pull request #1273 from tmooney/remove_getsubdirectories_gmt Remove "GetSubDirectories" GMT. | 29 February 2016, 14:07:35 UTC |
| 150c6a0 | Thomas B. Mooney | 29 February 2016, 14:07:26 UTC | Merge pull request #1274 from tmooney/remove_wiki_gmts Remove old GMTs for updating MediaWiki and indexing in Solr. | 29 February 2016, 14:07:26 UTC |
| 0e9e58e | Thomas B. Mooney | 29 February 2016, 14:07:13 UTC | Merge pull request #1276 from tmooney/remove_sword_gmts Remove unfinished "Sword" GMTs. | 29 February 2016, 14:07:13 UTC |
| c3f8cde | Thomas B. Mooney | 29 February 2016, 14:07:00 UTC | Merge pull request #1277 from tmooney/remove_text_gmt Remove head of "Text" GMT tree. | 29 February 2016, 14:07:00 UTC |
| 87c465e | Thomas B. Mooney | 29 February 2016, 14:06:47 UTC | Merge pull request #1279 from tmooney/remove_updatehistory Remove Genome::UpdateHistory. | 29 February 2016, 14:06:47 UTC |
| 2d34c8c | Thomas B. Mooney | 29 February 2016, 14:06:34 UTC | Merge pull request #1281 from tmooney/lsf_tmpdir_is_group_accessible Configure permissions on tempdir when using LSF location. | 29 February 2016, 14:06:34 UTC |
| df78ef7 | Susanna Kiwala | 26 February 2016, 20:20:18 UTC | Epitope length needs to be of Integer data type instead of Text | 26 February 2016, 20:20:18 UTC |
| fdfa20e | Anthony Brummett | 26 February 2016, 16:56:37 UTC | forgot "use Genonme" | 26 February 2016, 16:56:37 UTC |
| 02e80af | Chris Miller | 25 February 2016, 22:17:20 UTC | Merge pull request #1282 from chrisamiller/vscn adding name to the jobs for monitoring | 25 February 2016, 22:17:20 UTC |
| 20e92bc | Chris Miller | 25 February 2016, 21:50:40 UTC | adding name to the jobs for monitoring | 25 February 2016, 21:50:40 UTC |
| 519c00c | Thomas Mooney | 25 February 2016, 21:00:28 UTC | Configure permissions on tempdir when using LSF location. This will allow for easier debugging of jobs, while still restricting access to the authorized group. | 25 February 2016, 21:00:28 UTC |
| 3f444b4 | Thomas Mooney | 25 February 2016, 19:07:06 UTC | Remove last of DruggableGene namespace. Please see genome/dgi-db for the new and better version! | 25 February 2016, 19:08:43 UTC |
| 0adbbbd | Thomas Mooney | 25 February 2016, 19:06:44 UTC | Remove old DruggableGene importers. | 25 February 2016, 19:06:44 UTC |
| c2a9f6c | Thomas Mooney | 25 February 2016, 19:05:12 UTC | Remove old DruggableGene paths from web-app. | 25 February 2016, 19:05:12 UTC |
| 785f3c5 | Thomas Mooney | 25 February 2016, 19:02:07 UTC | Remove XSLT for non-existent classes. | 25 February 2016, 19:02:07 UTC |
| 167b646 | Anthony Brummett | 25 February 2016, 18:39:21 UTC | Lister command to list allocations of builds It's a bit of a hack on the standard lister. It allows --filter to apply to builds and fetches those builds. Then creates UR sets of allocations of those builds which is faster than iterating through the allocation objects directly. Finally, it applies the --show to those allocation sets. | 25 February 2016, 18:39:21 UTC |
| 998e884 | Anthony Brummett | 12 January 2016, 20:22:15 UTC | Constrain the valid values for a build's status This is the complete list of values currently present in the DB | 25 February 2016, 18:38:08 UTC |
| 8f85868 | David Morton | 25 February 2016, 17:33:09 UTC | Merge pull request #1266 from davidlmorton/inline_workflowbuilder Inline workflowbuilder DAG execution | 25 February 2016, 17:33:09 UTC |
| 2173780 | Thomas Mooney | 25 February 2016, 16:53:31 UTC | Remove Genome::UpdateHistory. It points to a non-existent table. | 25 February 2016, 16:53:31 UTC |
| 355c40a | Thomas Mooney | 25 February 2016, 16:15:40 UTC | AlignmentResult uses the AlignmentSummary GMT. | 25 February 2016, 16:15:40 UTC |
| 5f8bb80 | Thomas Mooney | 25 February 2016, 14:54:27 UTC | Remove head of "Text" GMT tree. The files under this were removed in 1bc1810154d2bebd11321dd2b833dd54cff62df8. | 25 February 2016, 15:03:26 UTC |
| 0d61450 | Thomas Mooney | 24 February 2016, 23:51:40 UTC | Remove unfinished "Sword" GMTs. | 24 February 2016, 23:51:40 UTC |
| 650d1eb | Thomas Mooney | 24 February 2016, 23:46:04 UTC | Remove "LiftOverMultipleColumns" GMT. The regular `gmt lift-over` remains available. | 24 February 2016, 23:46:04 UTC |
| 3f596f2 | Thomas Mooney | 24 February 2016, 23:36:13 UTC | Remove old GMTs for updating MediaWiki and indexing in Solr. | 24 February 2016, 23:36:13 UTC |
| b6a3bc2 | Thomas Mooney | 24 February 2016, 23:15:25 UTC | Remove "GetSubDirectories" GMT. | 24 February 2016, 23:15:25 UTC |
| dadcfee | Thomas Mooney | 24 February 2016, 22:56:46 UTC | Remove disused CompleteGenomics GMTs. | 24 February 2016, 22:56:46 UTC |
| 668ea67 | Thomas Mooney | 24 February 2016, 22:47:39 UTC | Remove disused "SeeFive" GMT tree. | 24 February 2016, 22:47:39 UTC |
| 0a2888f | David Morton | 24 February 2016, 20:35:43 UTC | Remove ptero_log_directory from genome-config | 24 February 2016, 20:35:43 UTC |
| 9fbc39e | Jason Walker | 24 February 2016, 19:02:54 UTC | Improvements to the BuildMetrics test case including the use of test factory. | 24 February 2016, 19:02:54 UTC |
| f7d1d61 | Jason Walker | 24 February 2016, 19:02:01 UTC | WIP: Addition of TSV reporting logic that was previously a stand-alone script. Also added exome metrics in addition to existing WGS. | 24 February 2016, 19:02:01 UTC |
| 98fa2d4 | Thomas Mooney | 18 February 2016, 23:11:44 UTC | Remove old way of generating per-lane alignments. | 23 February 2016, 23:46:38 UTC |
| c55d6cb | Thomas Mooney | 18 February 2016, 22:56:22 UTC | Remove old way of generating merged result. | 23 February 2016, 23:46:38 UTC |
| 1c04a41 | Thomas Mooney | 18 February 2016, 22:52:27 UTC | No more ReferenceAlignment events. | 23 February 2016, 23:46:38 UTC |
| 9075604 | Thomas Mooney | 18 February 2016, 22:51:59 UTC | Remove no-longer-supported QC events. CHANGELOG: ReferenceAlignment-based LaneQC models can no longer be built. | 23 February 2016, 23:46:17 UTC |
| 57b4a3a | Thomas Mooney | 18 February 2016, 22:00:09 UTC | ReferenceAlignment no longer uses staged workflow. | 23 February 2016, 23:46:17 UTC |
| 3ba73c4 | Thomas Mooney | 18 February 2016, 21:52:36 UTC | WIP: Convert RunReports event into a command. | 23 February 2016, 23:46:12 UTC |
| 11723ff | Thomas Mooney | 18 February 2016, 21:52:05 UTC | WIP: Convert Annotation events into a command. | 23 February 2016, 23:41:09 UTC |
| 64094a6 | Thomas Mooney | 18 February 2016, 21:51:18 UTC | WIP: Convert DetectVariants event to a command. | 23 February 2016, 23:41:08 UTC |
| dc19906 | Thomas Mooney | 18 February 2016, 21:49:58 UTC | WIP: Convert CoverageStats event to a command. | 23 February 2016, 23:41:08 UTC |
| 2601707 | Thomas Mooney | 18 February 2016, 21:49:31 UTC | WIP: Convert BamQC event to a command. | 23 February 2016, 23:41:08 UTC |
| 73d9c16 | Thomas Mooney | 18 February 2016, 21:48:00 UTC | WIP: Use Alignment dispatcher in ReferenceAlignment. | 23 February 2016, 23:41:08 UTC |
| 592fd00 | Thomas Mooney | 18 February 2016, 23:45:30 UTC | Base class for new pipeline commands. | 23 February 2016, 23:41:07 UTC |
| 303722a | Thomas B. Mooney | 23 February 2016, 23:35:05 UTC | Merge pull request #1264 from tmooney/refalign_uses_users_to_find_alignments ReferenceAlignment: Use user relationships to find alignments. | 23 February 2016, 23:35:05 UTC |
| 1c1d4b8 | Thomas B. Mooney | 23 February 2016, 23:33:49 UTC | Merge pull request #1265 from tmooney/remove_event_accessors_from_refalign_model Remove disused event accessors from ReferenceAlignment Model. | 23 February 2016, 23:33:49 UTC |
| b357582 | Thomas B. Mooney | 23 February 2016, 23:33:07 UTC | Merge pull request #1268 from tmooney/remove_referencecoverage_report_check_from_refalign_runreports ReferenceAlignment: Remove references to ReferenceCoverage report | 23 February 2016, 23:33:07 UTC |
| d95e0b4 | Eddie Belter | 23 February 2016, 22:54:52 UTC | use Genome before Test:: modules to avoid Carp bug | 23 February 2016, 22:54:52 UTC |
| 31117f4 | David Morton | 23 February 2016, 22:09:14 UTC | Allow backend=inline for parent_workflow_dir | 23 February 2016, 22:09:14 UTC |
| f3eebda | Eddie Belter | 23 February 2016, 21:57:52 UTC | Replace model uses config profile to get/create model for config | 23 February 2016, 21:57:52 UTC |
| 4d65e58 | Eddie Belter | 23 February 2016, 21:56:52 UTC | Fix bug in profile item is_current | 23 February 2016, 21:56:52 UTC |
| 115eccb | Eddie Belter | 23 February 2016, 21:56:16 UTC | Add create from profile config item | 23 February 2016, 21:56:16 UTC |
| d9ef356 | APipe Tester | 23 February 2016, 21:32:42 UTC | updated ur submodule to 939d091 | 23 February 2016, 21:32:42 UTC |
| 32d0007 | Eddie Belter | 23 February 2016, 20:43:03 UTC | Add create from config profile item | 23 February 2016, 20:43:03 UTC |
| f3e70b1 | Eddie Belter | 23 February 2016, 20:42:26 UTC | Move process models from CQID to profile | 23 February 2016, 20:42:30 UTC |
| 1499766 | Eddie Belter | 22 February 2016, 22:29:26 UTC | Fully process model hashes in config profile | 22 February 2016, 22:29:26 UTC |
| cbddc71 | Eddie Belter | 22 February 2016, 22:23:52 UTC | Move process_mapped_samples from CQID to profile | 22 February 2016, 22:23:52 UTC |
| 9c06e67 | Eddie Belter | 22 February 2016, 22:06:24 UTC | Move prepare_configuration_hashes_for_instrument_data from CQID to config class | 22 February 2016, 22:10:11 UTC |
| b964a45 | David Morton | 22 February 2016, 19:18:28 UTC | Don't try to commit in WorkflowBuilder/Command.pm The commit breaks things when running a DAG inline while inside of a UR Transaction. | 22 February 2016, 19:18:28 UTC |
| 35c3804 | David Morton | 22 February 2016, 18:37:46 UTC | use Genome instead of use above "Genome" The 'genome' cli already does a use above, so it is not needed here. | 22 February 2016, 18:37:46 UTC |
| b5cea18 | Chris Miller | 22 February 2016, 18:11:53 UTC | Merge pull request #1267 from chrisamiller/copyconfig don't copy config if to and from projects are the same | 22 February 2016, 18:11:53 UTC |
| 1c70ff3 | Thomas Mooney | 22 February 2016, 17:36:15 UTC | Fulfill review: Remove references to ReferenceCoverage report. | 22 February 2016, 17:36:15 UTC |
| baf6260 | Chris Miller | 22 February 2016, 16:58:06 UTC | return instead of return 0 | 22 February 2016, 16:58:06 UTC |
