| 9199acf | dmorton | 23 May 2013, 01:42:08 UTC | Update ClinSeq test expected output | 23 May 2013, 01:42:08 UTC |
| 618aa59 | dmorton | 22 May 2013, 23:08:13 UTC | Update ClinSeq data for test | 22 May 2013, 23:08:47 UTC |
| f403b8a | dmorton | 22 May 2013, 22:16:22 UTC | Make the GMTCuffDiffWrapper take different input It now takes condition_model_ids_string instead of bam_file_paths. This change was brought on by a 1000 character limit on the oracle database column which stores software result inputs. | 22 May 2013, 23:08:47 UTC |
| ba579e5 | Scott Smith | 22 May 2013, 22:46:43 UTC | fix typo in docs causing module compile fail | 22 May 2013, 22:46:43 UTC |
| 5316bd9 | Scott Smith | 22 May 2013, 22:45:48 UTC | updated docs for new "genome model copy" feature to take indirect params | 22 May 2013, 22:45:48 UTC |
| 02a894d | Scott Smith | 22 May 2013, 22:39:44 UTC | updated "genome model copy" to support input_model.other_input_model.blah=foo, and recursively make new underlying models as needed | 22 May 2013, 22:40:24 UTC |
| 9c9d506 | Scott Smith | 06 May 2013, 20:07:01 UTC | rename $exit_code variable to $sytem_retval, since this another variable actually contains the exit code | 22 May 2013, 22:40:23 UTC |
| 99c3cbd | dmorton | 22 May 2013, 22:09:54 UTC | Revert "update diag() code on diff failure for Strelka" This reverts commit 45073ff67d47621fd73bae4a4f43f4211bf7b838. | 22 May 2013, 22:14:52 UTC |
| 05db458 | dmorton | 22 May 2013, 21:40:58 UTC | Fix Test Sys-sw not doing what was intended. | 22 May 2013, 22:14:51 UTC |
| 7ee6ef2 | Eddie Belter | 22 May 2013, 15:52:19 UTC | Sample: remove is_control property | 22 May 2013, 18:31:38 UTC |
| 45073ff | Scott Smith | 22 May 2013, 18:25:24 UTC | update diag() code on diff failure for Strelka | 22 May 2013, 18:25:24 UTC |
| bbe74bc | Scott Smith | 22 May 2013, 18:24:03 UTC | don't complain about inputs w/o values when they are optional | 22 May 2013, 18:24:03 UTC |
| 684c364 | Scott Smith | 22 May 2013, 18:22:31 UTC | add Genome::Sys concatenate_files(), quote_for_shell() | 22 May 2013, 18:22:31 UTC |
| 371e7af | Eddie Belter | 22 May 2013, 14:44:33 UTC | DeNovo: scalar context bug in merge sx results | 22 May 2013, 14:55:54 UTC |
| b8cccd8 | Jim Weible | 22 May 2013, 13:15:09 UTC | wrapper for joinx vcf-normalize-indels | 22 May 2013, 13:15:21 UTC |
| 2c07fdb | Eddie Belter | 21 May 2013, 19:55:48 UTC | SX Processor: properly propogate DEFAULT processor | 21 May 2013, 19:55:48 UTC |
| 33e232f | Thomas Mooney | 21 May 2013, 18:17:31 UTC | Handle multiple BAM files since this is an "is_many" property. | 21 May 2013, 18:17:31 UTC |
| deb79c1 | Ian Ferguson | 20 May 2013, 20:33:32 UTC | Fix vcf symlinking in DV2 Don't unlink a vcf symlink and then recreate an identical symlink. Just leave the link alone if it already has the desired target. This should help prevent builds from failing because they tried to create symlinks on read-only volumes. | 20 May 2013, 20:33:32 UTC |
| f88bc72 | Thomas Mooney | 20 May 2013, 19:25:26 UTC | Defer checking inputs so build can be created (but unstartable). | 20 May 2013, 19:25:26 UTC |
| 5b8fe3c | dmorton | 18 May 2013, 13:14:43 UTC | Fix typo in DifferentialExpression pipeline | 18 May 2013, 13:15:39 UTC |
| 968b833 | Eddie Belter | 17 May 2013, 21:00:07 UTC | Sync RMU: run region 454 inherits from base | 17 May 2013, 21:00:07 UTC |
| d9f2b75 | Eddie Belter | 17 May 2013, 20:59:41 UTC | Sync RMU: handle setting attribute value to undef | 17 May 2013, 20:59:41 UTC |
| ba2aa8d | Eddie Belter | 17 May 2013, 20:59:01 UTC | Sync: rm db::single | 17 May 2013, 20:59:01 UTC |
| 106ed1a | Chris Miller | 17 May 2013, 17:01:38 UTC | removed incorrect default | 17 May 2013, 17:01:51 UTC |
| 662eb14 | Veena Bhonagiri | 17 May 2013, 14:55:22 UTC | Added code to copy contigs.cmt and gap.txt file to Sequence/Unmasked dirwhile running MGAP | 17 May 2013, 14:55:22 UTC |
| 6cb819f | APipe Tester | 17 May 2013, 03:53:42 UTC | Updated `genome` tab completion. | 17 May 2013, 03:53:42 UTC |
| 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 |
