| 76ddfac | nnutter | 25 April 2013, 20:03:00 UTC | update vendor/gatk-protected pointer | 25 April 2013, 20:03:15 UTC |
| a1dbeb2 | Gabriel Sanderson | 25 April 2013, 19:52:25 UTC | Merge branch 'master' into gb_master | 25 April 2013, 19:52:25 UTC |
| 42701ac | Gabriel Sanderson | 25 April 2013, 19:47:49 UTC | Updated default joinx version to .13 because .11 doesnt work for backfilling | 25 April 2013, 19:51:50 UTC |
| 8a45523 | Scott Smith | 25 April 2013, 18:39:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 April 2013, 18:39:39 UTC |
| 51b4e19 | Scott Smith | 25 April 2013, 18:37:20 UTC | fix warning | 25 April 2013, 18:37:20 UTC |
| 1766628 | Travis Abbott | 25 April 2013, 16:39:42 UTC | update blessed build | 25 April 2013, 16:40:29 UTC |
| d27cd04 | apregier | 25 April 2013, 16:38:27 UTC | CHORI libraries need their first 2 bases clipped | 25 April 2013, 16:39:04 UTC |
| 4b92653 | Travis Abbott | 25 April 2013, 16:30:48 UTC | updating blessed builds | 25 April 2013, 16:30:48 UTC |
| 74580b5 | Jim Weible | 25 April 2013, 15:37:50 UTC | Add a simple test for gmt vcf cleanup-vcf | 25 April 2013, 15:37:50 UTC |
| 4cdb428 | APipe Tester | 25 April 2013, 03:49:25 UTC | Updated `gmt` tab completion. | 25 April 2013, 03:49:25 UTC |
| 624a2be | APipe Tester | 25 April 2013, 03:48:26 UTC | Updated `genome` tab completion. | 25 April 2013, 03:48:26 UTC |
| defacbd | Chris Miller | 25 April 2013, 03:32:24 UTC | exposing minwidth option | 25 April 2013, 03:33:46 UTC |
| 41c0eaa | Malachi Griffith | 25 April 2013, 03:13:59 UTC | ClinSeq - build diffs check out, blessing new build | 25 April 2013, 03:13:59 UTC |
| 2aedc7d | Malachi Griffith | 24 April 2013, 21:32:07 UTC | Minor updates to clin-seq update-analysis and get-variant-sources | 24 April 2013, 21:32:07 UTC |
| b999c40 | APipe Tester | 24 April 2013, 20:57:48 UTC | Updated `gmt` tab completion. | 24 April 2013, 20:57:48 UTC |
| c46e5c8 | APipe Tester | 24 April 2013, 20:56:57 UTC | Updated `genome` tab completion. | 24 April 2013, 20:56:57 UTC |
| a87c055 | Cyriac Kandoth | 24 April 2013, 20:48:16 UTC | Switched to joinx1.7 | 24 April 2013, 20:52:32 UTC |
| df62cd3 | kmeltzst | 24 April 2013, 20:47:20 UTC | test file | 24 April 2013, 20:47:20 UTC |
| d37f9ab | kmeltzst | 24 April 2013, 20:46:38 UTC | added option for removing tmp files at end | 24 April 2013, 20:46:38 UTC |
| 2119981 | kmeltzst | 24 April 2013, 20:39:13 UTC | added option for output directory | 24 April 2013, 20:39:13 UTC |
| 17153ad | kmeltzst | 24 April 2013, 20:15:07 UTC | fixed bugs | 24 April 2013, 20:16:44 UTC |
| 76c4c75 | APipe Tester | 24 April 2013, 19:53:14 UTC | Updated `gmt` tab completion. | 24 April 2013, 19:53:14 UTC |
| c4b179c | APipe Tester | 24 April 2013, 19:52:17 UTC | Updated `genome` tab completion. | 24 April 2013, 19:52:17 UTC |
| 8f29e64 | Kyung Kim | 24 April 2013, 19:48:13 UTC | added soap v 2.23 | 24 April 2013, 19:48:13 UTC |
| ddeac02 | Jim Weible | 24 April 2013, 18:35:00 UTC | Fix the test I borked | 24 April 2013, 18:35:13 UTC |
| 0554026 | Gabriel Sanderson | 24 April 2013, 18:32:32 UTC | Merge branch 'master' into gb_master | 24 April 2013, 18:32:32 UTC |
| adb94ac | Gabriel Sanderson | 24 April 2013, 18:31:50 UTC | Allow the use of QC failed builds with a flag | 24 April 2013, 18:31:58 UTC |
| 37f5848 | Chris Miller | 24 April 2013, 18:22:24 UTC | works with version 0.4 | 24 April 2013, 18:23:11 UTC |
| 26667fc | kmeltzst | 24 April 2013, 18:11:34 UTC | modified tool | 24 April 2013, 18:13:12 UTC |
| 6ed199c | Eddie Belter | 24 April 2013, 16:02:43 UTC | GMT HTSEQ Count: change stranding terminology from "read" to "stranded" | 24 April 2013, 16:02:51 UTC |
| 227b10e | Scott Smith | 24 April 2013, 15:46:23 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 April 2013, 15:46:23 UTC |
| 2afd229 | Scott Smith | 24 April 2013, 15:46:02 UTC | add new file path formula for SOAPdenovo-63mer | 24 April 2013, 15:46:02 UTC |
| ebe9732 | Dan Koboldt | 24 April 2013, 15:31:52 UTC | New tool for converting VCF to PLINK | 24 April 2013, 15:31:52 UTC |
| 7af0d02 | Scott Smith | 24 April 2013, 14:26:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 April 2013, 14:26:08 UTC |
| 2dea78d | Scott Smith | 24 April 2013, 14:25:57 UTC | add custom lister for denovo assemblies | 24 April 2013, 14:25:57 UTC |
| c83709f | Todd Hepler | 23 April 2013, 20:23:40 UTC | basic tests for new picard tools | 23 April 2013, 20:35:17 UTC |
| 7c10d68 | Todd Hepler | 23 April 2013, 20:10:58 UTC | map basecalls_directory to basecalls_dir option also, java class changed -- some versions may be different | 23 April 2013, 20:35:16 UTC |
| 6d2061f | Todd Hepler | 23 April 2013, 20:09:32 UTC | made minimum_base_quality optional I think it may not be in some versions also, take out the output_files, I'm not sure how well this command maps to *_files | 23 April 2013, 20:35:16 UTC |
| 07d36bf | Todd Hepler | 22 April 2013, 20:08:00 UTC | first pass at gmt picard check-illumina-directory good for troubleshooting extract-illumina-barcodes | 23 April 2013, 20:35:15 UTC |
| 89aa148 | Todd Hepler | 22 April 2013, 17:30:30 UTC | first pass at picard demux tools | 23 April 2013, 20:35:15 UTC |
| 9695c0d | APipe Tester | 23 April 2013, 20:33:22 UTC | Updated `gmt` tab completion. | 23 April 2013, 20:33:22 UTC |
| 3918c0c | APipe Tester | 23 April 2013, 20:32:13 UTC | Updated `genome` tab completion. | 23 April 2013, 20:32:13 UTC |
| 925c967 | APipe Tester | 23 April 2013, 20:06:30 UTC | updated jenkins submodule to 6f61a9c | 23 April 2013, 20:06:30 UTC |
| 852ae2c | APipe Tester | 23 April 2013, 20:06:23 UTC | updated ur submodule to 9e47b40 | 23 April 2013, 20:06:23 UTC |
| 6cfa0e4 | APipe Tester | 23 April 2013, 20:01:31 UTC | updated ur submodule to da2ccbe | 23 April 2013, 20:01:31 UTC |
| 4affa36 | APipe Tester | 23 April 2013, 19:54:18 UTC | updated ur submodule to 111c33f | 23 April 2013, 19:54:18 UTC |
| 822d946 | Gabriel Sanderson | 23 April 2013, 19:50:05 UTC | Merge branch 'master' into gb_master | 23 April 2013, 19:50:05 UTC |
| 062a28f | Gabriel Sanderson | 23 April 2013, 19:48:58 UTC | Minor code updates to make the workflow run correctly. Make polymutt dir path expectation more flexible. | 23 April 2013, 19:49:12 UTC |
| 5f24f90 | Jim Weible | 23 April 2013, 19:41:52 UTC | Merge branch 'vcf-cleanup' | 23 April 2013, 19:41:52 UTC |
| 1bf4617 | Jim Weible | 23 April 2013, 19:41:07 UTC | increment VCF version to handle tag addition | 23 April 2013, 19:41:07 UTC |
| 3a0641f | Kyung Kim | 23 April 2013, 19:35:57 UTC | Fix typo changed sopa import to soap import | 23 April 2013, 19:35:57 UTC |
| b1c2fd8 | Jim Weible | 23 April 2013, 19:17:08 UTC | Add CleanupVcf, a tool to remove tagged per-detector columns fro a vcf file | 23 April 2013, 19:34:21 UTC |
| dce4ace | Jim Weible | 23 April 2013, 18:13:13 UTC | add square brackets to the per-caller columns on VCF combine for easily filtering | 23 April 2013, 19:34:21 UTC |
| de147a4 | Adam Coffman | 23 April 2013, 19:03:27 UTC | remove doc flag | 23 April 2013, 19:03:27 UTC |
| 977997e | Adam Coffman | 23 April 2013, 18:56:08 UTC | remove admin requirement for auto assign inst data | 23 April 2013, 18:56:08 UTC |
| 0dacc19 | Eddie Belter | 23 April 2013, 16:34:58 UTC | Inst Data Import: add orginal foramt attr; only add desc attr if defined; update tests | 23 April 2013, 16:34:58 UTC |
| 8b8bed3 | Eddie Belter | 22 April 2013, 23:15:07 UTC | InstData Import: dump sam from copied sra file | 22 April 2013, 23:15:07 UTC |
| f21d603 | Eddie Belter | 22 April 2013, 23:06:25 UTC | Sync: institutes a sync order for update apipe classes | 22 April 2013, 23:11:27 UTC |
| 7aa29b5 | Thomas Mooney | 22 April 2013, 21:12:40 UTC | Add some more abbreviations per RT#91971. | 22 April 2013, 21:12:40 UTC |
| 6bf4189 | APipe Tester | 22 April 2013, 18:18:54 UTC | updated jenkins submodule to 186aa31 | 22 April 2013, 18:18:54 UTC |
| 8fc5987 | apregier | 22 April 2013, 17:41:42 UTC | model input remove had bug for objects with display names | 22 April 2013, 17:41:42 UTC |
| b6321fe | APipe Tester | 22 April 2013, 14:46:16 UTC | updated jenkins submodule to 8d6d12d | 22 April 2013, 14:46:16 UTC |
| 274f264 | nnutter | 22 April 2013, 14:27:11 UTC | set copyCat pointer to master, old one was broken | 22 April 2013, 14:27:11 UTC |
| afe4940 | apregier | 19 April 2013, 22:53:12 UTC | Remove cp from debugging | 19 April 2013, 22:53:12 UTC |
| a2f1d3a | apregier | 19 April 2013, 21:56:35 UTC | Remove file copy from test | 19 April 2013, 21:57:16 UTC |
| 225bc1f | nnutter | 19 April 2013, 18:26:28 UTC | auto generate bare minimum tests | 19 April 2013, 21:22:01 UTC |
| 39d1e60 | nnutter | 19 April 2013, 19:28:12 UTC | should only look for .pm files This should only look for .pm files, tests will be added soon and they should not load. | 19 April 2013, 21:21:47 UTC |
| eb82a42 | Ben Oberkfell | 19 April 2013, 20:36:03 UTC | forgot to add this env module for query pausing | 19 April 2013, 20:36:03 UTC |
| 46e484e | Ben Oberkfell | 19 April 2013, 19:37:15 UTC | Set up pause blockers to stop querying & connects to Postgres. This will allow us to safely take down the PG server for sysadmin work and minimize disruption | 19 April 2013, 19:50:10 UTC |
| 4cbe84c | APipe Tester | 19 April 2013, 19:36:39 UTC | updated ur submodule to e1700d2 | 19 April 2013, 19:36:39 UTC |
| 1063e25 | nnutter | 19 April 2013, 19:26:02 UTC | add diag to help reproduce failure on apipe-ci | 19 April 2013, 19:26:02 UTC |
| 850e345 | nnutter | 19 April 2013, 18:37:40 UTC | load Test::* after 'use above' so we our Test::* | 19 April 2013, 18:44:38 UTC |
| 1be8ec4 | Ian Ferguson | 19 April 2013, 18:35:58 UTC | Modify Bwa memory request for certain ref builds Some reference sequence builds will consistently cause Bwa to reach its LSF memory limit. The AlignReads Event now provides the reference sequence build when calling the aligner module's required_rusage method. Bwa will now double the memory requirement from 8 to 16 GB when the provided reference sequence build matches a build that we have determined requires more memory. | 19 April 2013, 18:42:54 UTC |
| a73e6d5 | Ian Ferguson | 19 April 2013, 18:19:55 UTC | Increase bwamem memory rusage | 19 April 2013, 18:20:04 UTC |
| c5530f8 | Gabriel Sanderson | 19 April 2013, 18:11:48 UTC | Merge branch 'master' into gb_master | 19 April 2013, 18:11:48 UTC |
| 125f294 | Gabriel Sanderson | 18 April 2013, 23:04:49 UTC | Allow both gzipped and non gzipped vcfs as input | 19 April 2013, 18:11:10 UTC |
| 4c50713 | nnutter | 19 April 2013, 17:42:55 UTC | Merge branch 'test_more' | 19 April 2013, 17:42:55 UTC |
| dbbd532 | nnutter | 19 April 2013, 17:38:20 UTC | remove _subtest since we can now use Test::More's subtest | 19 April 2013, 17:38:20 UTC |
| 31bfc67 | nnutter | 19 April 2013, 17:37:05 UTC | remove sub_test since we can now use Test::More's subtest | 19 April 2013, 17:37:05 UTC |
| 9532180 | nnutter | 19 April 2013, 16:14:30 UTC | update to use Test::More's subtest | 19 April 2013, 16:22:38 UTC |
| 90e2546 | nnutter | 19 April 2013, 16:22:17 UTC | apply bugfix from Test::More 1.5 that hasn't been pulled into 0.98 | 19 April 2013, 16:22:38 UTC |
| 7bbae9e | nnutter | 19 April 2013, 16:21:34 UTC | pull in Test::More master @ 74efe123 | 19 April 2013, 16:22:37 UTC |
| 04096aa | nnutter | 19 April 2013, 15:20:45 UTC | whitespace | 19 April 2013, 15:47:39 UTC |
| 207c3f9 | nnutter | 19 April 2013, 15:18:47 UTC | make test pass even if UR_COMMAND_DUMP_STATUS_MESSAGES is set Since test depends on status messages not being shown we should also set $ENV{UR_COMMAND_DUMP_STATUS_MESSAGES} to 0 in case the tester has that enabled. | 19 April 2013, 15:47:38 UTC |
| d6db9c7 | nnutter | 19 April 2013, 15:20:31 UTC | add diagnostics | 19 April 2013, 15:47:38 UTC |
| 659c1fb | nnutter | 18 April 2013, 23:21:03 UTC | also get new lock The old lock includes subdirectories and should not. In order to transition to a new lock scheme we currently have to lock both schemes. Later we can remove the old scheme. | 18 April 2013, 23:40:44 UTC |
| 408c0d0 | nnutter | 18 April 2013, 23:11:08 UTC | refactor locking code Pull locking code into separate function. Same code is used in several modules so it still isn't completely refactored. Will fix that next. Moving towards fixing the fact that locks shouldn't contain subdirectories. | 18 April 2013, 23:40:42 UTC |
| 0b71bda | Ian Ferguson | 18 April 2013, 21:55:19 UTC | Add bwa-0.7.3a | 18 April 2013, 21:55:19 UTC |
| cc4ba0f | APipe Tester | 18 April 2013, 19:51:16 UTC | Updated `gmt` tab completion. | 18 April 2013, 19:51:16 UTC |
| fc422eb | APipe Tester | 18 April 2013, 19:49:58 UTC | Updated `genome` tab completion. | 18 April 2013, 19:49:58 UTC |
| a4d00c9 | Travis Abbott | 18 April 2013, 19:32:06 UTC | rename examples_values => example_values; add test | 18 April 2013, 19:32:06 UTC |
| 1941e02 | APipe Tester | 18 April 2013, 18:37:03 UTC | updated jenkins submodule to 63461be | 18 April 2013, 18:37:03 UTC |
| eda6d1f | Thomas Mooney | 18 April 2013, 18:16:40 UTC | This parameter is required. | 18 April 2013, 18:16:40 UTC |
| 7c5bfeb | Thomas Mooney | 18 April 2013, 18:14:02 UTC | Hardcode path to the rrna_database. This minimally restores the MGAP pipeline to functionality. | 18 April 2013, 18:14:02 UTC |
| 312a299 | apregier | 18 April 2013, 04:14:21 UTC | Bug fix | 18 April 2013, 04:14:50 UTC |
| 71f56cb | Travis Abbott | 17 April 2013, 21:44:41 UTC | update clinseq test data to fix broken test | 17 April 2013, 21:44:41 UTC |
| 1d27bde | Eddie Belter | 17 April 2013, 19:26:01 UTC | ClinSeq: update output for new builds | 17 April 2013, 20:08:25 UTC |
| 43cc8c3 | Ian Ferguson | 17 April 2013, 19:27:18 UTC | Added 1; to end of some aligner modules | 17 April 2013, 19:27:18 UTC |
| 04cf5df | Ian Ferguson | 17 April 2013, 19:24:25 UTC | Initial commit for Bwamem aligner module | 17 April 2013, 19:24:25 UTC |
| 107e345 | Ian Ferguson | 17 April 2013, 19:15:00 UTC | Refactoring in GMT::Bwa Tried to refactor GMT::Bwa to better manage the many different versions and features of Bwa. Includes tests. | 17 April 2013, 19:15:00 UTC |
