093d783 | apregier | 18 July 2013, 15:53:52 UTC | Disconnect db handle during long-running assembly operations | 18 July 2013, 15:53:52 UTC |
7552503 | APipe Tester | 18 July 2013, 15:18:25 UTC | Updated `gmt` tab completion. | 18 July 2013, 15:18:25 UTC |
446fc74 | APipe Tester | 18 July 2013, 15:17:31 UTC | Updated `genome` tab completion. | 18 July 2013, 15:17:31 UTC |
6145c18 | APipe Tester | 18 July 2013, 15:15:43 UTC | Updated class browser cache. | 18 July 2013, 15:15:43 UTC |
f0baef6 | Nathan Nutter | 18 July 2013, 14:45:54 UTC | Merge branch 'removal' | 18 July 2013, 15:06:17 UTC |
49e8778 | Nathan Nutter | 17 July 2013, 19:14:45 UTC | remove `gmt annotate genomic-regions` Command produces warnings when used and appears to have almost no usage: 2010/06/15 dkoboldt gmt annotate genomic-regions --help 2010/06/15 dkoboldt gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/06/02 ckandoth gmt annotate genomic-regions 2010/06/02 ckandoth gmt annotate genomic-regions --help 2010/06/02 ckandoth gmt annotate genomic-regions --help 2010/06/29 kchen gmt annotate genomic-regions 2010/06/30 wschierd gmt annotate genomic-regions --help 2010/06/30 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --help 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/07/02 wschierd gmt annotate genomic-regions --bed-file ... --output-directory ... 2010/08/11 jwalker gmt annotate genomic-regions --help 2010/08/11 jwalker gmt annotate genomic-regions --help 2011/01/12 jwallis gmt annotate genomic-regions --help 2012/07/24 dmorton gmt annotate genomic-regions --help 2013/07/10 jhundal gmt annotate genomic-regions --help | 18 July 2013, 15:06:15 UTC |
14077cd | Nathan Nutter | 16 July 2013, 19:12:43 UTC | remove unused/old code We believe these were either never really used or were only used experimentally so we are removing the code and archiving the database data. If one of these turns out to be needed then contact APIPE to coordinate a restore. Related classes: Genome::Disease Genome::Model::BuildSV Genome::Model::SV Genome::Model::VariantSource Genome::Model::VariantValidation Genome::SNVManualReview Genome::SequenceDiff Genome::SequenceDiffEval Genome::SequenceDiffPart Genome::UpdateHistory Genome::VRList Genome::VRListMember Genome::VariantOccurrence Genome::VariantReviewDetail Genome::VariantReviewDetailOld Genome::VariantReviewList Genome::VariantReviewListFilter Genome::VariantReviewListMember Related tables: DISEASE GENOME_MODEL_BUILD_SV GENOME_MODEL_SV GENOME_MODEL_VARIANT_SOURCE GENOME_MODEL_VARIANTVALIDATION SNV_MANUAL_REVIEW SEQUENCE_DIFF SEQUENCE_DIFF_EVAL SEQUENCE_DIFF_PART GENOME_VR_LIST GENOME_VR_LIST_MEMBER VARIANT_OCCURRENCE VARIANT_REVIEW_DETAIL VARIANT_REVIEW_DETAIL_OLD VARIANT_REVIEW_LIST VARIANT_REVIEW_LIST_FILTER VARIANT_REVIEW_LIST_MEMBER | 18 July 2013, 15:06:13 UTC |
a51290d | Jim Weible | 18 July 2013, 14:38:39 UTC | skip generate merged assemblies if we don't have a merged fasta file | 18 July 2013, 14:38:39 UTC |
e9d51d3 | APipe Tester | 17 July 2013, 18:37:22 UTC | Updated `gmt` tab completion. | 17 July 2013, 18:37:22 UTC |
232127d | APipe Tester | 17 July 2013, 18:36:27 UTC | Updated `genome` tab completion. | 17 July 2013, 18:36:27 UTC |
1255d4d | APipe Tester | 17 July 2013, 18:33:42 UTC | Updated class browser cache. | 17 July 2013, 18:33:42 UTC |
5814856 | Jasreet Hundal | 17 July 2013, 18:21:06 UTC | Renaming module | 17 July 2013, 18:21:06 UTC |
57fe376 | apregier | 17 July 2013, 17:27:01 UTC | Merge branch 'generator' into gb_master | 17 July 2013, 17:27:01 UTC |
f1fd599 | apregier | 11 July 2013, 15:07:54 UTC | Move CreateMutationDiagrams off of db | 17 July 2013, 17:23:52 UTC |
e32e9c1 | apregier | 10 July 2013, 21:50:40 UTC | Add a way to pass in data directories for somatic variation and annotation builds | 17 July 2013, 17:18:39 UTC |
1abfb82 | Thomas Mooney | 17 July 2013, 15:26:04 UTC | This...is...Pindel. | 17 July 2013, 15:26:04 UTC |
b5ebfe1 | Veena Bhonagiri | 17 July 2013, 15:08:03 UTC | removed version numbers from pipeline email | 17 July 2013, 15:08:03 UTC |
60b3779 | APipe Tester | 16 July 2013, 19:26:54 UTC | Updated `gmt` tab completion. | 16 July 2013, 19:26:54 UTC |
e5cb5c6 | APipe Tester | 16 July 2013, 19:25:58 UTC | Updated `genome` tab completion. | 16 July 2013, 19:25:58 UTC |
2de02f2 | APipe Tester | 16 July 2013, 19:23:49 UTC | Updated class browser cache. | 16 July 2013, 19:23:49 UTC |
ee6a7cd | Jasreet Hundal | 16 July 2013, 19:15:26 UTC | Output Cds sequence for annotated snv file | 16 July 2013, 19:15:26 UTC |
f40a60a | APipe Tester | 16 July 2013, 18:24:27 UTC | updated ur submodule to fc39b18 | 16 July 2013, 18:24:27 UTC |
58e488f | Ian Ferguson | 16 July 2013, 17:54:46 UTC | Bwamem now closes db handle during align and sort | 16 July 2013, 17:55:31 UTC |
b75157b | Nathan Nutter | 16 July 2013, 17:26:23 UTC | Sort::strverscmp is now packaged | 16 July 2013, 17:26:36 UTC |
16a0f0c | APipe Tester | 16 July 2013, 15:36:20 UTC | updated ur submodule to e8a55d2 | 16 July 2013, 15:36:20 UTC |
e72b646 | Thomas Mooney | 16 July 2013, 15:05:32 UTC | Make sure $@ doesn't get swallowed before we print our error. | 16 July 2013, 15:05:32 UTC |
692e155 | Ben Oberkfell | 15 July 2013, 22:14:00 UTC | Revert "pass the "force" param forward when copying models." This reverts commit ff03c8c755e7c34fc801cbc538f0cea133185c1e. | 15 July 2013, 22:14:00 UTC |
7af270b | Ben Oberkfell | 15 July 2013, 21:49:43 UTC | do not attempt to call properties where the model class does not define it | 15 July 2013, 21:49:43 UTC |
ff03c8c | Ben Oberkfell | 15 July 2013, 21:22:51 UTC | pass the "force" param forward when copying models. | 15 July 2013, 21:22:51 UTC |
0ae1e9b | Chris Miller | 15 July 2013, 17:08:02 UTC | updating help | 15 July 2013, 17:21:41 UTC |
a5b3daa | APipe Tester | 15 July 2013, 16:36:31 UTC | Updated `gmt` tab completion. | 15 July 2013, 16:36:50 UTC |
126a199 | APipe Tester | 15 July 2013, 16:34:37 UTC | Updated `genome` tab completion. | 15 July 2013, 16:36:50 UTC |
396bed1 | APipe Tester | 15 July 2013, 16:30:49 UTC | Updated class browser cache. | 15 July 2013, 16:36:49 UTC |
62c97f5 | Scott Smith | 15 July 2013, 16:30:30 UTC | fixed clinseq TestGenomeCommands for new input data | 15 July 2013, 16:30:30 UTC |
33bcbb6 | Scott Smith | 15 July 2013, 16:24:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 July 2013, 16:24:42 UTC |
1623f11 | Scott Smith | 15 July 2013, 16:24:32 UTC | updated clinseq convergeStats.t to use new output with different sorting | 15 July 2013, 16:24:32 UTC |
2448659 | Travis Abbott | 15 July 2013, 16:17:12 UTC | add breakdancer 1.4.2 | 15 July 2013, 16:17:12 UTC |
b1ef0c7 | APipe Tester | 15 July 2013, 15:50:58 UTC | Updated `gmt` tab completion. | 15 July 2013, 15:50:58 UTC |
b00b304 | APipe Tester | 15 July 2013, 15:49:45 UTC | Updated `genome` tab completion. | 15 July 2013, 15:49:45 UTC |
da78f7e | APipe Tester | 15 July 2013, 15:47:23 UTC | Updated class browser cache. | 15 July 2013, 15:47:23 UTC |
977ff34 | Chris Miller | 15 July 2013, 15:37:29 UTC | adding option for max clusters | 15 July 2013, 15:37:59 UTC |
2c19cbd | APipe Tester | 12 July 2013, 21:09:56 UTC | Updated `genome` tab completion. | 12 July 2013, 21:09:56 UTC |
5a5f456 | APipe Tester | 12 July 2013, 21:08:21 UTC | Updated class browser cache. | 12 July 2013, 21:08:21 UTC |
85b97ea | Malachi Griffith | 12 July 2013, 20:42:59 UTC | Clinseq - fix create-mutation-diagrams test to ingore fields contain floating point values and update test result to account for update to cosmic v65 | 12 July 2013, 20:42:59 UTC |
ba7dd28 | APipe Tester | 12 July 2013, 19:46:16 UTC | updated workflow submodule to 7bf85e2 | 12 July 2013, 19:46:16 UTC |
a85f660 | Nathan Nutter | 12 July 2013, 15:13:55 UTC | more aggressive abandoning of unstartable builds Change behavior so that it abandons Unstartable builds as soon as long as the latest_build was not Unstartable. This should lower "double counting" builds that have failures and unstartables. | 12 July 2013, 19:26:43 UTC |
e867197 | dmorton | 11 July 2013, 17:04:02 UTC | extracted methods in Genome::Model::Build::all_allocations | 12 July 2013, 16:27:37 UTC |
3baaece | dmorton | 10 July 2013, 18:56:08 UTC | Created 'genome instrument-data find-associated-builds' | 12 July 2013, 16:27:37 UTC |
d0bf02a | dmorton | 10 July 2013, 18:41:43 UTC | Fix error getting eaten in build.pm | 12 July 2013, 16:27:37 UTC |
d6cd4fa | APipe Tester | 12 July 2013, 13:37:39 UTC | updated workflow submodule to 81c111c | 12 July 2013, 13:37:39 UTC |
c7aa9bf | APipe Tester | 12 July 2013, 03:58:52 UTC | updated workflow submodule to 1985352 | 12 July 2013, 03:58:52 UTC |
f5845c6 | Malachi Griffith | 12 July 2013, 02:47:03 UTC | Update test data to accomodate updates to clin-seq update-analysis | 12 July 2013, 02:47:03 UTC |
13f1bd7 | Malachi Griffith | 12 July 2013, 02:10:35 UTC | Updated doc for clin-seq | 12 July 2013, 02:10:35 UTC |
9ce5304 | Malachi Griffith | 12 July 2013, 01:58:23 UTC | ClinSeq - add logic to improve handling of data additions | 12 July 2013, 01:58:23 UTC |
584a9c8 | Malachi Griffith | 11 July 2013, 22:53:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 July 2013, 22:53:03 UTC |
5eaeb43 | Malachi Griffith | 11 July 2013, 22:52:50 UTC | ClinSeq - Update test result for UpdateAnalysis | 11 July 2013, 22:52:50 UTC |
7e56672 | Scott Smith | 11 July 2013, 22:42:04 UTC | disabled test until test model completes building | 11 July 2013, 22:42:04 UTC |
2c8903b | Malachi Griffith | 11 July 2013, 21:51:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 11 July 2013, 21:51:54 UTC |
4662490 | Malachi Griffith | 11 July 2013, 21:51:44 UTC | Fix typo in clinseq annotation database variable name | 11 July 2013, 21:51:44 UTC |
27a3f5e | Scott Smith | 11 July 2013, 21:25:48 UTC | updated to match meta-data changes on samples | 11 July 2013, 21:25:48 UTC |
dfa5703 | Scott Smith | 11 July 2013, 21:22:07 UTC | update clinseq tests due to changing underlying data | 11 July 2013, 21:22:07 UTC |
d1ed931 | Scott Smith | 11 July 2013, 21:04:18 UTC | readme on constructing cancer annotation for clinseq | 11 July 2013, 21:04:18 UTC |
6c0746a | Scott Smith | 11 July 2013, 19:29:05 UTC | updated clinseq to use Genome::Db::Cosmic directly instead of the legacy files under the cancer annotation db. | 11 July 2013, 19:29:05 UTC |
2f1eb22 | apregier | 11 July 2013, 18:44:58 UTC | Merge branch 'annovar' into gb_master | 11 July 2013, 18:44:58 UTC |
c70a49e | apregier | 11 July 2013, 17:57:49 UTC | Include rsid in maf output | 11 July 2013, 18:18:25 UTC |
69fa554 | apregier | 11 July 2013, 17:26:35 UTC | Include regdb score in annot file | 11 July 2013, 18:18:25 UTC |
65b6e19 | apregier | 12 June 2013, 21:00:25 UTC | Annotate tier1 with regulatory variants as well | 11 July 2013, 18:18:24 UTC |
a209db0 | APipe Tester | 11 July 2013, 17:16:28 UTC | Updated `gmt` tab completion. | 11 July 2013, 17:16:39 UTC |
30b877a | APipe Tester | 11 July 2013, 17:15:38 UTC | Updated `genome` tab completion. | 11 July 2013, 17:16:39 UTC |
0c72cf4 | APipe Tester | 11 July 2013, 17:13:57 UTC | Updated class browser cache. | 11 July 2013, 17:16:39 UTC |
1a77f24 | Jason Walker | 11 July 2013, 17:15:24 UTC | Add a basic test for Sword SlidingWindowPileup | 11 July 2013, 17:15:24 UTC |
103716b | Jason Walker | 11 July 2013, 17:06:06 UTC | Add a new tree to genome model tools for Sword development | 11 July 2013, 17:06:06 UTC |
729ceef | APipe Tester | 11 July 2013, 14:14:22 UTC | updated workflow submodule to f58f5eb | 11 July 2013, 14:14:22 UTC |
9db1415 | Nathan Nutter | 11 July 2013, 06:28:29 UTC | rewrite strverscmp because the old one was broken | 11 July 2013, 06:28:29 UTC |
58b19de | APipe Tester | 11 July 2013, 03:19:13 UTC | Updated `gmt` tab completion. | 11 July 2013, 03:19:13 UTC |
35d8250 | APipe Tester | 11 July 2013, 03:18:13 UTC | Updated `genome` tab completion. | 11 July 2013, 03:18:13 UTC |
9a5936e | APipe Tester | 11 July 2013, 03:15:42 UTC | Updated class browser cache. | 11 July 2013, 03:15:42 UTC |
5778b7f | Dave Larson | 11 July 2013, 03:02:09 UTC | Query out the library name for BamQC summarization. | 11 July 2013, 03:02:09 UTC |
72bd7fe | Chris Miller | 11 July 2013, 00:22:19 UTC | fixing bed conversion issue | 11 July 2013, 00:22:58 UTC |
3c1032c | Scott Smith | 11 July 2013, 00:14:57 UTC | switch to specific subclasses of Genome::Db for clinseq inputs | 11 July 2013, 00:15:09 UTC |
efc8d54 | Gabriel Sanderson | 10 July 2013, 22:37:58 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:37:58 UTC |
bf36cd9 | Gabriel Sanderson | 10 July 2013, 22:37:43 UTC | Since this test uses shellcmd (and should not)... force a use of the module that is being tested so that test tracker can catch failures easier. | 10 July 2013, 22:37:43 UTC |
a94b24d | Gabriel Sanderson | 10 July 2013, 22:32:07 UTC | Merge branch 'master' into gb_master | 10 July 2013, 22:32:07 UTC |
4e821ba | Gabriel Sanderson | 10 July 2013, 22:28:01 UTC | Updated test for new required property | 10 July 2013, 22:30:56 UTC |
283cf91 | Feiyu Du | 10 July 2013, 21:41:46 UTC | skip bamqc for imported alignment bam | 10 July 2013, 21:41:46 UTC |
1612f25 | Scott Smith | 10 July 2013, 21:22:11 UTC | No longer require a .git subdirectory in a Genome::Db dir, or a "latest" symlink. A meta.yml file is sufficient. | 10 July 2013, 21:22:43 UTC |
7a0d6cc | APipe Tester | 10 July 2013, 20:46:53 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:46:53 UTC |
dd860d9 | APipe Tester | 10 July 2013, 20:45:58 UTC | Updated `genome` tab completion. | 10 July 2013, 20:45:58 UTC |
f38f394 | APipe Tester | 10 July 2013, 20:43:48 UTC | Updated class browser cache. | 10 July 2013, 20:43:48 UTC |
b248d55 | Scott Smith | 10 July 2013, 20:31:43 UTC | updated the blessed-build for clinseq: the diff changes when LIMS archives data, and this just occurred | 10 July 2013, 20:32:08 UTC |
808c854 | Scott Smith | 10 July 2013, 20:27:51 UTC | ensure that we only fabricate subclasses for things that inherit from Genome::Db | 10 July 2013, 20:32:08 UTC |
e819329 | Scott Smith | 10 July 2013, 20:24:39 UTC | merge error fix in Genome::Db | 10 July 2013, 20:32:07 UTC |
a7a889e | APipe Tester | 10 July 2013, 20:25:19 UTC | Updated `gmt` tab completion. | 10 July 2013, 20:25:19 UTC |
666055b | APipe Tester | 10 July 2013, 20:24:15 UTC | Updated `genome` tab completion. | 10 July 2013, 20:24:15 UTC |
6e30a5b | APipe Tester | 10 July 2013, 20:22:13 UTC | Updated class browser cache. | 10 July 2013, 20:22:13 UTC |
64c6193 | Scott Smith | 10 July 2013, 20:15:13 UTC | updated the clinseq pipeline to use Genome::Db entities instead of a hard-coded path to special annotation data | 10 July 2013, 20:15:13 UTC |
874aa4d | Scott Smith | 10 July 2013, 20:08:13 UTC | updated to sub-class by source and database | 10 July 2013, 20:08:50 UTC |
e892650 | APipe Tester | 10 July 2013, 18:54:59 UTC | Updated `gmt` tab completion. | 10 July 2013, 18:54:59 UTC |
d0c8d53 | APipe Tester | 10 July 2013, 18:53:45 UTC | Updated `genome` tab completion. | 10 July 2013, 18:53:45 UTC |
8bbb3b8 | APipe Tester | 10 July 2013, 18:51:33 UTC | Updated class browser cache. | 10 July 2013, 18:51:33 UTC |