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 |
1eb8bf5 | Feiyu Du | 10 July 2013, 18:26:26 UTC | bug fix | 10 July 2013, 18:26:26 UTC |
f84b75c | Jason Walker | 10 July 2013, 17:21:46 UTC | Merge t push branch 'master' of ssh://git/srv/git/genome | 10 July 2013, 17:21:46 UTC |
8666282 | Jason Walker | 10 July 2013, 17:21:37 UTC | Add PCT_CHIMERAS to the BamQcMetrics summary per refalign build. | 10 July 2013, 17:21:37 UTC |
eb01eb0 | Dave Larson | 10 July 2013, 03:04:16 UTC | Change workflow command construction to use ref($self) instead of __PACKAGE__ so inheritance does what we want. | 10 July 2013, 03:04:16 UTC |
4ee0e24 | APipe Tester | 09 July 2013, 22:07:12 UTC | updated ur submodule to bfb9399 | 09 July 2013, 22:07:12 UTC |
93e955a | Chris Miller | 09 July 2013, 21:38:21 UTC | removing depricated tool | 09 July 2013, 21:38:21 UTC |
5840552 | Eddie Belter | 09 July 2013, 21:05:07 UTC | SomVal: identify dnp result uses bam_path to get bam from aligned bam result | 09 July 2013, 21:05:07 UTC |
2c8f46c | Thomas Mooney | 09 July 2013, 20:47:53 UTC | Don't try to run coverage analysis without an ROI. | 09 July 2013, 20:47:53 UTC |
63f4c69 | Thomas Mooney | 09 July 2013, 20:47:13 UTC | Only restrict to target regions if we have an ROI. | 09 July 2013, 20:47:13 UTC |
ecc6fef | Thomas Mooney | 09 July 2013, 20:46:39 UTC | Change to parent class so we can operate on refined BAMs. | 09 July 2013, 20:46:39 UTC |
98c0ac8 | Jason Walker | 09 July 2013, 18:03:37 UTC | A new command line tool to summarize BamQc metrics per build by instrument data. | 09 July 2013, 18:03:37 UTC |
6982200 | Eddie Belter | 08 July 2013, 23:00:09 UTC | InstData GATK: base recalibrator uses allocation tmp dir for gatk print reads | 09 July 2013, 17:26:03 UTC |
c4dfa2f | Eddie Belter | 08 July 2013, 22:51:08 UTC | GMT GATK: add tmp dir option | 09 July 2013, 17:26:03 UTC |
9d3f59f | Eddie Belter | 08 July 2013, 21:39:36 UTC | Inst Data Refine Reads Gatk: use indel realigner as bam, source for base recalibrator | 09 July 2013, 17:26:03 UTC |
8a0aece | Eddie Belter | 08 July 2013, 20:33:14 UTC | InstData Aligned Bam: add bam_file alias | 09 July 2013, 17:26:02 UTC |
cdf746e | Eddie Belter | 08 July 2013, 20:27:33 UTC | InstData GATK: add inst data property to base | 09 July 2013, 17:26:02 UTC |
9825104 | Eddie Belter | 08 July 2013, 19:43:33 UTC | SomVal: use bam_path instead of merged_alignment_bam_path in align reads | 09 July 2013, 17:26:01 UTC |
85eb36c | Eddie Belter | 08 July 2013, 19:42:54 UTC | InstData Aligned Bam Result: rename bam_file to bam_path | 09 July 2013, 17:26:01 UTC |
f6fdf93 | Eddie Belter | 08 July 2013, 19:09:34 UTC | InstData Merge: create refiner command then call shortcut/execute | 09 July 2013, 17:26:00 UTC |
3affef7 | Eddie Belter | 08 July 2013, 19:08:58 UTC | Refine Read GATK: base recalibrator is now base recalibrator bam result | 09 July 2013, 17:26:00 UTC |
e33b239 | Thomas Mooney | 09 July 2013, 17:17:10 UTC | Can't filter on subclass now that we have an abstract parent class for merged results. | 09 July 2013, 17:17:10 UTC |
1a82f57 | Thomas Mooney | 09 July 2013, 16:57:11 UTC | Let apipe-builder clean up other people's builds in "cleanup-succeeded". | 09 July 2013, 16:57:11 UTC |
959dc44 | Feiyu Du | 09 July 2013, 15:05:49 UTC | add check to make sure normal and tumor model are not the same | 09 July 2013, 15:05:49 UTC |
eb4e1de | Thomas Mooney | 09 July 2013, 14:30:33 UTC | Tolerate tabs or other funny spacing in track line. | 09 July 2013, 14:30:33 UTC |
caa35c7 | Nathan Nutter | 09 July 2013, 01:53:02 UTC | typo | 09 July 2013, 01:53:02 UTC |
a493d82 | Nathan Nutter | 09 July 2013, 01:44:30 UTC | add methods to walk lineage | 09 July 2013, 01:46:06 UTC |
a668e7c | Thomas Mooney | 08 July 2013, 21:32:18 UTC | Use parent class so we can run refcov on refined BAMs, too. | 08 July 2013, 21:32:18 UTC |
431a3d8 | dmorton | 03 July 2013, 21:04:44 UTC | SoftwareResults generate lock-names more corectly: They will generate the same lock-name whether default params (those with default=undef anyways) are specified or not. | 08 July 2013, 20:46:28 UTC |
9535ddf | dmorton | 03 July 2013, 20:47:46 UTC | Added clarifying comment to SoftwareResult.pm | 08 July 2013, 20:46:28 UTC |
8758877 | dmorton | 03 July 2013, 19:36:45 UTC | SomaticValidation will not die if no somatic SVs are found to validate | 08 July 2013, 20:46:27 UTC |
4afe3bd | Nathan Nutter | 08 July 2013, 15:00:17 UTC | use throws_ok instead of eval | 08 July 2013, 15:00:17 UTC |
8b6ab63 | Nathan Nutter | 08 July 2013, 14:54:26 UTC | Merge branch 'RT/91739' CHANGELOG: New sort order in `gmt bed chrom-sort` which is used as the default sorter in DV2. This will correct a sort incompatability between some DV2 results and JoinX. Any existing DV2 results affected by the sort incompatability will need to be set aside. If you get a sort error from JoinX like 'Unsorted data found in stream...' then your DV2 results may be affected. Currently only builds that use GRCh37-lite-+-HPV_Redux-build (116426356) are known to be affected. | 08 July 2013, 14:54:26 UTC |
5a0d8af | Nathan Nutter | 05 July 2013, 20:08:32 UTC | use strverssort instead of nsort nsort, from Sort::Naturally, has a different sort preference compared to JoinX which uses GNU strverscmp. | 08 July 2013, 14:05:29 UTC |
32b7629 | Nathan Nutter | 05 July 2013, 19:23:15 UTC | add Sort::strverscmp | 08 July 2013, 14:05:29 UTC |
ea5ed9c | APipe Tester | 06 July 2013, 02:03:57 UTC | updated jenkins submodule to 7d4e5d2 | 06 July 2013, 02:03:57 UTC |
8662abb | Nathan Nutter | 05 July 2013, 20:21:11 UTC | rebuilt expected output per Malachi | 05 July 2013, 20:22:08 UTC |
ed5bb46 | Dave Larson | 05 July 2013, 20:21:16 UTC | point to latest version and docs | 05 July 2013, 20:21:16 UTC |
64efeb7 | Malachi Griffith | 05 July 2013, 19:44:16 UTC | ClinSeq - better handling of excluded data | 05 July 2013, 19:44:16 UTC |
565ccd0 | Chris Miller | 05 July 2013, 17:27:37 UTC | clarifications in the docs | 05 July 2013, 17:27:52 UTC |