| 16fda3e | dmorton | 17 May 2013, 03:34:16 UTC | Fix missing param in GMTCuffdiffWrapper | 17 May 2013, 03:34:43 UTC |
| 454dca1 | Thomas Mooney | 16 May 2013, 15:44:30 UTC | Convert to absolute paths before creating the result. (If the user supplied a relative path or other whatnot, result generation would fail.) | 16 May 2013, 21:02:56 UTC |
| 8d7bd8b | dmorton | 16 May 2013, 19:34:50 UTC | Fix where we look for the new DifferentialExpression command | 16 May 2013, 19:35:37 UTC |
| e31ea72 | Gabriel Sanderson | 16 May 2013, 19:04:08 UTC | Merge branch 'master' into gb_master | 16 May 2013, 19:04:08 UTC |
| c196edd | Gabriel Sanderson | 16 May 2013, 19:03:24 UTC | improved error messages | 16 May 2013, 19:03:24 UTC |
| ac4bf6e | APipe Tester | 16 May 2013, 17:48:59 UTC | Updated `genome` tab completion. | 16 May 2013, 17:50:01 UTC |
| d574b71 | Eddie Belter | 16 May 2013, 17:38:54 UTC | DeNovo: special diff for metrics files | 16 May 2013, 17:49:02 UTC |
| ae269eb | dmorton | 16 May 2013, 17:20:20 UTC | Fix check of stage_output in SoftwareResult::Default | 16 May 2013, 17:35:06 UTC |
| b2a4772 | dmorton | 15 May 2013, 22:54:07 UTC | SoftwareResultify DifferentialExpression's Cuffdiff | 16 May 2013, 17:35:06 UTC |
| 302ccfe | APipe Tester | 16 May 2013, 17:12:14 UTC | Updated `gmt` tab completion. | 16 May 2013, 17:12:14 UTC |
| b03da8f | APipe Tester | 16 May 2013, 17:11:11 UTC | Updated `genome` tab completion. | 16 May 2013, 17:11:11 UTC |
| c21f5f7 | Kyung Kim | 16 May 2013, 16:56:18 UTC | added option to remove scaffolds by min_length | 16 May 2013, 16:56:18 UTC |
| e016b41 | Thomas Mooney | 16 May 2013, 14:32:20 UTC | OK the ref.align diff. | 16 May 2013, 14:32:20 UTC |
| 0749f3f | Malachi Griffith | 16 May 2013, 04:40:20 UTC | Reactivate tests and update test results to account for correction of ALL1 sample common names | 16 May 2013, 04:40:20 UTC |
| f0131c2 | dmorton | 15 May 2013, 21:18:33 UTC | Disable some tests (blocking the model tests from being run) | 15 May 2013, 21:19:28 UTC |
| 51d9b1a | dmorton | 15 May 2013, 20:01:21 UTC | Remove incorrect comment | 15 May 2013, 21:19:28 UTC |
| d0c773e | dmorton | 15 May 2013, 20:00:13 UTC | Strengthen interface of DifferentialExpression command | 15 May 2013, 21:19:28 UTC |
| 833bc76 | dmorton | 15 May 2013, 14:21:33 UTC | Make ModelSummary have more flexible def of failed builds Useful for models with say one unstartable and one succeeded, the unstartable build should be cleaned up but since I wasn't flagged as a failed build the model had 0 failed builds and therefore the unstartable was not set to clean up. | 15 May 2013, 21:19:28 UTC |
| 991e3b1 | Eddie Belter | 15 May 2013, 20:57:11 UTC | SX: external command base will run the underlying command in back ticks | 15 May 2013, 21:08:34 UTC |
| ed42699 | Gabriel Sanderson | 15 May 2013, 21:02:37 UTC | Merge branch 'master' into gb_master | 15 May 2013, 21:02:37 UTC |
| 70e8ed1 | Gabriel Sanderson | 15 May 2013, 21:01:50 UTC | Output bam file paths that are missing | 15 May 2013, 21:01:50 UTC |
| 06c0902 | Thomas Mooney | 15 May 2013, 19:21:45 UTC | Reduce our tmp space request. RT#92318 It is believed that newer tophat versions and improvements to SX both contribute to reduced tmp space requirements. This change should be sufficient to schedule two jobs simultaneously [on our current systems]. | 15 May 2013, 19:21:45 UTC |
| 2f02641 | APipe Tester | 15 May 2013, 18:59:31 UTC | updated ur submodule to 926b226 | 15 May 2013, 18:59:31 UTC |
| d7942f1 | APipe Tester | 15 May 2013, 15:12:57 UTC | Updated `gmt` tab completion. | 15 May 2013, 15:12:57 UTC |
| dcec134 | APipe Tester | 15 May 2013, 15:11:53 UTC | Updated `genome` tab completion. | 15 May 2013, 15:11:53 UTC |
| 86dcaa8 | Thomas Mooney | 15 May 2013, 14:37:58 UTC | Switch the queue these land in so they don't compete with their parent. | 15 May 2013, 14:37:58 UTC |
| b5cc35f | Gabriel Sanderson | 14 May 2013, 21:28:05 UTC | Merge branch 'master' into gb_master | 14 May 2013, 21:28:05 UTC |
| 035e051 | Gabriel Sanderson | 14 May 2013, 21:27:24 UTC | Make fix_alt_and_gt optional so things are not broken. | 14 May 2013, 21:27:32 UTC |
| dd0b522 | APipe Tester | 14 May 2013, 21:02:20 UTC | updated getopt-complete submodule to 95e944c | 14 May 2013, 21:02:20 UTC |
| 8df0175 | APipe Tester | 14 May 2013, 20:47:25 UTC | updated graphite submodule to c3cea89 | 14 May 2013, 20:47:25 UTC |
| afeff7e | Jim Weible | 14 May 2013, 20:01:07 UTC | skip object creation for DGIDB GO importer | 14 May 2013, 20:01:07 UTC |
| 578cc23 | APipe Tester | 14 May 2013, 19:26:25 UTC | updated graphite submodule to 0c54926 | 14 May 2013, 19:26:25 UTC |
| 40a26f6 | APipe Tester | 14 May 2013, 18:35:02 UTC | updated ur submodule to 5112068 | 14 May 2013, 18:35:02 UTC |
| c8d4cd4 | APipe Tester | 14 May 2013, 17:57:29 UTC | Updated `gmt` tab completion. | 14 May 2013, 17:57:29 UTC |
| 7d24fd0 | APipe Tester | 14 May 2013, 17:56:36 UTC | Updated `genome` tab completion. | 14 May 2013, 17:56:36 UTC |
| 3c7faa5 | Adam Coffman | 14 May 2013, 17:50:55 UTC | add leading slash for file path | 14 May 2013, 17:50:55 UTC |
| ffdba60 | Adam Coffman | 14 May 2013, 17:46:51 UTC | fix typos, make code compile | 14 May 2013, 17:46:51 UTC |
| f75d13f | Chris Miller | 14 May 2013, 16:15:30 UTC | fixing thresholding problem | 14 May 2013, 16:15:38 UTC |
| d62bbd6 | APipe Tester | 14 May 2013, 16:12:31 UTC | Updated `gmt` tab completion. | 14 May 2013, 16:12:31 UTC |
| eab41ea | APipe Tester | 14 May 2013, 16:11:28 UTC | Updated `genome` tab completion. | 14 May 2013, 16:11:28 UTC |
| e2a58ec | kmeltzst | 14 May 2013, 15:39:09 UTC | added option for gzipped vcf file | 14 May 2013, 15:39:57 UTC |
| d5dfb4b | Malachi Griffith | 14 May 2013, 15:11:25 UTC | ClinSeq - SummarizeModels, diffs check out, updating test result | 14 May 2013, 15:11:25 UTC |
| d4ee502 | APipe Tester | 14 May 2013, 15:04:37 UTC | updated ur submodule to bbd15c4 | 14 May 2013, 15:04:37 UTC |
| 696be32 | Jason Walker | 14 May 2013, 14:15:34 UTC | Compile error. Add comma. | 14 May 2013, 14:15:34 UTC |
| 8f9c14e | Jason Walker | 14 May 2013, 13:28:40 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 May 2013, 13:28:40 UTC |
| c638adc | Jason Walker | 14 May 2013, 13:28:28 UTC | Changes to the metric keys caused missing values from the output metrics. | 14 May 2013, 13:28:28 UTC |
| 311982e | Malachi Griffith | 13 May 2013, 21:07:59 UTC | DumpIgvXml - Fix test result location so that old and new commits will pass test | 13 May 2013, 21:07:59 UTC |
| 082d315 | Malachi Griffith | 13 May 2013, 21:01:51 UTC | Update test result for clin-seq DumpIgvSessionXml | 13 May 2013, 21:01:51 UTC |
| 423cb59 | Ian Ferguson | 13 May 2013, 20:01:01 UTC | Bwa, Bwasw, Bwamem now respect thread count in PP. The Bwa, Bwasw, and Bwamem aligner modules now base their LSF CPU requirement off of the thread count argument (if specified) in read_aligner_params in the processing-profile. | 13 May 2013, 20:03:57 UTC |
| 649e2dc | Eddie Belter | 13 May 2013, 18:58:28 UTC | AQID mc16s.t: rm GSC from comments | 13 May 2013, 18:58:38 UTC |
| 99e4d9b | Veena Bhonagiri | 13 May 2013, 15:48:48 UTC | Added code so any version of acedb can be used | 13 May 2013, 15:48:48 UTC |
| a388067 | Kyung Kim | 10 May 2013, 22:05:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 May 2013, 22:05:03 UTC |
| 0bb37f1 | Kyung Kim | 10 May 2013, 21:13:42 UTC | DeNovo: update soap blessed build | 10 May 2013, 21:42:14 UTC |
| ae64b02 | Kyung Kim | 10 May 2013, 19:27:36 UTC | DeNovo: rm merge sx results and link result, they are in one step now | 10 May 2013, 21:42:14 UTC |
| de59666 | Kyung Kim | 10 May 2013, 19:19:45 UTC | SX: rm old processor test | 10 May 2013, 21:42:13 UTC |
| ee2cd26 | Kyung Kim | 10 May 2013, 19:02:13 UTC | Added new param to test | 10 May 2013, 21:42:13 UTC |
| 3321475 | apregier | 10 May 2013, 16:10:12 UTC | DeNovo: soap parallelizes process instrument data | 10 May 2013, 21:42:12 UTC |
| bb8673d | apregier | 10 May 2013, 16:09:07 UTC | Assemble step fails if assembler fails | 10 May 2013, 21:42:11 UTC |
| e21f328 | apregier | 10 May 2013, 16:08:10 UTC | Remove db::singles | 10 May 2013, 21:42:11 UTC |
| fc99bf1 | apregier | 10 May 2013, 16:02:47 UTC | Take average of insert size | 10 May 2013, 21:42:10 UTC |
| 9b588c0 | Eddie Belter | 10 May 2013, 14:47:04 UTC | DeNovo: get allpaths test to pass using merged SX results | 10 May 2013, 21:42:09 UTC |
| 3828ce4 | Eddie Belter | 10 May 2013, 14:46:38 UTC | DeNovo: add status msgs to assemble step | 10 May 2013, 21:42:09 UTC |
| 13bc2aa | Eddie Belter | 09 May 2013, 22:31:45 UTC | DeNovo: calculate reads attempted and processed in merge and link sx results step | 10 May 2013, 21:42:08 UTC |
| 585cbb7 | apregier | 09 May 2013, 20:35:11 UTC | Allpaths uses SxResults | 10 May 2013, 21:42:08 UTC |
| a034a3f | Eddie Belter | 09 May 2013, 21:10:15 UTC | DeNovo: update status msg on merge step | 10 May 2013, 21:42:07 UTC |
| a67f7a5 | Eddie Belter | 09 May 2013, 21:08:18 UTC | Sx Processor: make processor optional | 10 May 2013, 21:42:06 UTC |
| ff6ba58 | Eddie Belter | 09 May 2013, 21:00:41 UTC | DeNovo: new assemble build step | 10 May 2013, 21:42:06 UTC |
| 6eca376 | Eddie Belter | 09 May 2013, 21:00:12 UTC | SX Result: rm dumper statement | 10 May 2013, 21:42:04 UTC |
| 56086d5 | Eddie Belter | 09 May 2013, 20:59:24 UTC | DeNovo: merge and link sx results build step | 10 May 2013, 21:42:03 UTC |
| d030cb9 | Eddie Belter | 09 May 2013, 20:46:33 UTC | SX Result: update merged result to use new methods in base result | 10 May 2013, 21:42:02 UTC |
| 8cb0e9e | Eddie Belter | 09 May 2013, 19:24:26 UTC | SX Processor: complete final sx params method | 10 May 2013, 21:42:02 UTC |
| 05b1ac9 | Eddie Belter | 09 May 2013, 18:40:43 UTC | DeNovo: input_build is now just build. | 10 May 2013, 21:42:01 UTC |
| 03ffcd6 | Eddie Belter | 09 May 2013, 17:24:26 UTC | DeNovo: update workflow to use new build steps | 10 May 2013, 21:42:00 UTC |
| 6f601ff | Eddie Belter | 09 May 2013, 00:18:33 UTC | DeNovo: pass in command class name to add operation in pp | 10 May 2013, 21:42:00 UTC |
| 4cd2b62 | Eddie Belter | 09 May 2013, 00:10:54 UTC | DeNovo: update process inst data to use sx processor api | 10 May 2013, 21:41:59 UTC |
| 22e7f05 | Eddie Belter | 09 May 2013, 00:03:37 UTC | SX Processor: change API to be able to return merged sx result params and all final sx result params | 10 May 2013, 21:41:58 UTC |
| 9894dea | Eddie Belter | 08 May 2013, 17:25:35 UTC | SX Result: move resolve_merged_input_type from SX result to merged result | 10 May 2013, 21:41:58 UTC |
| b3dbc7e | Eddie Belter | 08 May 2013, 17:23:01 UTC | SX Result: reorged methods, updated status msgs | 10 May 2013, 21:41:57 UTC |
| 89d6c18 | Kyung Kim | 10 May 2013, 21:31:31 UTC | SX: sam and bam reader test reads 2 from sam/bam | 10 May 2013, 21:37:29 UTC |
| dc61a03 | Adam Coffman | 10 May 2013, 21:24:00 UTC | fix typo in error msg | 10 May 2013, 21:24:00 UTC |
| 0e46f18 | Kyung Kim | 10 May 2013, 21:17:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 May 2013, 21:17:08 UTC |
| f4d7162 | Kyung Kim | 10 May 2013, 21:16:41 UTC | SX: sam/bam reader complements seqs w/ reverse complemented flag | 10 May 2013, 21:16:41 UTC |
| 56e2726 | Kyung Kim | 10 May 2013, 21:13:17 UTC | SX: reader sorts seqs by name | 10 May 2013, 21:13:17 UTC |
| 6bea0c1 | Chris Miller | 10 May 2013, 20:25:51 UTC | added sanity checks to handle the case where no segs will be plot | 10 May 2013, 20:26:04 UTC |
| 30391a2 | Kyung Kim | 10 May 2013, 20:09:44 UTC | SX: add complement function | 10 May 2013, 20:09:44 UTC |
| f21a7f7 | Gabriel Sanderson | 09 May 2013, 22:45:22 UTC | Merge branch 'master' into gb_master | 09 May 2013, 22:45:22 UTC |
| d043a8d | Gabriel Sanderson | 09 May 2013, 22:43:54 UTC | added test case for convert_file_with_alpha_gt_values_to_numeric | 09 May 2013, 22:44:31 UTC |
| 8af948d | APipe Tester | 09 May 2013, 18:37:11 UTC | Updated `gmt` tab completion. | 09 May 2013, 18:37:11 UTC |
| 1eea829 | APipe Tester | 09 May 2013, 18:35:20 UTC | Updated `genome` tab completion. | 09 May 2013, 18:35:20 UTC |
| de572c5 | Jasreet Hundal | 09 May 2013, 18:22:26 UTC | New tool for parsing NetMHC3.2 stdout from web | 09 May 2013, 18:22:26 UTC |
| 718668d | APipe Tester | 09 May 2013, 17:39:10 UTC | Updated `genome` tab completion. | 09 May 2013, 17:39:10 UTC |
| 20786d8 | apregier | 09 May 2013, 17:17:02 UTC | Correctly get 1-based roi | 09 May 2013, 17:17:21 UTC |
| 901263a | Scott Smith | 09 May 2013, 14:28:47 UTC | make processing-profile diff flag differing properties | 09 May 2013, 14:28:47 UTC |
| 7d56809 | Scott Smith | 09 May 2013, 14:26:46 UTC | ensure changes to inputs or other model properties are applied to new models, not just processing profile changes | 09 May 2013, 14:26:46 UTC |
| 76ec43d | Thomas Mooney | 09 May 2013, 13:57:23 UTC | Bring back defaults required for MGAP pipeline... | 09 May 2013, 13:57:23 UTC |
| a4dc19a | Thomas Mooney | 08 May 2013, 14:48:45 UTC | Old data is gone again, so update blessed build blindly. | 09 May 2013, 13:55:54 UTC |
| 3fb56c7 | Dave Larson | 08 May 2013, 21:52:04 UTC | If we subtract one from the VCF coord then we need to add it back when we output it. Also, we should check that our filehandles opened. CHANGELOG: Fix VCF output for liftover tool (had an off by one error). | 08 May 2013, 21:52:04 UTC |
| 265973f | Ian Ferguson | 08 May 2013, 20:52:14 UTC | Better error checking for Bwasw | 08 May 2013, 20:52:29 UTC |
| 061b276 | Eddie Belter | 08 May 2013, 20:36:01 UTC | MC16s: add clusters to solexa inst data for est kb usage | 08 May 2013, 20:36:01 UTC |
| 1b44969 | APipe Tester | 08 May 2013, 20:05:42 UTC | Updated `gmt` tab completion. | 08 May 2013, 20:05:42 UTC |
