| b1b8472 | Scott Smith | 24 July 2013, 02:26:20 UTC | sciClone bmm and vendor/r-cran-normt3 update | 24 July 2013, 02:26:49 UTC |
| 599310d | Gabriel Sanderson | 23 July 2013, 22:40:25 UTC | Merge branch 'master' into gb_master | 23 July 2013, 22:40:25 UTC |
| 7432e89 | Gabriel Sanderson | 23 July 2013, 22:25:36 UTC | SamtoolsToBed now tries to get DP from the sample column if it cannot find it in INFO if the input is a vcf. | 23 July 2013, 22:39:42 UTC |
| ddfaa83 | Thomas Mooney | 23 July 2013, 22:34:52 UTC | Use alignment result accessor to get BAM file regardless of input model type. (whole_rmdup_bam_file was the old ref-align specific way to get at these) | 23 July 2013, 22:34:52 UTC |
| 961c8ff | APipe Tester | 23 July 2013, 20:06:51 UTC | updated ur submodule to 834d6c2 | 23 July 2013, 20:06:51 UTC |
| d355de6 | Nathan Nutter | 23 July 2013, 19:58:35 UTC | remove unnecessary files | 23 July 2013, 19:58:46 UTC |
| 64f13e6 | Eddie Belter | 23 July 2013, 19:32:58 UTC | Sample Import Manager: update expected values for launch command in test | 23 July 2013, 19:32:58 UTC |
| 9d02a75 | Todd Hepler | 23 July 2013, 18:52:56 UTC | use --inactivity-timeout so the job does not run indefinitely and make no progress | 23 July 2013, 18:53:19 UTC |
| cc36976 | Thomas Mooney | 23 July 2013, 14:28:22 UTC | Don't use backed up disk for indices of rederivable references. | 23 July 2013, 14:28:22 UTC |
| b8da544 | Eddie Belter | 22 July 2013, 22:19:21 UTC | Sample Manager: set sample status to import needed when creating sample | 22 July 2013, 22:19:31 UTC |
| 354d35c | Gabriel Sanderson | 22 July 2013, 22:11:34 UTC | Merge branch 'master' into gb_master | 22 July 2013, 22:11:34 UTC |
| 52e7909 | Gabriel Sanderson | 22 July 2013, 22:03:09 UTC | Correct dispatcher command dumping | 22 July 2013, 22:03:09 UTC |
| 31d4f22 | Nathan Nutter | 22 July 2013, 18:04:24 UTC | add our custom compiled DBD::Oracle This is DBD::Oracle 1.28 compiled with ORACLE_HOME=/opt/oracle-instantclient-11.2 | 22 July 2013, 21:40:19 UTC |
| 0b94f59 | Scott Smith | 22 July 2013, 21:17:49 UTC | disabled software result inputs_bx and params_bx, as the fields are never used, and break the SR lister | 22 July 2013, 21:17:49 UTC |
| 90dd934 | Scott Smith | 22 July 2013, 21:11:29 UTC | update link to bmm submodule | 22 July 2013, 21:11:29 UTC |
| a8c7e3e | Scott Smith | 22 July 2013, 21:09:23 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 22 July 2013, 21:09:23 UTC |
| 05dfd7e | Scott Smith | 22 July 2013, 21:09:00 UTC | add vendor/r-cran-normt3 | 22 July 2013, 21:09:00 UTC |
| 02029df | Eddie Belter | 22 July 2013, 19:56:47 UTC | Sample Manager: update test | 22 July 2013, 19:57:39 UTC |
| 6965744 | Eddie Belter | 18 July 2013, 17:00:03 UTC | Sample Manager: rework getting entities for samples | 22 July 2013, 19:57:39 UTC |
| 8b22e39 | Eddie Belter | 17 July 2013, 18:04:18 UTC | Sample Manager: status file is tab separated | 22 July 2013, 19:57:38 UTC |
| 20dc8af | Eddie Belter | 17 July 2013, 18:01:16 UTC | Sample Manager: add help for info file | 22 July 2013, 19:57:38 UTC |
| 6b7b37f | Eddie Belter | 17 July 2013, 17:42:57 UTC | Sample Manager: rename sample csv to info file and make it tsv | 22 July 2013, 19:57:37 UTC |
| 83b5986 | Eddie Belter | 17 July 2013, 17:21:12 UTC | Sample Manager: do not add model and build id to samples hash; add header to status file | 22 July 2013, 19:57:37 UTC |
| e4700f1 | Eddie Belter | 17 July 2013, 17:11:52 UTC | Sample Manager: add load status file when loading samples | 22 July 2013, 19:57:36 UTC |
| 67ece75 | Eddie Belter | 17 July 2013, 16:57:01 UTC | Sample Manager: save status file | 22 July 2013, 19:57:36 UTC |
| c187881 | Jim Weible | 22 July 2013, 19:46:30 UTC | update the BSmap test to account for fillmd | 22 July 2013, 19:46:30 UTC |
| 74d2a2c | Todd Hepler | 22 July 2013, 19:15:58 UTC | put rate limits back since we can run on more hosts now, we don't want to overload | 22 July 2013, 19:16:23 UTC |
| fc22b60 | Scott Smith | 22 July 2013, 19:06:40 UTC | updated error message when BamQc can't find its input file | 22 July 2013, 19:07:26 UTC |
| 58dcbd7 | Jim Weible | 22 July 2013, 19:05:51 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 22 July 2013, 19:05:51 UTC |
| 459ba29 | Jim Weible | 22 July 2013, 19:05:42 UTC | run fillmd_for_sam | 22 July 2013, 19:05:42 UTC |
| d2a022e | Todd Hepler | 22 July 2013, 18:38:56 UTC | use gtdowload from 3.8.3 deb package on 10.04 now we can use an LSF queue other than lims-datatransfer (more hosts we can run on) | 22 July 2013, 18:38:56 UTC |
| 82a4123 | Dave Larson | 22 July 2013, 16:26:48 UTC | which doesn't like it when you pass it absolute paths; so fall back if it doesn't work. | 22 July 2013, 16:27:05 UTC |
| 9fad62c | Scott Smith | 22 July 2013, 15:14:53 UTC | fix docs on GENOME_HOME environment variable: merge conflict cruft in the docs | 22 July 2013, 15:14:53 UTC |
| 4b1109c | APipe Tester | 22 July 2013, 05:33:49 UTC | updated ur submodule to 00898d4 | 22 July 2013, 05:33:49 UTC |
| 146887a | APipe Tester | 22 July 2013, 04:40:18 UTC | Updated `gmt` tab completion. | 22 July 2013, 04:40:18 UTC |
| 4a20059 | APipe Tester | 22 July 2013, 04:39:23 UTC | Updated `genome` tab completion. | 22 July 2013, 04:39:23 UTC |
| a218219 | APipe Tester | 22 July 2013, 04:37:27 UTC | Updated class browser cache. | 22 July 2013, 04:37:27 UTC |
| ceb6b18 | Scott Smith | 21 July 2013, 13:20:34 UTC | cleanup of gmt lift-over (much more needed) | 22 July 2013, 04:17:25 UTC |
| 30321db | Chris Miller | 21 July 2013, 20:48:56 UTC | whitespace fixing, changing splitting from tabs to whitespace | 21 July 2013, 20:49:13 UTC |
| d13fc9b | APipe Tester | 21 July 2013, 13:15:40 UTC | Updated `gmt` tab completion. | 21 July 2013, 13:15:40 UTC |
| 333dbdd | APipe Tester | 21 July 2013, 13:14:44 UTC | Updated `genome` tab completion. | 21 July 2013, 13:14:44 UTC |
| 7dfa80e | APipe Tester | 21 July 2013, 13:12:56 UTC | Updated class browser cache. | 21 July 2013, 13:12:56 UTC |
| 903db6a | Scott Smith | 21 July 2013, 12:59:10 UTC | added the "svold" file format to liftover to handle legacy SV annotation data | 21 July 2013, 12:59:10 UTC |
| a5e4679 | APipe Tester | 20 July 2013, 00:16:57 UTC | Updated `gmt` tab completion. | 20 July 2013, 00:16:57 UTC |
| 0a86af6 | APipe Tester | 20 July 2013, 00:16:00 UTC | Updated `genome` tab completion. | 20 July 2013, 00:16:00 UTC |
| 38ca1b7 | APipe Tester | 20 July 2013, 00:14:05 UTC | Updated class browser cache. | 20 July 2013, 00:14:05 UTC |
| c031b5b | Scott Smith | 19 July 2013, 23:52:53 UTC | Added a tst case for "gmt liftover", and did a little redundancy cleanup in the tool. Much more needed. Probably big help needed. | 19 July 2013, 23:52:53 UTC |
| 4bd3109 | Chris Miller | 19 July 2013, 22:43:44 UTC | depth for 2+ bp deletions was calculated incorrectly | 19 July 2013, 22:43:44 UTC |
| 6301965 | Obi Griffith | 19 July 2013, 21:24:00 UTC | Added fix for old annotation formats with reversed start-stop | 19 July 2013, 21:24:00 UTC |
| 8169c40 | Eddie Belter | 18 July 2013, 22:21:12 UTC | Reconcile Misc Update: add status messages | 18 July 2013, 22:21:54 UTC |
| b0e0b0c | APipe Tester | 18 July 2013, 22:09:02 UTC | updated ur submodule to 84b8b16 | 18 July 2013, 22:09:02 UTC |
| 6af95b3 | APipe Tester | 18 July 2013, 21:44:33 UTC | updated ur submodule to 2279fc2 | 18 July 2013, 21:44:33 UTC |
| 43bd8a1 | Scott Smith | 18 July 2013, 21:29:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 21:29:15 UTC |
| 602970e | Scott Smith | 18 July 2013, 21:28:37 UTC | added GENOME_HOME environment variable | 18 July 2013, 21:28:37 UTC |
| d1d0c49 | APipe Tester | 18 July 2013, 21:22:52 UTC | Updated `gmt` tab completion. | 18 July 2013, 21:22:52 UTC |
| 72741bb | APipe Tester | 18 July 2013, 21:21:48 UTC | Updated `genome` tab completion. | 18 July 2013, 21:21:48 UTC |
| 0a4876c | APipe Tester | 18 July 2013, 21:19:31 UTC | Updated class browser cache. | 18 July 2013, 21:19:31 UTC |
| c13cd1d | Feiyu Du | 18 July 2013, 20:56:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 20:56:26 UTC |
| 13bd912 | Feiyu Du | 18 July 2013, 20:54:52 UTC | add required field platform:illumina into intermediate novo breakdancer config file | 18 July 2013, 20:54:52 UTC |
| 5dd8ff2 | Dave Larson | 18 July 2013, 20:37:52 UTC | increase requested memory from LSF for the Pindel job | 18 July 2013, 20:38:05 UTC |
| 93c81c3 | Ben Oberkfell | 18 July 2013, 20:13:06 UTC | GENOME_HOME was not an available enviroment variable | 18 July 2013, 20:13:06 UTC |
| 174b965 | Scott Smith | 18 July 2013, 19:18:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 July 2013, 19:18:38 UTC |
| f46c39c | Scott Smith | 18 July 2013, 19:18:02 UTC | updated model-group copy to take indirect params | 18 July 2013, 19:18:02 UTC |
| 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 |
| 8d341e1 | Scott Smith | 17 July 2013, 19:05:03 UTC | add GENOME_HOME to Site::TGI | 17 July 2013, 19:05:03 UTC |
| c5cfb29 | Scott Smith | 17 July 2013, 18:43:00 UTC | "genome model export metadata" code and test | 17 July 2013, 18:43:00 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 |
| 391d85d | Scott Smith | 16 July 2013, 15:37:19 UTC | Mexport erge branch 'master' of ssh://git/srv/git/genome | 16 July 2013, 15:37:19 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 |
| fe4c0a7 | Scott Smith | 16 July 2013, 00:06:16 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 July 2013, 00:06:16 UTC |
| a1017c7 | Scott Smith | 16 July 2013, 00:04:40 UTC | Default GENOME_SYS_ID for TGI to 'GMS1' | 16 July 2013, 00:04:40 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 |
