| e53abf1 | Eddie Belter | 05 May 2014, 21:58:39 UTC | InstData Import: quote nomenclature in import command | 05 May 2014, 21:59:20 UTC |
| ad4fa33 | Nathaniel Nutter | 02 May 2014, 16:51:37 UTC | config TestTracker to use genome-prove | 05 May 2014, 21:55:51 UTC |
| cd6435c | Nathaniel Nutter | 05 May 2014, 20:18:27 UTC | use genome-perl instead of just perl | 05 May 2014, 21:46:35 UTC |
| 1bc64d0 | Nathaniel Nutter | 05 May 2014, 19:41:43 UTC | remove script that uses a non-existant package This script used a non-existant package, Workflow::Server::HTTPD, so does not compile. As such, the script is being removed. | 05 May 2014, 19:44:18 UTC |
| 7e7277d | Eddie Belter | 05 May 2014, 19:30:44 UTC | InstData: add library as input to sra to bam, use the sample name in the samtools cmd | 05 May 2014, 19:31:21 UTC |
| a8d247a | Eddie Belter | 05 May 2014, 19:30:02 UTC | InstData Import: add tmp placeholders for gtmp, mtmp and kbtmp | 05 May 2014, 19:31:21 UTC |
| 04ac950 | Eddie Belter | 22 April 2014, 00:42:55 UTC | InstData Import: tests use library instead of sample | 05 May 2014, 19:31:20 UTC |
| 54ba164 | Eddie Belter | 22 April 2014, 00:11:36 UTC | InstData Import: manager uses library instead of sample | 05 May 2014, 19:31:20 UTC |
| 1ff269f | Eddie Belter | 21 April 2014, 23:11:49 UTC | InstData Import: update manager doc | 05 May 2014, 19:31:19 UTC |
| 4b6622a | Eddie Belter | 21 April 2014, 23:06:28 UTC | Sample Import: updated to commnad v2 | 05 May 2014, 19:31:18 UTC |
| 7e394f6 | Eddie Belter | 14 April 2014, 22:59:47 UTC | InstData Import: cahnge tmp space spec to just by tmp, no kb or mb | 05 May 2014, 19:31:18 UTC |
| a6c1dc9 | Eddie Belter | 14 April 2014, 22:51:38 UTC | InstData Import: substitute tmp kb and mb in launch command using required amount of space needed | 05 May 2014, 19:31:17 UTC |
| 932a338 | Eddie Belter | 14 April 2014, 22:50:31 UTC | InstData Import: fix error message in helpers | 05 May 2014, 19:31:17 UTC |
| 0afaec7 | Eddie Belter | 14 April 2014, 22:16:44 UTC | InstData Import Manager: check if source file exists | 05 May 2014, 19:31:16 UTC |
| fb60216 | Eddie Belter | 14 April 2014, 21:51:48 UTC | InstData Import Manager: check for errors from separated value reader | 05 May 2014, 19:31:16 UTC |
| 5418869 | Ben Ainscough | 05 May 2014, 19:13:38 UTC | added check to rna-seq step | 05 May 2014, 19:13:38 UTC |
| c394e9d | Thomas Mooney | 05 May 2014, 19:01:54 UTC | Fix typo s/falgged/flagged/ | 05 May 2014, 19:01:54 UTC |
| b56dca6 | Chris Miller | 05 May 2014, 16:46:51 UTC | adding missing tab to header | 05 May 2014, 16:46:51 UTC |
| 0033736 | Thomas Mooney | 05 May 2014, 14:29:01 UTC | Remove trailing tab. | 05 May 2014, 14:29:01 UTC |
| 2fbc429 | Avinash Ramu | 02 May 2014, 21:03:45 UTC | handle case where tumor, normal arrays differ | 02 May 2014, 21:03:45 UTC |
| f7db0cd | Avinash Ramu | 02 May 2014, 20:44:01 UTC | remove BAMs from diff | 02 May 2014, 20:45:06 UTC |
| a4323b2 | APipe Tester | 02 May 2014, 19:17:13 UTC | updated jenkins submodule to fd08b91 | 02 May 2014, 19:17:13 UTC |
| c28fa6e | dmorton | 02 May 2014, 15:49:58 UTC | Fix missing use statement | 02 May 2014, 15:55:30 UTC |
| b7749cc | dmorton | 02 May 2014, 15:49:34 UTC | All Filters are now Interpreters too | 02 May 2014, 15:55:30 UTC |
| bc954d2 | dmorton | 02 May 2014, 02:39:42 UTC | Add user relationships between software-results | 02 May 2014, 15:55:30 UTC |
| 2c3082f | Avinash Ramu | 02 May 2014, 13:15:59 UTC | update clinseq blessed LIMS updated to the latest genome-snapshot which caused some of the alignment metrics to change. | 02 May 2014, 13:16:56 UTC |
| 9cf5a24 | APipe Tester | 02 May 2014, 12:18:18 UTC | Updated `gmt` tab completion. | 02 May 2014, 12:18:18 UTC |
| 3507bf0 | APipe Tester | 02 May 2014, 12:17:37 UTC | Updated `genome` tab completion. | 02 May 2014, 12:17:37 UTC |
| 3403e8e | APipe Tester | 02 May 2014, 12:16:06 UTC | Updated class browser cache. | 02 May 2014, 12:16:06 UTC |
| 676f052 | dmorton | 02 May 2014, 01:38:19 UTC | Add AnnotateBuild command | 02 May 2014, 02:31:45 UTC |
| aaa3226 | dmorton | 02 May 2014, 01:36:43 UTC | make feature_list_ids_and_tags an optional output | 02 May 2014, 02:31:45 UTC |
| 5a27e72 | dmorton | 02 May 2014, 01:35:50 UTC | Add logging info | 02 May 2014, 02:31:45 UTC |
| 69cb1b2 | dmorton | 02 May 2014, 01:34:31 UTC | Adaptors do their work in shortcut | 02 May 2014, 02:31:45 UTC |
| 04a66ac | dmorton | 02 May 2014, 01:20:58 UTC | Expert::CommandBase handles shortcut and execute | 02 May 2014, 02:31:45 UTC |
| e1e22fd | dmorton | 01 May 2014, 21:17:19 UTC | Add ability to write plan to file | 02 May 2014, 02:31:45 UTC |
| 8166bd6 | Eddie Belter | 01 May 2014, 22:39:14 UTC | GM: add checking vcf in extract to vcf tests | 01 May 2014, 22:39:14 UTC |
| 2bf9a69 | Eddie Belter | 01 May 2014, 22:36:10 UTC | GM: add tests for sample priority to extract to vcf fails | 01 May 2014, 22:36:10 UTC |
| 5b7edc2 | Eddie Belter | 01 May 2014, 22:30:26 UTC | GM: add extract to vcf from sample test | 01 May 2014, 22:30:26 UTC |
| c7d0364 | Eddie Belter | 01 May 2014, 22:30:06 UTC | GM: fixed external filter in extract to vcf | 01 May 2014, 22:30:06 UTC |
| 9d79302 | Eddie Belter | 01 May 2014, 21:57:26 UTC | GM: get all inst data for a sample via the microarry libs plus default genotype data in extract to vcf | 01 May 2014, 21:57:26 UTC |
| 9faf487 | Eddie Belter | 01 May 2014, 21:56:19 UTC | GM: add import_date to test inst data | 01 May 2014, 21:56:19 UTC |
| efd4554 | Gabriel Sanderson | 01 May 2014, 19:41:28 UTC | Attempt to get instrument data via default_genotype_data first before falling back to a library->get by name | 01 May 2014, 20:19:42 UTC |
| 8f624ab | dmorton | 01 May 2014, 19:46:37 UTC | Annotation Plan is passed in to Adaptors and Wrapper | 01 May 2014, 20:12:16 UTC |
| 73dbe1c | dmorton | 01 May 2014, 18:48:34 UTC | Allow plans to be serialized and deserialized using JSON | 01 May 2014, 20:12:15 UTC |
| 49375fd | Travis Abbott | 01 May 2014, 18:24:45 UTC | bless new som-val-sv build (due to new bam-readcount) | 01 May 2014, 18:24:45 UTC |
| fda1912 | Avinash Ramu | 01 May 2014, 18:12:25 UTC | update clinseq blessed build bam-readcounts was updated which changes some of the read-counting output. | 01 May 2014, 18:12:25 UTC |
| 886f002 | Avinash Ramu | 01 May 2014, 16:34:54 UTC | small mod to sciclone doc | 01 May 2014, 16:35:52 UTC |
| 1d61efa | APipe Tester | 01 May 2014, 16:17:34 UTC | updated jenkins submodule to f35ef3e | 01 May 2014, 16:17:34 UTC |
| 53b8847 | Nathaniel Nutter | 01 May 2014, 14:09:08 UTC | add lib/perl prefix to Genome blacklists and escape periods | 01 May 2014, 15:59:12 UTC |
| a6171a1 | dmorton | 01 May 2014, 15:20:46 UTC | Add execution test for MasterCommand | 01 May 2014, 15:49:50 UTC |
| 245b28d | dmorton | 01 May 2014, 15:20:10 UTC | Mocked build's tumor_build has a subject name | 01 May 2014, 15:49:49 UTC |
| 298ae86 | dmorton | 01 May 2014, 15:19:44 UTC | wrapper passes in tranlations | 01 May 2014, 15:49:49 UTC |
| 3c0bf84 | dmorton | 01 May 2014, 15:18:58 UTC | Make sure all inputs to workflow are provided | 01 May 2014, 15:49:49 UTC |
| 817537b | dmorton | 01 May 2014, 15:18:15 UTC | change name from single-vep to just vep | 01 May 2014, 15:49:49 UTC |
| c3ab42f | dmorton | 01 May 2014, 15:17:37 UTC | fix typo on valid_values | 01 May 2014, 15:49:49 UTC |
| ccfd768 | dmorton | 01 May 2014, 15:17:05 UTC | use required library | 01 May 2014, 15:49:49 UTC |
| 4328086 | dmorton | 01 May 2014, 15:16:39 UTC | Add checks around translation | 01 May 2014, 15:49:49 UTC |
| 8340f16 | dmorton | 01 May 2014, 15:15:27 UTC | builds have snv and indel annotation plans | 01 May 2014, 15:49:49 UTC |
| 3e1f083 | dmorton | 01 May 2014, 15:13:03 UTC | Add get_detailed_vcf_result accessor | 01 May 2014, 15:49:48 UTC |
| 16b73b1 | APipe Tester | 01 May 2014, 15:01:28 UTC | updated jenkins submodule to 26b3875 | 01 May 2014, 15:01:28 UTC |
| eebece3 | APipe Tester | 01 May 2014, 14:50:44 UTC | updated jenkins submodule to a188921 | 01 May 2014, 14:50:44 UTC |
| 66698e5 | apregier | 01 May 2014, 14:48:57 UTC | Rename class | 01 May 2014, 14:48:57 UTC |
| 0701aa4 | Gabriel Sanderson | 01 May 2014, 01:07:51 UTC | Print sample id instead of the object during error | 01 May 2014, 01:07:51 UTC |
| acd8ee9 | Gabriel Sanderson | 01 May 2014, 00:22:41 UTC | Die cleanly when we fail to get a library in _resolve_source_for_sample. | 01 May 2014, 00:22:41 UTC |
| d57343b | Thomas Mooney | 30 April 2014, 22:51:19 UTC | Be more lenient about which models to assign to the group. | 30 April 2014, 22:51:19 UTC |
| 145ecdd | APipe Tester | 30 April 2014, 22:10:25 UTC | updated jenkins submodule to bdc098f | 30 April 2014, 22:10:25 UTC |
| a125023 | APipe Tester | 30 April 2014, 21:55:38 UTC | updated jenkins submodule to 6cc06d5 | 30 April 2014, 21:55:38 UTC |
| 5f63a20 | Travis Abbott | 30 April 2014, 21:22:26 UTC | replace test that fails due to production data changing with one that doesn't | 30 April 2014, 21:23:28 UTC |
| ba6e6eb | dmorton | 30 April 2014, 20:42:55 UTC | Add test for vep expert | 30 April 2014, 21:03:57 UTC |
| 35db07e | dmorton | 30 April 2014, 20:41:57 UTC | Mock fasta_file accessor on reference_sequence_build | 30 April 2014, 21:03:57 UTC |
| be9e2ac | dmorton | 30 April 2014, 20:40:38 UTC | Add Vep adaptor and reduce params available to vep expert | 30 April 2014, 21:03:57 UTC |
| 8a8a95e | dmorton | 30 April 2014, 20:36:22 UTC | Finish Vep Expert | 30 April 2014, 21:03:56 UTC |
| 2f73567 | dmorton | 30 April 2014, 20:35:32 UTC | Remove unneeded use statements | 30 April 2014, 21:03:56 UTC |
| eb5012f | dmorton | 30 April 2014, 18:35:34 UTC | Added HasFeatureLists mixin to somatic val and var | 30 April 2014, 21:03:56 UTC |
| db78a31 | Chris Miller | 30 April 2014, 20:44:28 UTC | changing an ambiguous error message that has bugged me for years | 30 April 2014, 20:44:53 UTC |
| a9b3ad3 | apregier | 30 April 2014, 20:00:06 UTC | Only copy config directory if it is available | 30 April 2014, 20:00:26 UTC |
| 971d893 | Chris Miller | 30 April 2014, 18:30:35 UTC | handle the case where the user asks to restrict to target regions, but there are no target regions defined on the build. Cleaned up input validation section | 30 April 2014, 18:32:00 UTC |
| 97098c0 | APipe Tester | 30 April 2014, 15:44:15 UTC | updated workflow submodule to 44229b0 | 30 April 2014, 15:44:15 UTC |
| 5cead8e | APipe Tester | 30 April 2014, 15:32:46 UTC | updated ur submodule to fa27dd0 | 30 April 2014, 15:32:46 UTC |
| b90dd7c | apregier | 30 April 2014, 14:51:38 UTC | Merge branch 'updated' into gb_master | 30 April 2014, 14:51:38 UTC |
| f803d3a | apregier | 30 April 2014, 14:43:46 UTC | Add translations hash to plan This allows us to override certain param values in filters with a build-specific value at runtime | 30 April 2014, 14:46:03 UTC |
| 8400154 | apregier | 30 April 2014, 14:42:18 UTC | Memoize object instead of caching | 30 April 2014, 14:46:03 UTC |
| 8d59897 | apregier | 30 April 2014, 14:40:33 UTC | Add get_class method on plan | 30 April 2014, 14:46:02 UTC |
| 41cb0f6 | apregier | 30 April 2014, 14:37:23 UTC | Add optional overrides parameter to get_object Any properties specified in the second hashref will override property values in the original params hashref | 30 April 2014, 14:46:02 UTC |
| 8e37f06 | apregier | 30 April 2014, 14:33:34 UTC | Move sample_name functionality into a base class | 30 April 2014, 14:46:01 UTC |
| 83947ef | apregier | 29 April 2014, 21:02:01 UTC | Build has snvs_ and indels_annotation_plans | 30 April 2014, 14:46:00 UTC |
| 31bb532 | Thomas Mooney | 29 April 2014, 14:38:47 UTC | Require an explicit strategy for getting the samtools result to use. The previous strategy of grabbing a bunch of results and picking one, aside from being non-deterministic, occasionally pulled back an indel filter result, which specifically does not work for this tool. | 30 April 2014, 14:01:02 UTC |
| 739a5cd | Nathaniel Nutter | 29 April 2014, 19:28:49 UTC | allow Nessy to be specified as mandatory based on environment variable | 29 April 2014, 21:08:08 UTC |
| c83ed81 | dmorton | 29 April 2014, 19:35:29 UTC | Add ReportGeneratorWrapper and MasterCommand | 29 April 2014, 19:35:29 UTC |
| 2eff93b | dmorton | 29 April 2014, 19:34:36 UTC | Fix order of arguments to compare_ok | 29 April 2014, 19:34:36 UTC |
| 8e431fb | dmorton | 29 April 2014, 19:34:24 UTC | Remove unused option to _link | 29 April 2014, 19:34:24 UTC |
| 2c0e5cc | dmorton | 29 April 2014, 19:20:51 UTC | Factory doesn't need to specify search_path so specifically | 29 April 2014, 19:20:51 UTC |
| 67c41b8 | dmorton | 29 April 2014, 19:17:20 UTC | Adaptors don't provide an output_result | 29 April 2014, 19:19:55 UTC |
| beb1661 | dmorton | 29 April 2014, 18:56:18 UTC | Add die message, rebase this out later | 29 April 2014, 19:19:55 UTC |
| 5a213ce | dmorton | 29 April 2014, 18:09:26 UTC | Get input_result from the input_connector instead of from the build-adaptor | 29 April 2014, 19:19:54 UTC |
| 03e388c | dmorton | 29 April 2014, 18:08:42 UTC | Add priority to ExpertBase This will be used to determine the order in which experts run. | 29 April 2014, 18:56:46 UTC |
| 5fe36c0 | Feiyu Du | 29 April 2014, 18:48:25 UTC | add vendor/star to submodules | 29 April 2014, 18:48:25 UTC |
| a87b811 | apregier | 29 April 2014, 18:29:28 UTC | Merge branch 'updated' into gb_master | 29 April 2014, 18:29:28 UTC |
| fc3253e | apregier | 29 April 2014, 18:27:33 UTC | Move experts into subdir | 29 April 2014, 18:27:58 UTC |
| 3049942 | apregier | 29 April 2014, 17:55:48 UTC | Move filters to subdir | 29 April 2014, 18:27:57 UTC |
