| a32e222 | APipe Tester | 28 March 2013, 05:11:48 UTC | updated ur submodule to f25dca5 | 28 March 2013, 05:11:48 UTC |
| 00959da | Malachi Griffith | 28 March 2013, 02:37:10 UTC | ClinSeq - add date of last analysis to status report on finding complete clinseq analysis using update-analysis | 28 March 2013, 02:37:10 UTC |
| 9b41b17 | Malachi Griffith | 28 March 2013, 02:23:19 UTC | ClinSeq - add additional checks for models that need to be updated in update-analysis | 28 March 2013, 02:23:19 UTC |
| 82b53eb | Malachi Griffith | 28 March 2013, 02:02:37 UTC | ClinSeq - add additional checks for models that need to be updated in update-analysis | 28 March 2013, 02:02:37 UTC |
| 322ef32 | Eddie Belter | 27 March 2013, 22:35:59 UTC | Sample Import: rearrange getting the extraction type | 27 March 2013, 22:36:08 UTC |
| 09bd9c6 | Eddie Belter | 27 March 2013, 22:35:58 UTC | Subject: do not use // when setting nomenclature | 27 March 2013, 22:36:08 UTC |
| ddbe372 | Gabriel Sanderson | 27 March 2013, 22:00:37 UTC | Merge branch 'master' into gb_master | 27 March 2013, 22:00:37 UTC |
| 8a635b5 | Gabriel Sanderson | 27 March 2013, 22:00:02 UTC | do not overwrite default samtools version if the processing profile does not contain one | 27 March 2013, 22:00:17 UTC |
| cd83524 | Eddie Belter | 27 March 2013, 21:48:59 UTC | Sample Import: update configs and tests for incoinsistant naming | 27 March 2013, 21:48:59 UTC |
| 5a47032 | Eddie Belter | 27 March 2013, 21:13:40 UTC | TCGA Bam import: use sample importer | 27 March 2013, 21:13:40 UTC |
| e0e02ac | Eddie Belter | 27 March 2013, 21:08:17 UTC | Sample Import: rm DACC importer, can not find examples that were imported | 27 March 2013, 21:10:15 UTC |
| 98a9b3a | Eddie Belter | 27 March 2013, 21:00:23 UTC | Sample Import: update doc for name | 27 March 2013, 21:10:15 UTC |
| 68eae8d | Eddie Belter | 27 March 2013, 20:48:34 UTC | Sample Import: update help | 27 March 2013, 21:10:15 UTC |
| 5ba05f6 | Eddie Belter | 27 March 2013, 20:28:05 UTC | Sample Import: mv tcga to import.pm | 27 March 2013, 21:10:14 UTC |
| 3faaa0c | Eddie Belter | 27 March 2013, 18:52:00 UTC | Sample Import: mv metahit to import.pm | 27 March 2013, 21:10:14 UTC |
| 6c3c032 | Eddie Belter | 27 March 2013, 18:45:17 UTC | Sample Import: mv embl-ebi to import.pm | 27 March 2013, 21:10:13 UTC |
| ff12e88 | Eddie Belter | 27 March 2013, 18:07:19 UTC | Sample Import: add taxon name to config | 27 March 2013, 21:10:13 UTC |
| 423e4c3 | Eddie Belter | 27 March 2013, 17:55:19 UTC | Sample Import: add fucntionality for same named attributes; add more tests for property metas | 27 March 2013, 21:10:13 UTC |
| 8949c80 | Eddie Belter | 27 March 2013, 17:00:51 UTC | Sample Import: conbine ind name match and sample name match into name_regexp | 27 March 2013, 21:10:12 UTC |
| c53a86e | Eddie Belter | 26 March 2013, 22:12:04 UTC | Sample Import: fix sample/ind attr names; add ATCC namespace | 27 March 2013, 21:10:12 UTC |
| c7ab756 | Eddie Belter | 26 March 2013, 21:56:06 UTC | Sample Import: move nomenclature from base to import | 27 March 2013, 21:10:11 UTC |
| 7f98aa5 | Eddie Belter | 26 March 2013, 21:45:06 UTC | Sample Import: take array or hash for sample/individual attrs | 27 March 2013, 21:10:11 UTC |
| f7a8c72 | Eddie Belter | 26 March 2013, 21:06:36 UTC | Sample Import: extraction type now has default and valid values | 27 March 2013, 21:10:11 UTC |
| 4d476b1 | Eddie Belter | 26 March 2013, 21:01:36 UTC | Sample Import: use one regexp to validate name and get source name; add tests for invalid names | 27 March 2013, 21:10:10 UTC |
| 9564d5b | Eddie Belter | 26 March 2013, 19:10:38 UTC | Sample Import: put import command creation and config loading into methods | 27 March 2013, 21:10:10 UTC |
| 013295e | Eddie Belter | 26 March 2013, 18:42:06 UTC | Sample Import: use entity class to get meta to get properties | 27 March 2013, 21:10:09 UTC |
| e9a3dcc | Eddie Belter | 26 March 2013, 18:36:23 UTC | Sample Import: require nomenclature, derive namespace | 27 March 2013, 21:10:09 UTC |
| 4afea3f | Eddie Belter | 26 March 2013, 18:32:58 UTC | Sample Import: add extraction type "genomic dna" to sample attrs if none set | 27 March 2013, 21:10:09 UTC |
| 3ae1c24 | Eddie Belter | 26 March 2013, 18:30:50 UTC | Sample Import: switch ATCC to use import config | 27 March 2013, 21:10:08 UTC |
| 162e998 | Eddie Belter | 25 March 2013, 22:28:48 UTC | Sample Import: gather all attrs for sample and individual attrs | 27 March 2013, 21:10:08 UTC |
| 4ea1b8c | Eddie Belter | 25 March 2013, 19:41:09 UTC | Sample Import: change sample/ind attrs to names | 27 March 2013, 21:10:07 UTC |
| 87f1fb7 | Eddie Belter | 25 March 2013, 19:30:55 UTC | Sample import: use config to add commands | 27 March 2013, 21:10:07 UTC |
| 0c0e60a | Eddie Belter | 22 March 2013, 21:38:37 UTC | Sample Import: import command generates sub commands for namespaces | 27 March 2013, 21:10:06 UTC |
| 887a308 | Eddie Belter | 22 March 2013, 20:43:09 UTC | Sample Import: update update attrributes | 27 March 2013, 21:10:06 UTC |
| b63725e | Eddie Belter | 22 March 2013, 18:26:59 UTC | Sample Import: add ind and sample attrs to base | 27 March 2013, 21:10:06 UTC |
| ca458f4 | Eddie Belter | 22 March 2013, 17:50:25 UTC | Sample Import: remove _bail method | 27 March 2013, 21:10:05 UTC |
| 2d211ec | Eddie Belter | 22 March 2013, 17:48:38 UTC | Sample Import: removed commits | 27 March 2013, 21:10:05 UTC |
| 3e6c352 | Eddie Belter | 20 March 2013, 22:54:52 UTC | Subject: use bool exp to pull out undeclared attrs; set nomenclature when creating attrs | 27 March 2013, 21:10:04 UTC |
| edad3b6 | Eddie Belter | 20 March 2013, 22:24:31 UTC | Sample: add delete method to delete libraries | 27 March 2013, 21:10:04 UTC |
| 880a2e4 | Malachi Griffith | 27 March 2013, 20:51:12 UTC | Minor update to cn-view figures | 27 March 2013, 20:51:12 UTC |
| e45b94f | Malachi Griffith | 27 March 2013, 20:41:05 UTC | Clin | 27 March 2013, 20:41:05 UTC |
| 542bf94 | Malachi Griffith | 27 March 2013, 20:40:15 UTC | Fix bug to handle ref-align models with now dbsnp build associated | 27 March 2013, 20:40:15 UTC |
| dd4af6e | APipe Tester | 27 March 2013, 20:13:07 UTC | updated jenkins submodule to 2cf8523 | 27 March 2013, 20:13:07 UTC |
| 4ddbf03 | APipe Tester | 27 March 2013, 20:05:03 UTC | updated jenkins submodule to b92b92a | 27 March 2013, 20:05:03 UTC |
| 10c20f6 | APipe Tester | 27 March 2013, 20:02:10 UTC | updated jenkins submodule to da4770c | 27 March 2013, 20:02:10 UTC |
| c41d0ad | APipe Tester | 27 March 2013, 19:33:28 UTC | updated jenkins submodule to ecb044d | 27 March 2013, 19:33:28 UTC |
| 0905421 | APipe Tester | 27 March 2013, 19:33:23 UTC | updated workflow submodule to adde3cf | 27 March 2013, 19:33:23 UTC |
| f4df943 | nnutter | 27 March 2013, 18:31:30 UTC | remove some DRY comments | 27 March 2013, 18:31:49 UTC |
| a7396f3 | nnutter | 27 March 2013, 18:29:58 UTC | simplify test with run_ok | 27 March 2013, 18:31:49 UTC |
| 3d86a14 | nnutter | 27 March 2013, 18:00:37 UTC | improve after test failed due to additional file - Check that we got the expected number of files so it will be clearer if something underneath changed. - Check that the file exists in the $temp_dir. - Check that the file exists in the $expected_output_dir. - Add name to the compare_ok tests. | 27 March 2013, 18:31:48 UTC |
| 26d1c55 | Scott Smith | 27 March 2013, 18:12:25 UTC | lister for current Genome::Db::Base entities | 27 March 2013, 18:12:57 UTC |
| 93abefa | Scott Smith | 26 March 2013, 20:26:01 UTC | test case for htseq results requiring merge of multiple underlying results | 27 March 2013, 18:12:57 UTC |
| 2ea7462 | apregier | 27 March 2013, 16:51:02 UTC | Fix REBUILD option on model define docs test | 27 March 2013, 16:51:02 UTC |
| be17feb | apregier | 27 March 2013, 16:49:59 UTC | Fix expected help output for reference alignment | 27 March 2013, 16:49:59 UTC |
| ca837f6 | apregier | 27 March 2013, 16:29:11 UTC | Remove default for add-tiers | 27 March 2013, 16:29:11 UTC |
| dabebae | apregier | 27 March 2013, 16:24:42 UTC | Revert "Remove deprecated tiering tool and a somatic pipeline tool that used it" This reverts commit 236c1b04e1ea91397577ca81bb16a94478ab7cd8. | 27 March 2013, 16:24:42 UTC |
| 210542a | apregier | 27 March 2013, 16:10:02 UTC | Remove default from long-indels-part-two. This means that you will always have to specify the tiering file location | 27 March 2013, 16:10:02 UTC |
| 236c1b0 | apregier | 27 March 2013, 16:02:46 UTC | Remove deprecated tiering tool and a somatic pipeline tool that used it | 27 March 2013, 16:02:46 UTC |
| b1ad411 | apregier | 27 March 2013, 15:56:14 UTC | Remove deprecated annotator tool | 27 March 2013, 15:56:14 UTC |
| 15634da | apregier | 27 March 2013, 15:48:22 UTC | Remove default from define reference-alignment | 27 March 2013, 15:48:22 UTC |
| f00be22 | apregier | 27 March 2013, 15:30:04 UTC | Remove default value from gmt sv sv-annot | 27 March 2013, 15:30:04 UTC |
| e1f2f4e | apregier | 27 March 2013, 15:24:29 UTC | Remove defaults from annotate sv tools | 27 March 2013, 15:24:29 UTC |
| 52c851f | apregier | 27 March 2013, 14:54:17 UTC | Fix typo | 27 March 2013, 14:54:30 UTC |
| 07dedd5 | nnutter | 27 March 2013, 04:05:54 UTC | fix alarm | 27 March 2013, 04:05:54 UTC |
| bc74aeb | nnutter | 27 March 2013, 02:51:50 UTC | Merge branch 'update_classes' This is all prep work for upcoming UR changes and for running `ur update classes-from-db`. | 27 March 2013, 02:51:50 UTC |
| aa59f2e | nnutter | 26 March 2013, 22:27:20 UTC | only add wingspan option to command if defined | 27 March 2013, 02:51:41 UTC |
| 5f3419e | nnutter | 08 March 2013, 15:49:22 UTC | sort section in preperation for update classes-from-db | 27 March 2013, 02:51:41 UTC |
| ad65b53 | Nathan Nutter | 28 February 2013, 16:28:05 UTC | property without column should be marked transient | 27 March 2013, 02:51:40 UTC |
| 4dbacf2 | nnutter | 06 March 2013, 21:09:05 UTC | add missing my | 27 March 2013, 02:51:40 UTC |
| 3e9011b | nnutter | 05 March 2013, 22:55:08 UTC | fix case where no PATHS_TO_REMOVE | 27 March 2013, 02:51:40 UTC |
| c2bcbc3 | Nathan Nutter | 01 March 2013, 00:35:25 UTC | ignore two more tables | 27 March 2013, 02:51:39 UTC |
| 37eb1f8 | Nathan Nutter | 27 February 2013, 21:03:29 UTC | trying to hide class from UR | 27 March 2013, 02:51:39 UTC |
| d735d00 | nnutter | 26 March 2013, 21:13:53 UTC | pre-fix for dependency on UR bug This currently depends on a bug in UR that will soon be fixed and will then need to fall back onto Workflow::DataSource::InstanceSchema as a consequence of our Postgres/Oracle syncing. | 27 March 2013, 02:51:38 UTC |
| dbad428 | Nathan Nutter | 27 February 2013, 21:41:04 UTC | move _ignore_table back to GMSchema | 27 March 2013, 02:51:38 UTC |
| 66752a1 | Nathan Nutter | 27 February 2013, 21:40:23 UTC | whitespace | 27 March 2013, 02:51:37 UTC |
| 97a248b | nnutter | 26 March 2013, 20:44:00 UTC | fix directories being made without group write due to restricted umask | 27 March 2013, 01:09:19 UTC |
| 3e2d435 | apregier | 26 March 2013, 23:23:57 UTC | Move references to the cancer gene list to dbpath | 26 March 2013, 23:23:57 UTC |
| ee6c34d | apregier | 26 March 2013, 21:44:06 UTC | Add documentation for annotate sv | 26 March 2013, 21:44:13 UTC |
| 5bafd53 | APipe Tester | 26 March 2013, 21:11:48 UTC | updated workflow submodule to ea4a2bf | 26 March 2013, 21:11:48 UTC |
| 22e70f4 | Jasreet Hundal | 26 March 2013, 20:38:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 March 2013, 20:38:15 UTC |
| 773eab0 | Jasreet Hundal | 26 March 2013, 20:38:06 UTC | removed debugging print statements | 26 March 2013, 20:38:06 UTC |
| f9a3565 | Ben Oberkfell | 26 March 2013, 20:28:52 UTC | Merge branch 'master' of git:/srv/git/genome | 26 March 2013, 20:28:52 UTC |
| b5b7c2a | Ben Oberkfell | 26 March 2013, 20:28:19 UTC | CHANGELOG: Tighter coupling of timing of Postgres & Oracle commits. Register a commit callback on the Oracle side to wait until Postgres has fully committed. Intent is to reduce race conditions in instances where shell commands are called that create entities that are queried for right away. For example, allocations. | 26 March 2013, 20:28:24 UTC |
| d4bc7f0 | Feiyu Du | 26 March 2013, 20:20:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 March 2013, 20:20:15 UTC |
| 11885d0 | Feiyu Du | 26 March 2013, 20:20:07 UTC | Blessing som-var-sv-detection build test for new sv annotation | 26 March 2013, 20:20:07 UTC |
| e6080c7 | Eddie Belter | 26 March 2013, 19:48:38 UTC | Solexa: add read trimmer version to all single SX comands if present | 26 March 2013, 19:48:47 UTC |
| d608a91 | Feiyu Du | 26 March 2013, 19:05:40 UTC | Blessing som-var-short build test for new sv annotation | 26 March 2013, 19:05:40 UTC |
| 9d28b85 | Feiyu Du | 25 March 2013, 19:42:46 UTC | syntax error fixed | 26 March 2013, 15:58:57 UTC |
| 996088d | Feiyu Du | 22 March 2013, 20:40:36 UTC | More update to plug new sv annotation to som var pipeline | 26 March 2013, 15:58:57 UTC |
| 3c16b47 | Feiyu Du | 20 March 2013, 15:32:58 UTC | Implement new sv annotation into somatic variation pipeline | 26 March 2013, 15:58:56 UTC |
| b2afc2c | Thomas Mooney | 26 March 2013, 15:28:57 UTC | Stop sending mail every minute when there's nothing to build. | 26 March 2013, 15:28:57 UTC |
| daf32f0 | Gabriel Sanderson | 26 March 2013, 00:06:22 UTC | Merge branch 'master' into gb_master | 26 March 2013, 00:06:22 UTC |
| bf57884 | Gabriel Sanderson | 25 March 2013, 23:58:19 UTC | Clean up many varscan modules. Rely less on samtools_path and more on the pileup_command method. ValidateSmallIndels -add samtools_use_baq flag to pass to varscan validation Add a samtools_path method instead of it being a copypasted param everywhere which was confusing with samtools_version. pileup_command_for_reference_and_bam method now takes an arrayref of bams so it can work for mpileup | 26 March 2013, 00:04:43 UTC |
| cfbd49f | Cyriac Kandoth | 24 March 2013, 20:45:53 UTC | ImportedAnnotation: Support subtracting bps using param flank_size | 24 March 2013, 20:45:53 UTC |
| a330e4c | Gabriel Sanderson | 22 March 2013, 23:26:56 UTC | Merge branch 'nobaq' into gb_master | 22 March 2013, 23:26:56 UTC |
| 5c30788 | Gabriel Sanderson | 22 March 2013, 23:03:33 UTC | DV2 Varscan now recognizes samtools params delimited with : before its own params. There is now the concept of samtools_version, samtools_use_baq, and other samtools params in the varscan base class. | 22 March 2013, 23:14:54 UTC |
| cfc83a3 | Malachi Griffith | 22 March 2013, 22:00:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 22 March 2013, 22:00:34 UTC |
| 251a992 | Malachi Griffith | 22 March 2013, 22:00:15 UTC | Blessing clin-seq build to accomodate recent update to cn-view | 22 March 2013, 22:00:15 UTC |
| c6a3706 | nnutter | 22 March 2013, 21:38:00 UTC | more refactoring/testing | 22 March 2013, 21:38:00 UTC |
| 89cb6f6 | dmorton | 22 March 2013, 20:45:06 UTC | Use GENOME_ALIGNER_INDEX_TEST_NAME for chimerascan index instead of GENOME_SOFTWARE_RESULT_TEST_NAME so we can make a test model that doesn't recalculate the index and take forever. | 22 March 2013, 20:45:06 UTC |
