| dc69835 | APipe Tester | 10 May 2014, 12:19:39 UTC | Updated `genome` tab completion. | 10 May 2014, 12:19:39 UTC |
| 1cd8ae3 | APipe Tester | 10 May 2014, 12:18:04 UTC | Updated class browser cache. | 10 May 2014, 12:18:04 UTC |
| e4c0271 | dmorton | 09 May 2014, 21:45:58 UTC | Update genome_base_dir after file move | 09 May 2014, 21:45:58 UTC |
| ac4d15a | dmorton | 09 May 2014, 21:24:26 UTC | Move base class We have to 'hide' this base class in a folder to keep the model define subcommand factory from attempting to generate a subcommand. | 09 May 2014, 21:39:10 UTC |
| ebf5e50 | dmorton | 09 May 2014, 19:37:56 UTC | Bugfix: stop use_ok'ing non-existent class | 09 May 2014, 21:39:10 UTC |
| a12533b | dmorton | 09 May 2014, 18:18:06 UTC | Replaced temp-variables with methods | 09 May 2014, 21:39:09 UTC |
| 0b40f85 | dmorton | 09 May 2014, 17:56:12 UTC | Make sure we create the output_directory | 09 May 2014, 21:39:09 UTC |
| ce389a9 | dmorton | 08 May 2014, 21:53:46 UTC | Remove MasterCommand | 09 May 2014, 21:39:09 UTC |
| bcaf786 | dmorton | 08 May 2014, 21:32:11 UTC | Create Dag module to generate the annotation-dag This will soon replace the MasterCommand->dag method | 09 May 2014, 21:39:09 UTC |
| 7d75188 | dmorton | 08 May 2014, 20:58:45 UTC | Remove unused (dummy) input from GetInitialVcfResult | 09 May 2014, 21:39:09 UTC |
| be79e10 | dmorton | 08 May 2014, 20:06:43 UTC | Integrate Annotation Plan into Somatic Validation/Variation builds | 09 May 2014, 21:39:09 UTC |
| d0f861e | dmorton | 08 May 2014, 19:56:52 UTC | Params shouldn't be listed as inputs for commands They are for SoftwareResults, but not for commands | 09 May 2014, 21:39:09 UTC |
| 806ad52 | dmorton | 08 May 2014, 17:23:11 UTC | Make command for getting the vcf-result from DV2 at runtime We couldn't pass this in when we launch the workflow because it hasn't been created yet at that point. | 09 May 2014, 21:39:08 UTC |
| a39f030 | dmorton | 08 May 2014, 17:22:04 UTC | Add use statements for WorkflowBuilder | 09 May 2014, 21:39:08 UTC |
| 9bf1665 | Anthony Brummett | 09 May 2014, 18:39:35 UTC | remove debugging variable causing a void context warning | 09 May 2014, 20:27:58 UTC |
| 7ff5390 | Eddie Belter | 09 May 2014, 20:23:01 UTC | MC16s: adjust est kb usage | 09 May 2014, 20:23:01 UTC |
| 715f103 | Nathaniel Nutter | 09 May 2014, 19:56:36 UTC | exit prevents TestTracker from working | 09 May 2014, 19:56:36 UTC |
| c8a7085 | Nathaniel Nutter | 09 May 2014, 19:02:54 UTC | refactor has_bit to reuse mode | 09 May 2014, 19:35:55 UTC |
| f4fe221 | Nathaniel Nutter | 09 May 2014, 19:02:34 UTC | add missing dependency | 09 May 2014, 19:35:53 UTC |
| 98c6832 | Nathaniel Nutter | 09 May 2014, 18:47:48 UTC | refactor all_results to use ancestors, remove duplicate code | 09 May 2014, 19:35:18 UTC |
| e63f317 | Nathaniel Nutter | 09 May 2014, 17:39:54 UTC | remove unused variable | 09 May 2014, 19:35:17 UTC |
| 68afe6e | Nathaniel Nutter | 09 May 2014, 17:36:24 UTC | convert eval to subtest | 09 May 2014, 19:35:15 UTC |
| 1511d24 | Nathaniel Nutter | 09 May 2014, 17:32:10 UTC | refactor has_group_write for reuse of has_bit | 09 May 2014, 19:35:14 UTC |
| 1adfe0a | Nathaniel Nutter | 09 May 2014, 17:29:22 UTC | s/has_group_write/group_write/ | 09 May 2014, 19:35:12 UTC |
| d9327ae | Nathaniel Nutter | 09 May 2014, 18:58:41 UTC | blacklist genome-re.pl | 09 May 2014, 18:58:41 UTC |
| 32623c6 | Anthony Brummett | 09 May 2014, 17:50:34 UTC | remove properties corresponding to dropped columns analysis_menu_item_id and configuration_set_id | 09 May 2014, 17:50:34 UTC |
| cef18af | Anthony Brummett | 09 May 2014, 15:26:57 UTC | Remove the table name override - The class has the right table after all | 09 May 2014, 17:30:15 UTC |
| 0e9a045 | Adam Coffman | 09 May 2014, 16:11:26 UTC | migration for removing unused apconfig tables | 09 May 2014, 16:11:26 UTC |
| 751b713 | APipe Tester | 09 May 2014, 14:14:49 UTC | updated ur submodule to fdb054f | 09 May 2014, 14:14:49 UTC |
| 7f0cba1 | Anthony Brummett | 08 May 2014, 18:44:52 UTC | use autogenerated IDs instead of IDs that already exist in the DB | 09 May 2014, 14:13:35 UTC |
| ca52cfd | Anthony Brummett | 07 May 2014, 21:37:50 UTC | Populate the validation values in the timeline.analysis_project_event_type table | 09 May 2014, 14:13:34 UTC |
| d1f9e48 | Anthony Brummett | 07 May 2014, 21:28:46 UTC | Populate the validation values in the timeline.allocation_event_type table | 09 May 2014, 14:13:34 UTC |
| 4910151 | Anthony Brummett | 01 May 2014, 14:43:58 UTC | Pass in the alternate DB details in the env var instead of hard-coding it Also, we don't need the GENOME_TEST_USEDB env var - just use the existing env vars for server, user, passwd | 09 May 2014, 14:13:33 UTC |
| 1085ffa | Anthony Brummett | 01 May 2014, 14:42:48 UTC | Show the STDERR output when the test fails | 09 May 2014, 14:13:32 UTC |
| 01d79f8 | Anthony Brummett | 04 April 2014, 21:43:23 UTC | WIP getting the Genome tests to create the seed data for a test database Changes in Config/AnalysisProject.pm are to get the alternate DB loader to see some foreign keys that didn't have delegated properties. | 09 May 2014, 14:13:32 UTC |
| be97fe0 | Anthony Brummett | 14 March 2014, 22:26:03 UTC | Enviroment variables to fill and use test databases | 09 May 2014, 14:13:31 UTC |
| 1ebe4a8 | APipe Tester | 09 May 2014, 12:19:10 UTC | Updated `gmt` tab completion. | 09 May 2014, 12:19:10 UTC |
| ca19339 | APipe Tester | 09 May 2014, 12:18:29 UTC | Updated `genome` tab completion. | 09 May 2014, 12:18:29 UTC |
| c26d698 | APipe Tester | 09 May 2014, 12:17:09 UTC | Updated class browser cache. | 09 May 2014, 12:17:09 UTC |
| ce95801 | Thomas Mooney | 08 May 2014, 22:16:32 UTC | Enable no-commit to avoid locking in dummy library creation. | 08 May 2014, 22:16:32 UTC |
| 011798b | Gabriel Sanderson | 08 May 2014, 21:21:01 UTC | another place where instrument_data_segment_id could be 0 | 08 May 2014, 21:21:01 UTC |
| 64c26da | Gabriel Sanderson | 08 May 2014, 21:06:02 UTC | account for instrument_data_segment_id being 0 sometimes. | 08 May 2014, 21:06:16 UTC |
| 0e35264 | Thomas Mooney | 08 May 2014, 20:59:28 UTC | Use the segment if it's defined even if it's not truthy. | 08 May 2014, 20:59:28 UTC |
| 73e25b8 | Thomas Mooney | 08 May 2014, 20:14:57 UTC | Save the error before $@ is overwritten. | 08 May 2014, 20:14:57 UTC |
| 02ffbd5 | Eddie Belter | 08 May 2014, 19:16:59 UTC | MC16s: reduce est kb requested | 08 May 2014, 19:43:40 UTC |
| 14bfc30 | Nathaniel Nutter | 08 May 2014, 19:33:46 UTC | remove xgmt that probably got committed by accident | 08 May 2014, 19:34:29 UTC |
| 29a2efd | Nathaniel Nutter | 08 May 2014, 18:05:24 UTC | work-around to allow listing of CLE volumes (and vice-versa) | 08 May 2014, 18:07:02 UTC |
| d719d81 | Nathaniel Nutter | 08 May 2014, 18:04:58 UTC | refactor validation of disk group names to site | 08 May 2014, 18:07:01 UTC |
| 84f03ab | Nathaniel Nutter | 08 May 2014, 17:13:56 UTC | refactor Genome::Env | 08 May 2014, 17:13:56 UTC |
| 8717653 | Nathaniel Nutter | 08 May 2014, 14:26:08 UTC | change globals to subs | 08 May 2014, 17:13:34 UTC |
| 1fe7592 | Nathaniel Nutter | 08 May 2014, 14:25:21 UTC | remove undefined default values | 08 May 2014, 17:13:33 UTC |
| d2dd6e5 | Nathaniel Nutter | 08 May 2014, 14:23:46 UTC | fix default value overwriting existing value | 08 May 2014, 17:13:32 UTC |
| 2c62150 | Nathaniel Nutter | 08 May 2014, 00:12:13 UTC | add test for Genome::Env | 08 May 2014, 17:13:32 UTC |
| f212e5a | Nathaniel Nutter | 08 May 2014, 00:06:31 UTC | refactor Genome::Env to use Set::Scalar and Module::Find | 08 May 2014, 17:13:30 UTC |
| 949caec | Nathaniel Nutter | 08 May 2014, 14:07:10 UTC | fix bad copy-paste | 08 May 2014, 17:13:29 UTC |
| c35f375 | Thomas Mooney | 07 May 2014, 22:46:51 UTC | Replace defined(@refiners) with scalar(@refiners) to quiet warning. | 07 May 2014, 22:46:51 UTC |
| ee25cc2 | Ian Ferguson | 07 May 2014, 21:38:21 UTC | Update samtools version check in DV2/Samtools.pm Samtools mpileup version check was checking for versions newer than 'r599', but didn't take into account versions like '0.1.19'. Ideally version and capability checks should be centralized in some place like GMT/Sam.pm. | 07 May 2014, 21:38:21 UTC |
| 8d0d203 | Nathaniel Nutter | 07 May 2014, 19:57:40 UTC | change genome-re.pl to use genome-perl instead CHANGELOG: genome-re.pl now uses genome-perl instead of symlinking to /usr/bin/re.pl which uses a '/usr/bin/env perl' hashbang so does not correctly use /usr/bin/perl (genome-perl). | 07 May 2014, 20:46:55 UTC |
| ff2d8e2 | Chris Miller | 07 May 2014, 19:52:10 UTC | Escaping filenames with special characters when shelling out | 07 May 2014, 20:18:47 UTC |
| 483e700 | Thomas Mooney | 07 May 2014, 20:00:35 UTC | Start migration to new status columns. | 07 May 2014, 20:00:35 UTC |
| cb72ccf | Thomas Mooney | 07 May 2014, 18:28:31 UTC | A trigger to keep the new columns in synch during the transition. | 07 May 2014, 19:50:40 UTC |
| fb26c00 | Thomas Mooney | 07 May 2014, 17:35:07 UTC | Add direct status columns to model.build | 07 May 2014, 19:50:39 UTC |
| da347ad | Avinash Ramu | 07 May 2014, 16:28:26 UTC | remove spaces from dir names | 07 May 2014, 18:22:00 UTC |
| e57d4be | Travis Abbott | 07 May 2014, 18:19:08 UTC | Subtree merge of gstat repo from Qunyuan | 07 May 2014, 18:19:08 UTC |
| 1596eb3 | Travis Abbott | 07 May 2014, 18:19:08 UTC | Squashed 'lib/perl/Genome/Model/Tools/Germline/gstat/' changes from 5482dd7..4d208d9 4d208d9 whitespace bbf7ed4 solving mixed types of covar problem for binary trait in call.skat() git-subtree-dir: lib/perl/Genome/Model/Tools/Germline/gstat git-subtree-split: 4d208d908305f22bb1c0249e7074a9f87a30694a | 07 May 2014, 18:19:08 UTC |
| 8e7ff72 | Avinash Ramu | 07 May 2014, 16:03:25 UTC | update clinseq blessed-cnmops updated | 07 May 2014, 16:03:25 UTC |
| 56e9159 | Avinash Ramu | 07 May 2014, 03:57:26 UTC | update test-dir and fix small bug | 07 May 2014, 03:58:15 UTC |
| b40acc1 | Avinash Ramu | 07 May 2014, 03:56:59 UTC | update exome cnv calling | 07 May 2014, 03:58:15 UTC |
| a618667 | Avinash Ramu | 06 May 2014, 20:12:35 UTC | revert changes to prior value. | 07 May 2014, 03:58:15 UTC |
| 689f1de | Avinash Ramu | 06 May 2014, 19:41:45 UTC | update cnv calling parameters | 07 May 2014, 03:58:14 UTC |
| 41dd20c | Avinash Ramu | 06 May 2014, 19:41:05 UTC | add GMB ClinSeq | 07 May 2014, 03:58:14 UTC |
| 675725b | Avinash Ramu | 06 May 2014, 19:38:37 UTC | add Clinseq class to gmt analysis | 07 May 2014, 03:58:14 UTC |
| b6066ba | Avinash Ramu | 05 May 2014, 04:10:15 UTC | fix fn | 07 May 2014, 03:58:13 UTC |
| 3673bc4 | Avinash Ramu | 05 May 2014, 04:09:46 UTC | minor update to cnv calling | 07 May 2014, 03:58:13 UTC |
| d835c99 | Avinash Ramu | 05 May 2014, 04:08:45 UTC | update test dir | 07 May 2014, 03:58:12 UTC |
| 650ebc1 | Malachi Griffith | 06 May 2014, 22:30:11 UTC | clin-seq - bless new test build | 06 May 2014, 22:30:11 UTC |
| 22b6714 | dmorton | 06 May 2014, 22:12:36 UTC | Commit after resolve_bed_for_reference since it can create SRs | 06 May 2014, 22:13:25 UTC |
| 0260452 | Dave Larson | 06 May 2014, 21:37:04 UTC | cut down on error messages from bam-readcount | 06 May 2014, 21:37:04 UTC |
| 947ca14 | APipe Tester | 06 May 2014, 21:13:14 UTC | updated jenkins submodule to 3c0805d | 06 May 2014, 21:13:14 UTC |
| 7fe795a | Jim Weible | 06 May 2014, 20:02:17 UTC | add profile item status to ShowConfig | 06 May 2014, 20:02:17 UTC |
| 1fee2f8 | Ben Ainscough | 06 May 2014, 19:45:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome forgot to push | 06 May 2014, 19:45:14 UTC |
| cd3317d | Thomas Mooney | 06 May 2014, 18:30:03 UTC | Add sequencing_platform filter afterwards so it doesn't get overwritten. | 06 May 2014, 18:30:03 UTC |
| 3e0f211 | APipe Tester | 06 May 2014, 17:43:14 UTC | updated jenkins submodule to 7d9b110 | 06 May 2014, 17:43:14 UTC |
| dcf738c | APipe Tester | 06 May 2014, 17:40:15 UTC | updated jenkins submodule to 5d959e3 | 06 May 2014, 17:40:15 UTC |
| 66c4741 | APipe Tester | 06 May 2014, 17:34:58 UTC | updated jenkins submodule to 1e815df | 06 May 2014, 17:34:58 UTC |
| f3299dc | dmorton | 06 May 2014, 15:44:27 UTC | Do not keep around the uncompressed vcf file | 06 May 2014, 16:55:24 UTC |
| 03f0ab8 | dmorton | 06 May 2014, 15:43:52 UTC | Various optimizations to improve Reporter performance | 06 May 2014, 16:55:23 UTC |
| 24052c6 | dmorton | 02 May 2014, 17:08:35 UTC | Stop tabix indexing Vep vcf file Apparently the vcf output that vep produces isn't always sorted, so if we want to keep this we'll have to sort the vcf first. None of the other experts tabix index their vcfs, so if this expert isn't run last the final vcf won't be tabix indexed anyways. | 06 May 2014, 16:55:23 UTC |
| 2a96540 | Chris Miller | 06 May 2014, 16:39:19 UTC | typo | 06 May 2014, 16:39:34 UTC |
| 52bdfce | Chris Miller | 06 May 2014, 16:17:30 UTC | handling the case where bam-readcount returns lowercase alleles from a soft-masked genome | 06 May 2014, 16:39:30 UTC |
| 2489365 | Thomas Mooney | 06 May 2014, 16:32:43 UTC | Add caller info to auto-unarchive reason. | 06 May 2014, 16:32:43 UTC |
| 28533db | Malachi Griffith | 06 May 2014, 15:49:16 UTC | clin-seq - clean up GMAF values in snv-indel-report | 06 May 2014, 15:49:16 UTC |
| 3fb73f1 | Nathaniel Nutter | 06 May 2014, 15:04:39 UTC | add the requested_at time to user_data in Nessy lock | 06 May 2014, 15:04:39 UTC |
| e11d5fc | Nathaniel Nutter | 06 May 2014, 14:46:20 UTC | reorder statements | 06 May 2014, 14:46:20 UTC |
| e767990 | APipe Tester | 06 May 2014, 12:17:06 UTC | Updated `genome` tab completion. | 06 May 2014, 12:17:06 UTC |
| ac2ee06 | APipe Tester | 06 May 2014, 12:15:38 UTC | Updated class browser cache. | 06 May 2014, 12:15:38 UTC |
| 9dfeab4 | APipe Tester | 05 May 2014, 23:58:38 UTC | updated jenkins submodule to 00a6639 | 05 May 2014, 23:58:38 UTC |
| 6e498d8 | Eddie Belter | 05 May 2014, 22:37:25 UTC | Site TGI: Fix sanger run creation in genome | 05 May 2014, 22:43:01 UTC |
| 1259164 | Eddie Belter | 05 May 2014, 22:36:31 UTC | MC16s: print error msg from eval | 05 May 2014, 22:42:58 UTC |
| c12b56d | Eddie Belter | 05 May 2014, 22:31:01 UTC | InstData Import: remove some of the old importers | 05 May 2014, 22:31:01 UTC |
