| 8e98317 | Nathan Nutter | 22 December 2012, 17:14:46 UTC | add TestTracker config | 22 December 2012, 17:14:46 UTC |
| 921e141 | Nathan Nutter | 22 December 2012, 02:58:22 UTC | whitespace | 22 December 2012, 02:58:44 UTC |
| f808fa4 | Nathan Nutter | 22 December 2012, 02:58:03 UTC | fix void context warning | 22 December 2012, 02:58:43 UTC |
| 411f82b | dmorton | 21 December 2012, 17:39:56 UTC | Add option to Gatk/RealignIndels.pm to make bam index Remove step in ValidateSmallIndels that was doing the same. | 21 December 2012, 17:39:56 UTC |
| 96b9830 | dmorton | 21 December 2012, 17:12:40 UTC | Remove Utility::Text from Sys.pm It wasn't being used. | 21 December 2012, 17:14:10 UTC |
| 60e461e | Jason Walker | 21 December 2012, 17:12:53 UTC | Add the deduplication_handler param for RnaSeq models. | 21 December 2012, 17:12:53 UTC |
| cc07cd3 | Gabriel Sanderson | 21 December 2012, 00:32:30 UTC | Merge branch 'polymuttheaderfix' into gb_master | 21 December 2012, 00:32:30 UTC |
| 3d003df | Gabriel Sanderson | 21 December 2012, 00:32:15 UTC | Add a couple more header fixes. We should no longer have duplicate DQ or missing DS headers | 21 December 2012, 00:32:22 UTC |
| 8c1ab9d | Gabriel Sanderson | 21 December 2012, 00:05:03 UTC | Merge branch 'master' into gb_master | 21 December 2012, 00:05:03 UTC |
| 4dfc246 | Gabriel Sanderson | 21 December 2012, 00:04:54 UTC | Fixed a spammy common warning | 21 December 2012, 00:04:59 UTC |
| 8d3fb4d | Gabriel Sanderson | 21 December 2012, 00:01:16 UTC | Merge branch 'validation' into gb_master | 21 December 2012, 00:01:16 UTC |
| 4a1f154 | Gabriel Sanderson | 21 December 2012, 00:01:02 UTC | Added a test case for gmt gatk realign-indels. | 21 December 2012, 00:01:02 UTC |
| f9af56c | Gabriel Sanderson | 20 December 2012, 21:38:07 UTC | Merge branch 'validation' into gb_master | 20 December 2012, 21:38:07 UTC |
| efb19f0 | Gabriel Sanderson | 20 December 2012, 21:19:33 UTC | Added a gmt gatk realign-indels command to run -T IndelRealigner. ValidateSmallIndels is refactored to use this new command. Added some functionality to gmt gatk to be more useful as a base class. | 20 December 2012, 21:38:00 UTC |
| 8c2cc78 | Thomas Mooney | 20 December 2012, 21:06:21 UTC | Tighten the regexes now that there are two alignment directories. | 20 December 2012, 21:06:55 UTC |
| 2cf0e7b | Jim Weible | 20 December 2012, 21:03:14 UTC | Serialize the uniprot mapping | 20 December 2012, 21:03:20 UTC |
| 6f800f3 | Nathan Dees | 20 December 2012, 16:34:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 December 2012, 16:34:35 UTC |
| 99c3e87 | Nathan Dees | 20 December 2012, 16:34:30 UTC | new joinx version plus case-independent checking of ref sequence at cpg loci | 20 December 2012, 16:34:30 UTC |
| ba54aac | Feiyu Du | 20 December 2012, 16:07:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 December 2012, 16:07:20 UTC |
| 025661f | Feiyu Du | 20 December 2012, 16:06:46 UTC | add FT subfield to FORMAT and populate it in sample columns for strelka detector vcf output | 20 December 2012, 16:06:46 UTC |
| a58e614 | Thomas Mooney | 20 December 2012, 14:18:16 UTC | Only require a reference if we're going to run the step. | 20 December 2012, 14:18:16 UTC |
| 8310a2d | Gabriel Sanderson | 19 December 2012, 23:41:18 UTC | Merge branch 'validation' into gb_master | 19 December 2012, 23:41:18 UTC |
| 0516d90 | Gabriel Sanderson | 19 December 2012, 23:41:04 UTC | Refactored the a section of code in PullOneTwoBpIndels that is relevant for SomaticValidation models into a new module in G:M:SomaticValidation::Command::ValidateSmallIndels. | 19 December 2012, 23:41:14 UTC |
| 9a2a45f | Thomas Mooney | 19 December 2012, 23:16:52 UTC | Fix typo. | 19 December 2012, 23:16:52 UTC |
| 5a7168d | Gabriel Sanderson | 19 December 2012, 22:56:54 UTC | Merge branch 'master' into gb_master | 19 December 2012, 22:56:54 UTC |
| de5a57f | Gabriel Sanderson | 19 December 2012, 22:56:40 UTC | The previous commit did not actually include AD and BQ information in the vcf line. Fixed this and updated the test case | 19 December 2012, 22:56:46 UTC |
| 7755e2a | Malachi Griffith | 19 December 2012, 22:51:32 UTC | clinseq - fixed summarize-builds to get samples associated with a clinseq model more accurately | 19 December 2012, 22:51:32 UTC |
| 60b07ab | Malachi Griffith | 19 December 2012, 22:50:56 UTC | CnView - added plot that is scaled consistently and more suitable for comparison across multiple tumors | 19 December 2012, 22:50:56 UTC |
| 8a896f3 | Thomas Mooney | 19 December 2012, 22:27:55 UTC | Split SV validation into steps to eliminate nested refalign model. The reference-sequence generation still delegates to a new build. It was moved to a separate step in order to have it be committed before the alignments try to use it. | 19 December 2012, 22:27:55 UTC |
| a05338c | Thomas Mooney | 19 December 2012, 22:24:30 UTC | Prevent a few failures in error handling. A nested workflow in a pure-workflow build may match the three-part format without having an event or stage for each step, so just bail if we don't get something that looks like an ID. | 19 December 2012, 22:24:30 UTC |
| 451cf39 | Gabriel Sanderson | 19 December 2012, 21:36:11 UTC | Merge branch 'master' into gb_master | 19 December 2012, 21:36:11 UTC |
| 6acd2e3 | Gabriel Sanderson | 19 December 2012, 21:36:02 UTC | Reversing a hack in order to try something else | 19 December 2012, 21:36:02 UTC |
| d8892dc | APipe Tester | 19 December 2012, 21:20:17 UTC | updated ur submodule to 7dec1ff | 19 December 2012, 21:20:17 UTC |
| a76407b | Gabriel Sanderson | 19 December 2012, 21:17:03 UTC | Merge branch 'master' into gb_master | 19 December 2012, 21:17:03 UTC |
| 851c457 | Gabriel Sanderson | 19 December 2012, 21:16:47 UTC | Updated test data | 19 December 2012, 21:16:47 UTC |
| 478181e | Ben Oberkfell | 19 December 2012, 20:57:31 UTC | dont auto-abort for bad postgres driver if you are running a LIMS command, because you still have to use ancient perl to run it. | 19 December 2012, 20:57:31 UTC |
| 2603e2b | Ben Oberkfell | 19 December 2012, 20:56:43 UTC | always use genome-perl when shelling out. | 19 December 2012, 20:56:43 UTC |
| 35594cc | Ben Oberkfell | 19 December 2012, 20:20:36 UTC | Merge branch 'master' of git:/srv/git/genome | 19 December 2012, 20:20:36 UTC |
| 6ec0fc4 | Ben Oberkfell | 19 December 2012, 20:20:30 UTC | make new picard module available | 19 December 2012, 20:20:30 UTC |
| c19ebb8 | Gabriel Sanderson | 19 December 2012, 19:41:07 UTC | Merge branch 'master' into gb_master | 19 December 2012, 19:41:07 UTC |
| 52a586d | Gabriel Sanderson | 19 December 2012, 19:40:47 UTC | Increment vcf version. | 19 December 2012, 19:40:47 UTC |
| 2c5284d | Ben Oberkfell | 19 December 2012, 17:38:36 UTC | fix postgres syncing on sample attribute stomper for real | 19 December 2012, 17:38:50 UTC |
| 4bb4333 | Dan Koboldt | 19 December 2012, 17:33:13 UTC | Changes to improve the way VarScan output is converted to VCF fields | 19 December 2012, 17:33:13 UTC |
| a52c018 | Dan Koboldt | 19 December 2012, 17:01:16 UTC | Updated line 34 to force PhenotypeCorrelation models to always proceed as if QC-passed | 19 December 2012, 17:01:16 UTC |
| 8203901 | Thomas Mooney | 19 December 2012, 14:12:55 UTC | Add category to the newer somatic-validation pipeline steps. | 19 December 2012, 14:12:55 UTC |
| 5cc9590 | Malachi Griffith | 19 December 2012, 01:21:04 UTC | clinseq: update to converge scripts - added SV fusion converge script | 19 December 2012, 01:21:04 UTC |
| ee0d3d3 | apregier | 18 December 2012, 23:08:11 UTC | Merge branch 'fix' into gb_master | 18 December 2012, 23:08:11 UTC |
| 5deb7f1 | apregier | 18 December 2012, 23:07:51 UTC | Get the tiering directory from the annotation build | 18 December 2012, 23:07:51 UTC |
| dacd33b | apregier | 18 December 2012, 23:03:18 UTC | Merge branch 'fix' into gb_master | 18 December 2012, 23:03:18 UTC |
| 0d12c3d | apregier | 18 December 2012, 23:02:43 UTC | Fix CountContigs command so it handles contig names with parens | 18 December 2012, 23:02:56 UTC |
| c7517c3 | Gabriel Sanderson | 18 December 2012, 21:36:36 UTC | Merge branch 'validation' into gb_master | 18 December 2012, 21:36:36 UTC |
| 87f7d0c | Gabriel Sanderson | 17 December 2012, 22:53:49 UTC | Add run-inline option to PullOneTwoBpIndels so that one part may be run inline for testing purposes. Added a test case | 18 December 2012, 21:35:21 UTC |
| 0afbb87 | Eddie Belter | 18 December 2012, 21:00:51 UTC | MC16s: process inst data event calls seq platform on model | 18 December 2012, 21:04:15 UTC |
| ba7ac37 | Malachi Griffith | 18 December 2012, 20:23:43 UTC | ClinSeq: various patches to fix converge steps broken by recent updates to the pipeline | 18 December 2012, 20:23:43 UTC |
| 10d1446 | Eddie Belter | 18 December 2012, 20:13:43 UTC | MC16s: rm broken test in command.t | 18 December 2012, 20:13:43 UTC |
| ba50428 | Eddie Belter | 18 December 2012, 19:54:41 UTC | MC16s: rm list runs command | 18 December 2012, 19:54:41 UTC |
| 4424c7f | Thomas Mooney | 18 December 2012, 18:52:37 UTC | Produce a GFF file at the end of the GenePrediction::Eukaryotic pipeline. | 18 December 2012, 18:52:37 UTC |
| 21112ee | Brian Derickson | 18 December 2012, 17:24:59 UTC | fixed memory instance size in grid jobs finished | 18 December 2012, 17:25:04 UTC |
| 1a23670 | Brian Derickson | 17 December 2012, 18:36:35 UTC | check that input value exists before calling isa on it | 18 December 2012, 17:25:04 UTC |
| ef3abd1 | Thomas Mooney | 18 December 2012, 14:57:27 UTC | Update one more build parameter to support arbitrary references. | 18 December 2012, 14:57:27 UTC |
| 7c7f9e4 | Eddie Belter | 18 December 2012, 00:27:47 UTC | MC16s: Merge branch | 18 December 2012, 00:27:47 UTC |
| a54852c | Eddie Belter | 17 December 2012, 23:42:13 UTC | MC16s: rm sequencing center | 17 December 2012, 23:42:13 UTC |
| 0cfcac2 | Eddie Belter | 17 December 2012, 23:25:01 UTC | MC16s: combine calculate kg usage for each platform into one method; update getting seq platform to get amplicon sets; add to base build test; rm subclass tests | 17 December 2012, 23:25:01 UTC |
| d3a3919 | Eddie Belter | 17 December 2012, 22:50:43 UTC | Mc16s: update test to use build from factory | 17 December 2012, 22:50:43 UTC |
| cb8664e | Thomas Mooney | 17 December 2012, 22:49:11 UTC | Fix another caller... | 17 December 2012, 22:49:11 UTC |
| 1cc827b | Eddie Belter | 17 December 2012, 22:47:04 UTC | MC16s: remove unneeded methods | 17 December 2012, 22:47:19 UTC |
| 7528305 | Eddie Belter | 17 December 2012, 22:42:13 UTC | MC16s: rm unused methods | 17 December 2012, 22:42:13 UTC |
| b72e605 | Eddie Belter | 17 December 2012, 22:34:35 UTC | MC16s: add generate reports to build steps | 17 December 2012, 22:34:35 UTC |
| 58ae1a3 | Thomas Mooney | 17 December 2012, 22:31:04 UTC | Support arbitrary references in SV validation. Cleanup involved in making this change: *Use samtools faidx instead of expiece. *Use \t as delimeter instead of . which may appear in contig names. *Call into ReadRemap as class methods (to prevent AUTOLOAD warnings). | 17 December 2012, 22:31:04 UTC |
| 3f313c5 | Eddie Belter | 17 December 2012, 22:04:20 UTC | MC16s: rm Test module | 17 December 2012, 22:04:20 UTC |
| 72ecf4f | Eddie Belter | 17 December 2012, 21:52:05 UTC | MC16s: rm individual report tests, they are tested in the reports event | 17 December 2012, 21:52:05 UTC |
| c1c35d7 | Malachi Griffith | 17 December 2012, 21:51:21 UTC | clinseq: fixed bug in which the mutation diagram plots did not specify the property name for the build input | 17 December 2012, 21:51:21 UTC |
| 89f9cc4 | Eddie Belter | 17 December 2012, 21:49:53 UTC | MC16s: rm report base class | 17 December 2012, 21:49:53 UTC |
| 792c3ad | Nathan Nutter | 17 December 2012, 19:36:37 UTC | remove old debug exit | 17 December 2012, 21:03:08 UTC |
| a3d4d61 | Nathan Nutter | 17 December 2012, 19:15:06 UTC | remove commented out code and comment about it | 17 December 2012, 21:03:07 UTC |
| 584c8ae | Nathan Nutter | 17 December 2012, 20:58:23 UTC | use __FILE__ instead of FindBin to infer path | 17 December 2012, 21:03:07 UTC |
| a754633 | Nathan Nutter | 17 December 2012, 20:57:43 UTC | whitespace | 17 December 2012, 21:02:56 UTC |
| 07963c0 | Nathan Nutter | 17 December 2012, 19:13:06 UTC | tests must return 1 for tracking - test tracking uses a 'do' which must not return undef for error checking purposes - skip returns undef | 17 December 2012, 21:02:16 UTC |
| 1380772 | Nathan Nutter | 17 December 2012, 19:11:12 UTC | use above | 17 December 2012, 20:52:25 UTC |
| 23439fb | Nathan Nutter | 17 December 2012, 19:11:03 UTC | load class so it can be tracked for test dependencies | 17 December 2012, 20:52:24 UTC |
| 19e2a2f | Nathan Nutter | 17 December 2012, 19:08:11 UTC | add hostname to error message | 17 December 2012, 20:52:24 UTC |
| 65d11c5 | Nathan Nutter | 17 December 2012, 16:37:54 UTC | add newline to print, missing newline breaks test | 17 December 2012, 20:52:23 UTC |
| f43cac8 | Nathan Nutter | 17 December 2012, 16:17:41 UTC | improve die message | 17 December 2012, 20:52:22 UTC |
| 98e9cc8 | Nathan Nutter | 17 December 2012, 16:17:23 UTC | add column to LocalDataSource | 17 December 2012, 20:52:21 UTC |
| 10f21a4 | Eddie Belter | 17 December 2012, 19:45:48 UTC | MC16s: add sanger build to test build factory | 17 December 2012, 19:45:48 UTC |
| 4c5b1b7 | Eddie Belter | 17 December 2012, 19:45:29 UTC | MC16s: cleanup process sanger inst data; add test | 17 December 2012, 19:45:29 UTC |
| f7e3e62 | Eddie Belter | 17 December 2012, 19:44:03 UTC | MC16s: rm edit and chromat dir from build | 17 December 2012, 19:44:03 UTC |
| 69671c6 | Gabriel Sanderson | 17 December 2012, 18:36:09 UTC | Merge branch 'validation' into gb_master | 17 December 2012, 18:36:09 UTC |
| b60d5ad | Gabriel Sanderson | 17 December 2012, 18:25:41 UTC | Skip if the long indel bed file doesnt exist, rather than dying. This made test builds / anything without indel output fail. | 17 December 2012, 18:36:04 UTC |
| d89ab54 | Ben Oberkfell | 17 December 2012, 18:34:42 UTC | more detailed error messages; bomb out on sync if you are using a bad DBD::Pg driver. | 17 December 2012, 18:34:42 UTC |
| bca4858 | Thomas Mooney | 17 December 2012, 14:59:35 UTC | Make a symlink so data appears in some arbitrary data directory. This makes the pipeline act more like the non-pipelined version. | 17 December 2012, 14:59:35 UTC |
| b78436b | Gabriel Sanderson | 17 December 2012, 06:21:19 UTC | Merge branch 'largeindel' into gb_master | 17 December 2012, 06:21:19 UTC |
| b852d4a | Gabriel Sanderson | 30 November 2012, 19:01:48 UTC | CHANGELOG: Added large indel validation to the somatic validation pipeline. | 17 December 2012, 06:20:29 UTC |
| 7fc1693 | Scott Smith | 14 December 2012, 21:44:56 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 December 2012, 21:44:56 UTC |
| 3028155 | Scott Smith | 14 December 2012, 21:44:49 UTC | replaced hard-coded workflow,apipe queue names with configurable variables in Genome/Env | 14 December 2012, 21:44:49 UTC |
| f83f47e | dmorton | 14 December 2012, 20:24:53 UTC | Removed spurious exit from tests. They were a problem for an upcomming feature Nathan and I are working on to let you determine what tests need to be run after you've changed some files. | 14 December 2012, 21:29:43 UTC |
| b586d17 | Scott Smith | 14 December 2012, 21:05:06 UTC | fix typos in override of default workflow LSF queues | 14 December 2012, 21:05:06 UTC |
| 2e1a80a | Nathan Nutter | 14 December 2012, 20:25:01 UTC | add option to exclude either total_kb or unallocated_kb | 14 December 2012, 20:26:50 UTC |
| 6998dfd | Nathan Nutter | 14 December 2012, 20:24:38 UTC | split sync_usage into two smaller units | 14 December 2012, 20:26:50 UTC |
| 028c7dc | Nathan Nutter | 13 December 2012, 23:17:33 UTC | unallocated_kb call should occur after total_kb is updated | 14 December 2012, 20:26:49 UTC |
