| 22fc8ad | apregier | 19 November 2013, 23:05:53 UTC | Merge branch 'copy' into gb_master | 19 November 2013, 23:05:53 UTC |
| e20a193 | apregier | 19 November 2013, 23:00:46 UTC | Don't need to pass around idf anymore | 19 November 2013, 23:05:14 UTC |
| cf4da21 | apregier | 19 November 2013, 22:57:17 UTC | Sdrf object has an idf object | 19 November 2013, 23:05:14 UTC |
| 639e6ed | apregier | 19 November 2013, 22:48:52 UTC | Separate resolving and adding protocols | 19 November 2013, 23:05:13 UTC |
| b3545be | apregier | 19 November 2013, 22:41:59 UTC | Add processing profiles to the idf separate from resolving them | 19 November 2013, 23:05:13 UTC |
| bd0030e | apregier | 19 November 2013, 21:34:33 UTC | Extract complete_archive_name method | 19 November 2013, 23:05:12 UTC |
| f3e57c6 | apregier | 19 November 2013, 21:21:00 UTC | Extract an SDRF class | 19 November 2013, 23:05:11 UTC |
| bf0ca4e | Avinash Ramu | 19 November 2013, 22:17:56 UTC | update clinseq to copy over unfiltered fusion file, and change fusion directory within Clinseq | 19 November 2013, 22:18:12 UTC |
| ae3d936 | Eddie Belter | 19 November 2013, 17:29:01 UTC | Build: moved circos conf diffing to clinseq model | 19 November 2013, 22:07:32 UTC |
| def17e6 | apregier | 19 November 2013, 20:27:18 UTC | Merge branch 'copy' into gb_master | 19 November 2013, 20:27:18 UTC |
| 6d7c41b | apregier | 19 November 2013, 20:21:14 UTC | Generic method for resolving protocols with processing profiles | 19 November 2013, 20:23:42 UTC |
| 1dfd994 | apregier | 19 November 2013, 20:05:36 UTC | library preparation is a hard-coded protocol | 19 November 2013, 20:23:42 UTC |
| 2f6a8be | apregier | 19 November 2013, 20:00:23 UTC | All hard-coded protocols are resolved in the same way | 19 November 2013, 20:23:41 UTC |
| c2dae00 | apregier | 19 November 2013, 18:45:35 UTC | Stop passing around protocol_db | 19 November 2013, 20:23:41 UTC |
| ec5492f | apregier | 19 November 2013, 18:11:50 UTC | Replace protocols_db data structure with idf object | 19 November 2013, 20:23:40 UTC |
| b30dbc7 | apregier | 18 November 2013, 23:02:58 UTC | Move printIdf to idf object | 19 November 2013, 20:23:40 UTC |
| 38fd08b | apregier | 18 November 2013, 20:55:39 UTC | Resolve_*_protocol methods only take processing profiles when needed | 19 November 2013, 20:23:39 UTC |
| f9325ca | apregier | 18 November 2013, 20:47:10 UTC | Move resolve_*_protocol to IDF object | 19 November 2013, 20:23:38 UTC |
| fb97c3a | Avinash Ramu | 19 November 2013, 19:24:41 UTC | updated clinseq's blessed build, it now uses the default ver of GMT transcript annotator which finds different transcripts compared to the ones found before. | 19 November 2013, 19:24:41 UTC |
| 36c3ea2 | Thomas Mooney | 19 November 2013, 15:07:00 UTC | Skip test that is failing for lack of a software licence. | 19 November 2013, 15:07:00 UTC |
| 8aa2722 | Mark Burnett | 19 November 2013, 14:12:55 UTC | make WorkflowBuilder save prettier XML | 19 November 2013, 14:40:47 UTC |
| 72890f2 | APipe Tester | 19 November 2013, 13:16:50 UTC | Updated `genome` tab completion. | 19 November 2013, 13:16:50 UTC |
| a19a3b2 | APipe Tester | 19 November 2013, 13:15:04 UTC | Updated class browser cache. | 19 November 2013, 13:15:04 UTC |
| feb39c7 | dmorton | 19 November 2013, 03:31:33 UTC | rewrite justify in Utility::Text There were bugs like where: justify('12345', 'right', 6) would be '12345 ' instead of ' 12345' | 19 November 2013, 03:31:33 UTC |
| d5423f3 | dmorton | 19 November 2013, 02:38:21 UTC | Add Command::V2 to WorkflowMixin This allows the command line options specified there to get inhertited by subclasses | 19 November 2013, 02:38:21 UTC |
| 3ac4e3c | dmorton | 19 November 2013, 02:17:28 UTC | Stop referring to self->build in WorkflowMixin | 19 November 2013, 02:17:28 UTC |
| 6ef712d | dmorton | 19 November 2013, 01:37:15 UTC | Factored out Workflow portion of build view | 19 November 2013, 01:44:22 UTC |
| bca5920 | apregier | 19 November 2013, 01:35:02 UTC | Merge branch 'fireteam2' into gb_master | 19 November 2013, 01:35:02 UTC |
| 48ebc96 | apregier | 18 November 2013, 16:03:38 UTC | Fix whitespace | 19 November 2013, 01:34:07 UTC |
| 2574e44 | APipe Tester | 18 November 2013, 22:16:02 UTC | updated workflow submodule to 1758ca3 | 18 November 2013, 22:16:02 UTC |
| 8e08bec | APipe Tester | 18 November 2013, 22:04:49 UTC | updated ur submodule to 356ca1b | 18 November 2013, 22:04:49 UTC |
| 2940e10 | Eddie Belter | 18 November 2013, 21:34:40 UTC | ClinSeq: update circos conf diff | 18 November 2013, 21:34:40 UTC |
| ebf96aa | Eddie Belter | 18 November 2013, 21:07:26 UTC | Build: rm circos conf from custom regex diff | 18 November 2013, 21:07:34 UTC |
| 2bb0085 | Eddie Belter | 18 November 2013, 21:07:07 UTC | ClinSeq: add custom diff for circos conf | 18 November 2013, 21:07:34 UTC |
| 9e89d07 | Eddie Belter | 18 November 2013, 21:02:01 UTC | Build: look in model class for diff methods if it does not exist in build class | 18 November 2013, 21:07:33 UTC |
| 689aa70 | Eddie Belter | 18 November 2013, 19:34:44 UTC | Build: add addtional_regex_for_custom_diff call to model class when getting regex_for_custom_diff | 18 November 2013, 21:07:32 UTC |
| db3d6da | Eddie Belter | 18 November 2013, 19:28:03 UTC | Build: files_ignored_by_diff uses model_class method | 18 November 2013, 21:07:32 UTC |
| 33cf3b1 | Eddie Belter | 18 November 2013, 19:21:01 UTC | Build: Add model_class method | 18 November 2013, 21:07:31 UTC |
| 0a99733 | Avinash Ramu | 18 November 2013, 20:56:55 UTC | Update CreateMutationSpectrum.pm to use the default version of the GMT Transcript Annotator:wq | 18 November 2013, 20:58:55 UTC |
| dd96a0a | Ben Ainscough | 18 November 2013, 19:59:58 UTC | added exception to diff blessed that accounts for changes in circos.conf | 18 November 2013, 19:59:58 UTC |
| eff48a7 | Feiyu Du | 18 November 2013, 18:16:38 UTC | modify smallRNA pipeline to be better error-handling | 18 November 2013, 18:17:57 UTC |
| 92fe4d4 | APipe Tester | 18 November 2013, 15:07:15 UTC | updated graphite submodule to 633dbaf | 18 November 2013, 15:07:15 UTC |
| 18591f4 | APipe Tester | 18 November 2013, 15:07:10 UTC | updated jenkins submodule to b02fcf4 | 18 November 2013, 15:07:10 UTC |
| 88a7b77 | APipe Tester | 18 November 2013, 15:07:05 UTC | updated workflow submodule to 5853124 | 18 November 2013, 15:07:05 UTC |
| d486d79 | APipe Tester | 16 November 2013, 13:17:11 UTC | Updated `genome` tab completion. | 16 November 2013, 13:17:11 UTC |
| 8d0cabf | APipe Tester | 16 November 2013, 13:15:28 UTC | Updated class browser cache. | 16 November 2013, 13:15:28 UTC |
| 8605f80 | apregier | 15 November 2013, 22:37:33 UTC | Merge branch 'fireteam2' into gb_master | 15 November 2013, 22:37:33 UTC |
| 8b4a328 | apregier | 15 November 2013, 22:37:14 UTC | Add docs for the command line | 15 November 2013, 22:37:14 UTC |
| 91b8a75 | apregier | 15 November 2013, 22:25:32 UTC | Merge branch 'fireteam2' into gb_master | 15 November 2013, 22:25:32 UTC |
| 66fcae5 | apregier | 15 November 2013, 22:25:12 UTC | Update test based on production db change | 15 November 2013, 22:25:12 UTC |
| 94344ba | apregier | 15 November 2013, 21:57:10 UTC | Merge branch 'fireteam2' into gb_master | 15 November 2013, 21:57:10 UTC |
| 9cafa37 | apregier | 15 November 2013, 21:54:26 UTC | Fully test the archive creation and a small refactor | 15 November 2013, 21:54:50 UTC |
| ad7a403 | apregier | 15 November 2013, 21:53:33 UTC | compare_ok will replace all regex matches on the line | 15 November 2013, 21:54:50 UTC |
| f1c03e1 | apregier | 15 November 2013, 20:01:33 UTC | Several extract method refactorings | 15 November 2013, 21:54:49 UTC |
| cbcc633 | Eddie Belter | 15 November 2013, 18:29:15 UTC | CQID: create models with user_name apipe-builder | 15 November 2013, 18:29:25 UTC |
| 0a86bf7 | Gabriel Sanderson | 15 November 2013, 16:47:34 UTC | Merge branch 'workflowbuilder' into gb_master | 15 November 2013, 16:47:34 UTC |
| ad54bac | Gabriel Sanderson | 15 November 2013, 16:46:11 UTC | WorkflowBuilder bug fix. It would break when using both parallel_by/is_many and singular links to the same operation. | 15 November 2013, 16:46:28 UTC |
| 1d4c50a | Ben Ainscough | 15 November 2013, 16:08:21 UTC | added MakecircosPlot.pm to the clinseq pipeline | 15 November 2013, 16:08:21 UTC |
| 36ceaeb | APipe Tester | 15 November 2013, 13:17:50 UTC | Updated `gmt` tab completion. | 15 November 2013, 13:17:50 UTC |
| 67cdc34 | APipe Tester | 15 November 2013, 13:17:08 UTC | Updated `genome` tab completion. | 15 November 2013, 13:17:08 UTC |
| b92eaee | APipe Tester | 15 November 2013, 13:15:27 UTC | Updated class browser cache. | 15 November 2013, 13:15:27 UTC |
| 1c2f32a | Avinash Ramu | 15 November 2013, 03:24:22 UTC | use build variable | 15 November 2013, 03:24:22 UTC |
| 84da588 | Avinash Ramu | 15 November 2013, 03:05:37 UTC | update clinseq to intersect RNA fusions with DNA SV's only if WGS build is specified | 15 November 2013, 03:18:11 UTC |
| 087e8b4 | Thomas Mooney | 14 November 2013, 23:27:16 UTC | Another check for the build to exist before asking for its data directory. | 14 November 2013, 23:27:16 UTC |
| 5a2f8b5 | Thomas Mooney | 14 November 2013, 23:24:02 UTC | Ensure we have a WGS build before asking for its data directory. | 14 November 2013, 23:24:43 UTC |
| fccd76c | Thomas Mooney | 14 November 2013, 23:23:28 UTC | More variable use instead of repeated accessor calls | 14 November 2013, 23:24:42 UTC |
| 8ff1528 | Thomas Mooney | 14 November 2013, 23:20:11 UTC | Use the variables we made instead of reasking the build every time. | 14 November 2013, 23:24:41 UTC |
| 1b0d549 | apregier | 14 November 2013, 23:22:06 UTC | Merge branch 'fireteam2' into gb_master | 14 November 2013, 23:22:06 UTC |
| 24998b5 | apregier | 14 November 2013, 22:21:31 UTC | Add a log directory for the workflow | 14 November 2013, 22:48:50 UTC |
| d02eaf8 | apregier | 14 November 2013, 21:33:37 UTC | Preload substructures for speed | 14 November 2013, 22:48:49 UTC |
| 53401d1 | apregier | 14 November 2013, 21:32:36 UTC | Run workflow with workflow object rather than xml | 14 November 2013, 22:48:48 UTC |
| 14015c7 | apregier | 13 November 2013, 20:10:28 UTC | Simplify annotate-chromosome workflow | 14 November 2013, 22:48:48 UTC |
| 692bc44 | apregier | 12 November 2013, 19:33:15 UTC | Fix bug in file format | 14 November 2013, 22:48:47 UTC |
| 9b9f649 | apregier | 10 November 2013, 21:16:15 UTC | Add "translated_processed_pseudogene" to biotype hash | 14 November 2013, 22:48:46 UTC |
| 0b5cba8 | apregier | 08 November 2013, 17:54:19 UTC | Need to create sub-directories | 14 November 2013, 22:48:46 UTC |
| 52fd443 | apregier | 08 November 2013, 17:39:56 UTC | AnnotationStructures object was not moved to Command dir | 14 November 2013, 22:48:45 UTC |
| 2d9196d | apregier | 08 November 2013, 17:31:49 UTC | Db commands were moved into Command dir | 14 November 2013, 22:48:44 UTC |
| db65891 | Jim Weible | 14 November 2013, 20:03:13 UTC | move method from old AQID | 14 November 2013, 20:03:13 UTC |
| 46ae3d5 | Eddie Belter | 14 November 2013, 18:27:00 UTC | InstData Import: add lane with value of 1 to fastq inst data when importing | 14 November 2013, 18:27:00 UTC |
| e4af768 | apregier | 14 November 2013, 17:19:01 UTC | Merge branch 'copy' into gb_master | 14 November 2013, 17:19:01 UTC |
| c56d3db | apregier | 13 November 2013, 22:50:13 UTC | Create archive tarball when requested | 14 November 2013, 16:55:12 UTC |
| 8fd983a | apregier | 12 November 2013, 22:33:27 UTC | Get the tcga-compliant files | 14 November 2013, 16:55:11 UTC |
| 0bf84eb | apregier | 12 November 2013, 16:16:24 UTC | Revise vcf file naming | 14 November 2013, 16:55:11 UTC |
| ffe5735 | apregier | 08 November 2013, 20:44:21 UTC | Add some tests | 14 November 2013, 16:55:10 UTC |
| 0b322bf | apregier | 07 November 2013, 21:14:31 UTC | Use archive name as mage-tab file names | 14 November 2013, 16:55:10 UTC |
| 6207fe9 | apregier | 06 November 2013, 21:53:37 UTC | Add option to load cghub id by tcga-name rather than just bam file | 14 November 2013, 16:55:09 UTC |
| b8441a6 | apregier | 06 November 2013, 19:29:38 UTC | Use somatic variation vcfs rather than refalign | 14 November 2013, 16:55:08 UTC |
| a81b20e | apregier | 06 November 2013, 15:39:11 UTC | Look up CGHub based on bam file | 14 November 2013, 16:55:08 UTC |
| ae1bce8 | apregier | 05 November 2013, 21:28:34 UTC | Take SomVar models as inputs | 14 November 2013, 16:55:07 UTC |
| f6d2260 | apregier | 05 November 2013, 20:46:57 UTC | Pass in cghub ids for builds | 14 November 2013, 16:55:06 UTC |
| ce626aa | apregier | 04 November 2013, 22:34:30 UTC | Hard-code capture reagent info | 14 November 2013, 16:55:06 UTC |
| 850a8d4 | apregier | 29 October 2013, 21:40:35 UTC | Add some more required sdrf columns | 14 November 2013, 16:55:05 UTC |
| c0df558 | apregier | 28 October 2013, 16:26:45 UTC | Add a couple hard-coded values | 14 November 2013, 16:55:04 UTC |
| 3bc3d98 | apregier | 25 October 2013, 21:49:44 UTC | Add some more columns to the vcf row | 14 November 2013, 16:55:04 UTC |
| 555c591 | apregier | 25 October 2013, 21:06:35 UTC | Use a string object so we can preserve quoting | 14 November 2013, 16:55:02 UTC |
| daaefab | apregier | 25 October 2013, 20:05:22 UTC | Cleanup from travis | 14 November 2013, 16:55:01 UTC |
| 2efe6c9 | apregier | 25 October 2013, 20:02:54 UTC | Use undef instead of fancy string | 14 November 2013, 16:55:00 UTC |
| a8e4aff | apregier | 25 October 2013, 19:58:30 UTC | Add sample barcode and uuid to row | 14 November 2013, 16:55:00 UTC |
| 2b82e70 | apregier | 25 October 2013, 18:55:15 UTC | Vcf Header parses arbitrary metainfo lines | 14 November 2013, 16:54:59 UTC |
| 0a7f40b | apregier | 25 October 2013, 18:43:42 UTC | Allow almost everything in regular strings | 14 November 2013, 16:54:58 UTC |
