| 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 |
| b9e1e8e | Anthony Brummett | 14 December 2012, 17:45:18 UTC | Merge branch 'chunk' | 14 December 2012, 17:45:18 UTC |
| e020e1e | Anthony Brummett | 14 December 2012, 17:44:46 UTC | Avoid uninitialized warnings | 14 December 2012, 17:44:46 UTC |
| 2ede499 | Anthony Brummett | 14 December 2012, 17:42:54 UTC | The output directory now has permissions based in the user's umask File::Temp makes directories with mode 700. This change makes the perms as permissive as the user's umask specifies, after the chunking is complete | 14 December 2012, 17:42:54 UTC |
| 8d921ab | Chris Miller | 14 December 2012, 17:32:10 UTC | Added submodule bam-window | 14 December 2012, 17:32:10 UTC |
| 42443d2 | Anthony Brummett | 14 December 2012, 17:24:47 UTC | Fail more gracefully when SUPER::create() fails This way, the user won't get an additional error message about calling a method on an undefined value | 14 December 2012, 17:24:47 UTC |
| 0f734f9 | Scott Smith | 14 December 2012, 16:11:56 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 December 2012, 16:11:56 UTC |
| 23195c1 | Scott Smith | 14 December 2012, 16:11:46 UTC | Added an env for GENOME_SYS_ID. Most of these really need to be moved to a config file, but sticking with this approach until we can make a global change. | 14 December 2012, 16:11:46 UTC |
| ac763f0 | APipe Tester | 14 December 2012, 00:04:06 UTC | updated workflow submodule to 32a3a01 | 14 December 2012, 00:04:06 UTC |
| 615c376 | APipe Tester | 13 December 2012, 23:55:13 UTC | updated workflow submodule to 9252020 | 13 December 2012, 23:55:13 UTC |
| b0113cb | Gabriel Sanderson | 13 December 2012, 23:37:32 UTC | Merge branch 'master' into gb_master | 13 December 2012, 23:37:32 UTC |
| 9250c66 | Gabriel Sanderson | 13 December 2012, 23:37:17 UTC | Ignore indel_validation for now, since this is produced by bsubs (and thus it will not always be done by the time the build is done). We should remove this once we are no longer bsubbing. | 13 December 2012, 23:37:21 UTC |
| 55fbf38 | Scott Smith | 13 December 2012, 23:07:53 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 December 2012, 23:07:53 UTC |
| 0e03447 | Scott Smith | 13 December 2012, 23:07:36 UTC | added TGI-centric workflow environment variables | 13 December 2012, 23:07:36 UTC |
| 69e4ed9 | Ben Oberkfell | 13 December 2012, 21:56:38 UTC | filter changed objects for bad tables | 13 December 2012, 21:56:38 UTC |
| e9a43fe | Eddie Belter | 13 December 2012, 21:37:05 UTC | AQID: add inst data property to force [re]processing of specific inst data | 13 December 2012, 21:37:11 UTC |
| c7afa43 | Thomas Mooney | 13 December 2012, 21:05:51 UTC | Add a mechanism for automatic locus suffixes for testing. | 13 December 2012, 21:05:51 UTC |
| ec904e0 | Scott Smith | 13 December 2012, 21:04:09 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 December 2012, 21:04:09 UTC |
| a2e6f99 | Scott Smith | 13 December 2012, 21:04:00 UTC | removed size constraints on event id, parent_event_id and prior_event_id since they are bigger in postgres with UUIDs | 13 December 2012, 21:04:00 UTC |
| 205e010 | Thomas Mooney | 13 December 2012, 20:53:03 UTC | Remove TODO The comment describes what the line currently does. | 13 December 2012, 20:53:03 UTC |
| 98da2da | Kyung Kim | 13 December 2012, 20:03:00 UTC | update to set qual format as sanger when inst data qual format is sanger fastq .. previously it was set as illumina which was probably a bug | 13 December 2012, 20:03:00 UTC |
| 7801421 | Kyung Kim | 13 December 2012, 20:00:49 UTC | Update bam_path method to not return the bam_file location when bam file is not actually present | 13 December 2012, 20:00:49 UTC |
