| 6462e53 | Ben Oberkfell | 11 April 2013, 16:51:50 UTC | account for extra newline added so as to not break TAP | 11 April 2013, 16:51:50 UTC |
| 439cd64 | nnutter | 11 April 2013, 16:22:01 UTC | update config for new home dirs | 11 April 2013, 16:22:35 UTC |
| a46d069 | nnutter | 11 April 2013, 16:03:11 UTC | add a new line so that bad programs don't break TAP, etc. | 11 April 2013, 16:04:42 UTC |
| 5c67dce | nnutter | 11 April 2013, 14:57:13 UTC | example values were added in 6af42ec | 11 April 2013, 14:57:13 UTC |
| b4a1731 | nnutter | 11 April 2013, 14:35:48 UTC | Vep.d moved | 11 April 2013, 14:35:48 UTC |
| 5b529a2 | nnutter | 11 April 2013, 14:30:14 UTC | new build looks OK to me It looks like a new alignment was done that had a few insignificant changes in the results. | 11 April 2013, 14:30:14 UTC |
| 9b2f47b | nnutter | 11 April 2013, 14:13:16 UTC | blacklist all Db/Ensembl/Vep.d from being compile tested | 11 April 2013, 14:13:51 UTC |
| 6af42ec | Scott Smith | 11 April 2013, 13:42:28 UTC | Restructure Genome/Db tree. | 11 April 2013, 13:42:28 UTC |
| f92de5e | nnutter | 11 April 2013, 02:30:52 UTC | revert default => example_values change This probably needs to be backfilled on SomaticValidation processing profiles and converted to an input to the model's workflow. | 11 April 2013, 02:30:52 UTC |
| 9d8d256 | nnutter | 11 April 2013, 02:15:57 UTC | approved apipe-test-reference-alignment This model just started running with GENOME_SOFTWARE_RESULT_TEST_NAME so the alignments were regenerated for the first time in awhile. BWA alignments now use however many CPUs are available when submitted to LSF so the -t option changed to 4 and that was the only diff. diff -U0 <(samtools view -h /gscmnt/gc13001/info/model_data/2880887847/build133133153/alignments/112032366.bam) <(samtools view -h /gscmnt/gc9006/info/model_data/2880887847/build136534477/alignments/136537547.bam) --- /dev/fd/63 2013-04-10 21:12:53.057852876 -0500 +++ /dev/fd/62 2013-04-10 21:12:53.057852876 -0500 @@ -116 +116 @@ -@PG ID:2851949190 VN:0.5.9 CL:bwa aln -t4 -q 5; bwa sampe -a 462 +@PG ID:2851949190 VN:0.5.9 CL:bwa aln -t2 -q 5; bwa sampe -a 462 | 11 April 2013, 02:15:57 UTC |
| d5de8a0 | nnutter | 10 April 2013, 19:59:44 UTC | updated expected outputs Updated `genome-model-rnaseq-list2.out` because a model has a new build. | 10 April 2013, 19:59:44 UTC |
| 96da6fa | Gabriel Sanderson | 10 April 2013, 19:24:48 UTC | Merge branch 'master' into gb_master | 10 April 2013, 19:24:48 UTC |
| baaa8e1 | Gabriel Sanderson | 10 April 2013, 19:23:54 UTC | Increment vcf_version because old vcf results had no sample name set | 10 April 2013, 19:24:04 UTC |
| 293b831 | Ben Oberkfell | 10 April 2013, 18:57:45 UTC | return to the previous behavior that didnt include the post-commit handler, while i figure out why it is janky | 10 April 2013, 18:57:45 UTC |
| 7b9f451 | nnutter | 10 April 2013, 03:19:02 UTC | simplify | 10 April 2013, 03:19:02 UTC |
| 583a792 | apregier | 10 April 2013, 02:50:26 UTC | Can't call object method before object is instantiated | 10 April 2013, 02:50:26 UTC |
| 451e577 | nnutter | 10 April 2013, 01:28:46 UTC | rename function so it doesn't override instance method | 10 April 2013, 01:31:29 UTC |
| 14658a4 | nnutter | 09 April 2013, 20:54:37 UTC | updated expected outputs Updated `genome-model-rnaseq-list2.out` because several models have had new builds. | 09 April 2013, 20:54:37 UTC |
| 0a74b16 | Chris Miller | 09 April 2013, 19:39:19 UTC | create output dir if doesn't exist | 09 April 2013, 19:41:11 UTC |
| 54d29af | nnutter | 09 April 2013, 19:23:36 UTC | add blacklist for exceptions | 09 April 2013, 19:23:47 UTC |
| 2d31a19 | nnutter | 09 April 2013, 19:23:22 UTC | label test | 09 April 2013, 19:23:46 UTC |
| e3c229a | Jim Weible | 08 April 2013, 18:59:33 UTC | respect reference-fasta param for build purposes | 09 April 2013, 19:18:21 UTC |
| 651e1a9 | Jim Weible | 08 April 2013, 15:46:43 UTC | MergeFile became MergeFiles and remove useless is_many | 09 April 2013, 19:18:21 UTC |
| b5908f5 | nnutter | 09 April 2013, 19:11:09 UTC | temporary bypass | 09 April 2013, 19:11:09 UTC |
| a21b631 | nnutter | 09 April 2013, 19:05:09 UTC | enable quiet option on VEP Enable quiet option so Bio::EnsEMBL::Variation::Utils::VEP doesn't spam logs with progress bar. | 09 April 2013, 19:05:09 UTC |
| d500927 | nnutter | 09 April 2013, 18:56:29 UTC | whitespace | 09 April 2013, 18:56:29 UTC |
| a7b2dc0 | nnutter | 09 April 2013, 18:53:16 UTC | limit output for test so it doesn't spam | 09 April 2013, 18:54:34 UTC |
| 3da234f | APipe Tester | 09 April 2013, 18:12:45 UTC | updated jenkins submodule to 35ad2c1 | 09 April 2013, 18:12:45 UTC |
| d322d31 | APipe Tester | 09 April 2013, 17:59:07 UTC | updated jenkins submodule to decd4bb | 09 April 2013, 17:59:07 UTC |
| cb829ca | Malachi Griffith | 09 April 2013, 01:07:28 UTC | Bringing R code used by ClonalityPlot.pm under source control | 09 April 2013, 01:07:28 UTC |
| e994e16 | Malachi Griffith | 09 April 2013, 01:06:35 UTC | ClonalityPlot.pm used to use a default path to some random R code on network that was then sourced, this was refactored to be specified as a required parameter. This broke a clin-seq command that wants to run this command automatically. I have refactored to bring the random code under source control and find it automatically instead of specifying at command line. | 09 April 2013, 01:06:35 UTC |
| b5f1d8c | Malachi Griffith | 09 April 2013, 00:56:41 UTC | ClinSeq - Added ad hoc ensembl API script to assist in creation of PCR primer design files | 09 April 2013, 00:56:41 UTC |
| ea18fbe | nnutter | 08 April 2013, 23:57:47 UTC | update expected output Updated `genome-model-rnaseq-list2.out` now that several builds have completed so several columns are now filled in with values instead of nulls. | 08 April 2013, 23:57:47 UTC |
| 9d03000 | nnutter | 08 April 2013, 22:47:58 UTC | reapply most of Gabe's commit to remove default_values I mistakenly reverted a previous commit instead of only a couple files in it. This reapplies the rest of the changes. Erroneous Revert: 1da947a655ceb82bc450766333b21260ca20885d Original Change: 935b04397f9b925fac4b80aacbdcbcf79d70dea8 | 08 April 2013, 23:00:56 UTC |
| a210fc8 | Eddie Belter | 08 April 2013, 21:42:15 UTC | InstData import: only dump primary alignemnts from sra | 08 April 2013, 21:42:48 UTC |
| 45bc9bd | Eddie Belter | 05 April 2013, 22:16:06 UTC | InstData Import: check ncbi config file | 08 April 2013, 21:42:48 UTC |
| cf348ec | Eddie Belter | 04 April 2013, 16:18:25 UTC | InstData Import: Add SRA functionality | 08 April 2013, 21:42:48 UTC |
| 5d44179 | Eddie Belter | 01 April 2013, 18:40:36 UTC | InstData Import: mv bam sort into separate method | 08 April 2013, 21:42:47 UTC |
| 18e77b9 | Eddie Belter | 01 April 2013, 18:27:37 UTC | InstData Import: make method to verify and move bam | 08 April 2013, 21:42:47 UTC |
| 2df4013 | Eddie Belter | 29 March 2013, 20:05:33 UTC | InstData Import: move flagstat into separate method | 08 April 2013, 21:42:46 UTC |
| a2562c9 | Eddie Belter | 29 March 2013, 18:11:02 UTC | InstData Import: remove moved fail and bam tests from fastq | 08 April 2013, 21:42:46 UTC |
| 2f9619c | Eddie Belter | 29 March 2013, 18:09:33 UTC | InstData Import: mv fail tests from fastq into separate file | 08 April 2013, 21:42:46 UTC |
| c45f462 | Eddie Belter | 29 March 2013, 18:03:26 UTC | InstData Import: mv bam test from fastq into separate file | 08 April 2013, 21:42:45 UTC |
| 58e6b87 | Eddie Belter | 29 March 2013, 17:58:01 UTC | InstData Import: rename basic test | 08 April 2013, 21:42:45 UTC |
| fc317e4 | Eddie Belter | 29 March 2013, 17:49:49 UTC | InstData Import Basic: convert format into original_format and import_format | 08 April 2013, 21:42:43 UTC |
| c94d40b | APipe Tester | 08 April 2013, 21:30:13 UTC | updated jenkins submodule to bad136a | 08 April 2013, 21:30:13 UTC |
| 89cf28e | APipe Tester | 08 April 2013, 20:43:34 UTC | updated jenkins submodule to 6fdbd47 | 08 April 2013, 20:43:34 UTC |
| 5b9814a | APipe Tester | 08 April 2013, 20:43:27 UTC | updated ur submodule to 318fcdc | 08 April 2013, 20:43:27 UTC |
| 1da947a | nnutter | 08 April 2013, 17:17:53 UTC | restore default_values This tool is using defaults to find compatible models or creating new models if needed (which would then validate their inputs as well). So I think it may be an exception to the "no defaults" rule. That commit did not convert several defaults which possibly should have been converted (if this is ever unreverted). This reverts commit 935b04397f9b925fac4b80aacbdcbcf79d70dea8. | 08 April 2013, 17:33:25 UTC |
| fb75798 | Feiyu Du | 08 April 2013, 16:14:49 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 April 2013, 16:14:49 UTC |
| 0d04edb | nnutter | 08 April 2013, 15:57:48 UTC | updated expected data Updated several files expected outputs: genome-instrument-data-list2.out genome-model-clinseq-list1.out genome-model-clinseq-list3.out genome-model-rnaseq-list2.out genome-instrument-data-list2.out was because insert size information was added to the instrument data. The other three are all related to rebuilding of dependent builds due to some issue with the alignments (tmooney handled that). | 08 April 2013, 16:02:04 UTC |
| f5f07e2 | Feiyu Du | 08 April 2013, 15:57:50 UTC | bug fix get_default_alignment_results method | 08 April 2013, 15:58:25 UTC |
| cd7849a | Dave Larson | 08 April 2013, 15:40:23 UTC | rename method for grabbing blessed build and remove use above | 08 April 2013, 15:40:23 UTC |
| db48199 | nnutter | 08 April 2013, 15:02:40 UTC | output changed because default value was made to an example value | 08 April 2013, 15:02:40 UTC |
| af0a8ec | Dave Larson | 08 April 2013, 14:18:12 UTC | added test for DiffBlessed refactor | 08 April 2013, 14:18:12 UTC |
| 026b382 | Scott Smith | 06 April 2013, 20:55:32 UTC | Revamp Genome::Model::ReferenceSequence. * Updated to use newer input handling. * Legacy "*Imported*" modules still are in place but are empty. * Genome::Model::Build::ReferenceSequence exists but is smaller. | 06 April 2013, 21:02:13 UTC |
| 0d9b7ea | Anthony Brummett | 05 April 2013, 22:07:57 UTC | Avoid uninitialized value warnings | 05 April 2013, 22:31:41 UTC |
| 334847f | Anthony Brummett | 05 April 2013, 21:46:46 UTC | command_execute_ok doesn't work with this kind of command | 05 April 2013, 22:31:41 UTC |
| e6a023b | Anthony Brummett | 05 April 2013, 21:28:15 UTC | make tests less chatty | 05 April 2013, 22:31:40 UTC |
| 45573e9 | Anthony Brummett | 05 April 2013, 21:27:14 UTC | Forgot to use Sub::Install | 05 April 2013, 22:31:40 UTC |
| 4b0db30 | Anthony Brummett | 05 April 2013, 18:51:44 UTC | Add test command_execute_fail_ok() that passes if the command execution returns false | 05 April 2013, 22:31:40 UTC |
| 1283565 | Anthony Brummett | 05 April 2013, 18:11:23 UTC | Make the output from vep go to /dev/null in the test | 05 April 2013, 22:31:39 UTC |
| 0b55d56 | APipe Tester | 05 April 2013, 22:10:26 UTC | updated ur submodule to ffdf52f | 05 April 2013, 22:10:26 UTC |
| cd4d2ef | Dave Larson | 05 April 2013, 21:44:14 UTC | add some file accessors to clinseq | 05 April 2013, 21:55:18 UTC |
| 314eff7 | Dave Larson | 05 April 2013, 21:33:27 UTC | refactored to have methods | 05 April 2013, 21:55:17 UTC |
| 23f272e | Dave Larson | 05 April 2013, 21:32:42 UTC | remove accessors from tool (moved to ClinSeq) | 05 April 2013, 21:55:17 UTC |
| e607fd4 | Malachi Griffith | 05 April 2013, 21:03:12 UTC | ClinSeq - Extra input file checking in converge all-events | 05 April 2013, 21:03:12 UTC |
| 0ac2520 | Gabriel Sanderson | 05 April 2013, 20:47:31 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:47:31 UTC |
| 85eb548 | Gabriel Sanderson | 05 April 2013, 20:47:16 UTC | Remove default parameters. Remove unused CeuYri module. | 05 April 2013, 20:47:26 UTC |
| 2eee6b7 | nnutter | 05 April 2013, 20:23:56 UTC | add runtime check for ambiguous property definitions | 05 April 2013, 20:45:00 UTC |
| 035674a | Jason Walker | 05 April 2013, 20:44:47 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 20:44:47 UTC |
| 5ec0475 | Jason Walker | 05 April 2013, 20:44:40 UTC | Get or create the to model-group. | 05 April 2013, 20:44:40 UTC |
| 3cd1671 | Ben Oberkfell | 05 April 2013, 20:44:09 UTC | actually capture this in a closure | 05 April 2013, 20:44:09 UTC |
| af219a8 | Gabriel Sanderson | 05 April 2013, 20:38:44 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:38:44 UTC |
| 935b043 | Gabriel Sanderson | 05 April 2013, 20:25:38 UTC | remove default values | 05 April 2013, 20:38:40 UTC |
| 8bbb520 | APipe Tester | 05 April 2013, 20:32:48 UTC | updated ur submodule to a12ce7f | 05 April 2013, 20:32:48 UTC |
| 5b2fc40 | Gabriel Sanderson | 05 April 2013, 20:19:10 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:19:10 UTC |
| e031351 | Gabriel Sanderson | 05 April 2013, 20:16:39 UTC | remove default values | 05 April 2013, 20:16:39 UTC |
| cdb0224 | Gabriel Sanderson | 05 April 2013, 20:09:53 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:09:53 UTC |
| 98df15b | Gabriel Sanderson | 05 April 2013, 20:08:38 UTC | eliminate default values | 05 April 2013, 20:08:38 UTC |
| 301fc93 | Gabriel Sanderson | 05 April 2013, 20:03:45 UTC | Merge branch 'default' into gb_master | 05 April 2013, 20:03:45 UTC |
| 54e92af | Gabriel Sanderson | 05 April 2013, 20:03:18 UTC | remove default values | 05 April 2013, 20:03:18 UTC |
| 552408b | Gabriel Sanderson | 05 April 2013, 19:09:46 UTC | Merge branch 'default' into gb_master | 05 April 2013, 19:09:46 UTC |
| ddd8618 | Jason Walker | 05 April 2013, 19:07:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 19:07:35 UTC |
| 3b64e6b | Gabriel Sanderson | 05 April 2013, 18:55:43 UTC | removed default values | 05 April 2013, 18:55:43 UTC |
| 34369dd | Gabriel Sanderson | 05 April 2013, 18:49:38 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:49:38 UTC |
| 55e2a00 | Gabriel Sanderson | 05 April 2013, 18:45:13 UTC | remove default values | 05 April 2013, 18:49:28 UTC |
| d420a07 | Gabriel Sanderson | 05 April 2013, 18:41:11 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:41:11 UTC |
| def2737 | Gabriel Sanderson | 05 April 2013, 18:38:26 UTC | remove default values | 05 April 2013, 18:38:26 UTC |
| 75502c0 | Gabriel Sanderson | 05 April 2013, 18:34:35 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:34:35 UTC |
| 4a16edf | Gabriel Sanderson | 05 April 2013, 18:33:03 UTC | eliminate default values | 05 April 2013, 18:33:03 UTC |
| eea6596 | Gabriel Sanderson | 05 April 2013, 18:30:25 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:30:25 UTC |
| 8ca25e0 | Gabriel Sanderson | 05 April 2013, 18:29:16 UTC | remove default values | 05 April 2013, 18:29:16 UTC |
| 1a858f1 | Gabriel Sanderson | 05 April 2013, 18:25:49 UTC | Merge branch 'default' into gb_master | 05 April 2013, 18:25:49 UTC |
| 87369b3 | Gabriel Sanderson | 05 April 2013, 18:24:46 UTC | Eliminate default values | 05 April 2013, 18:24:46 UTC |
| 622f225 | Scott Smith | 05 April 2013, 15:22:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 15:22:13 UTC |
| 872d00e | Scott Smith | 05 April 2013, 15:22:02 UTC | remove debug code | 05 April 2013, 15:22:02 UTC |
| 1cc4c36 | Malachi Griffith | 05 April 2013, 15:13:47 UTC | clin-seq ignore R files in test case diff | 05 April 2013, 15:13:47 UTC |
| e5f05dc | Scott Smith | 05 April 2013, 15:03:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 April 2013, 15:03:08 UTC |
| 2c3157f | Scott Smith | 05 April 2013, 15:02:48 UTC | Builds now get properties from the model even if a build module with some code exists. | 05 April 2013, 15:03:01 UTC |
