08b7a20 | Eddie Belter | 09 December 2015, 21:08:13 UTC | Merge pull request #1153 from ernfrid/blessed_process_update update blessed process to account for new N-caller and VAF fixes | 09 December 2015, 21:08:13 UTC |
a3beeff | Dave Larson | 09 December 2015, 19:24:47 UTC | update blessed process to account for new N-caller and VAF fixes | 09 December 2015, 19:24:47 UTC |
44ce7eb | Feiyu Du | 09 December 2015, 18:33:21 UTC | Merge pull request #1149 from dufeiyu/tcga TCGA Priorities: Add dump_vcfs option to create sdrf file only | 09 December 2015, 18:33:21 UTC |
86ff863 | Thomas B. Mooney | 09 December 2015, 18:26:04 UTC | Merge pull request #1148 from tmooney/somatic_validation_subject_mapping_exporter SomaticValidation SubjectMapping Exporter | 09 December 2015, 18:26:04 UTC |
3981829 | Anthony Brummett | 09 December 2015, 14:26:45 UTC | Merge pull request #1066 from brummett/model-create-delete Model create delete | 09 December 2015, 14:26:45 UTC |
6dd2e61 | Feiyu Du | 08 December 2015, 19:45:20 UTC | print vcf manifest only if dump_vcfs is true | 08 December 2015, 19:45:20 UTC |
179a670 | Dave Larson | 08 December 2015, 19:41:12 UTC | Merge pull request #1096 from ernfrid/readcount_annotation_fix Readcount annotation fix | 08 December 2015, 19:41:12 UTC |
e08bbac | Dave Larson | 08 December 2015, 19:27:24 UTC | Merge pull request #1098 from ernfrid/igv_session_labeling Attempt to fix Trio Reporting IGV labels | 08 December 2015, 19:27:24 UTC |
6a111cd | Dave Larson | 08 December 2015, 19:27:12 UTC | Merge pull request #1080 from apregier/ncallers-fix Ncallers fix | 08 December 2015, 19:27:12 UTC |
e1b44e8 | Feiyu Du | 08 December 2015, 19:17:51 UTC | more changes requested by Mike | 08 December 2015, 19:17:51 UTC |
65adb3d | Feiyu Du | 08 December 2015, 16:33:44 UTC | add dump_vcfs option to create sdrf file only | 08 December 2015, 16:33:44 UTC |
7c6f95a | Thomas Mooney | 08 December 2015, 16:03:14 UTC | Use a common test for both importing and exporting somval mappings. | 08 December 2015, 16:03:14 UTC |
e2147c9 | Thomas Mooney | 08 December 2015, 16:00:58 UTC | Don't print warnings for missing values. | 08 December 2015, 16:00:58 UTC |
0b58923 | Thomas Mooney | 08 December 2015, 15:57:40 UTC | New command to export subject mappings back out. (This will only work for somatic-validation subject mappings previously created with the import command. Any others will produce a bad file.) | 08 December 2015, 15:57:40 UTC |
c45c580 | Thomas Mooney | 08 December 2015, 15:13:07 UTC | Remove unused "use Genome::Command::Crud". | 08 December 2015, 15:13:07 UTC |
ce86c75 | APipe Tester | 07 December 2015, 22:56:31 UTC | updated ur submodule to 1eb3c02 | 07 December 2015, 22:56:31 UTC |
9d99a0e | Chris Miller | 07 December 2015, 22:43:28 UTC | Merge pull request #1138 from chrisamiller/cn updating path to bam-window cmd in help | 07 December 2015, 22:43:28 UTC |
0cd0ed1 | Adam Coffman | 07 December 2015, 20:58:47 UTC | Merge pull request #1147 from acoffman/alias_metric_name Make name/value accessors consistent for differing metric types. | 07 December 2015, 20:58:47 UTC |
8c1247c | Adam Coffman | 04 December 2015, 22:18:05 UTC | alias metric name and value for a consistent interface | 07 December 2015, 16:41:44 UTC |
c66de64 | Thomas B. Mooney | 07 December 2015, 16:32:23 UTC | Merge pull request #1143 from tmooney/remove_disk_allocations_from_test_db_remembers_testdb RemoveDiskAllocationsFromTestDb remembers which TestDB was used. | 07 December 2015, 16:32:23 UTC |
4443f2b | Thomas B. Mooney | 07 December 2015, 15:01:46 UTC | Merge pull request #1145 from tmooney/analysis_project_view_includes_status Include status in `genome analysis-project view` output | 07 December 2015, 15:01:46 UTC |
d68906e | APipe Tester | 04 December 2015, 22:25:36 UTC | updated ur submodule to 3f3ca68 | 04 December 2015, 22:25:36 UTC |
eb1c0f6 | Feiyu Du | 04 December 2015, 20:10:01 UTC | Merge pull request #1146 from dufeiyu/tcga TCGA Priorities: Put lookup hash by bam base name in cache | 04 December 2015, 20:10:01 UTC |
187baeb | Feiyu Du | 04 December 2015, 19:03:24 UTC | Put lookup hash by bam base name in cache | 04 December 2015, 19:03:24 UTC |
a5da876 | Dave Larson | 04 December 2015, 18:58:02 UTC | revert calculated vaf changes. These don't count properly for SNVs when bam-readcount isn't run in insertion-centric mode. bam-readcount needs to be fixed. | 04 December 2015, 18:58:02 UTC |
8d5e553 | Feiyu Du | 04 December 2015, 16:52:07 UTC | Merge pull request #1144 from dufeiyu/tcga TCGA Priorities: Add alternative way to get cghub id | 04 December 2015, 16:52:07 UTC |
eabac6a | Feiyu Du | 03 December 2015, 22:07:01 UTC | use scalar variable | 03 December 2015, 22:07:01 UTC |
fcca81f | Thomas Mooney | 03 December 2015, 22:05:00 UTC | Include status in Analysis Project view. | 03 December 2015, 22:05:00 UTC |
2d74b02 | Feiyu Du | 03 December 2015, 21:49:24 UTC | change the order | 03 December 2015, 21:49:24 UTC |
3cfbcc9 | Feiyu Du | 03 December 2015, 21:22:00 UTC | name_in_vcf is the right way to get TCGA names | 03 December 2015, 21:22:00 UTC |
00f66c6 | Feiyu Du | 03 December 2015, 21:06:50 UTC | add an alternative way by using bam base to search | 03 December 2015, 21:06:50 UTC |
1ba62d1 | Eddie Belter | 03 December 2015, 18:15:29 UTC | Merge pull request #1140 from ebelter/anp-release-status AnP: Add status message to release command | 03 December 2015, 18:15:29 UTC |
4646361 | APipe Tester | 03 December 2015, 13:16:46 UTC | Updated `genome` tab completion. | 03 December 2015, 13:16:46 UTC |
fa706f3 | APipe Tester | 03 December 2015, 13:15:11 UTC | Updated class browser cache. | 03 December 2015, 13:15:11 UTC |
0153e30 | Thomas Mooney | 02 December 2015, 21:53:40 UTC | Localize before deleting values. | 02 December 2015, 21:53:40 UTC |
63d7f03 | Eddie Belter | 02 December 2015, 19:19:59 UTC | AnP: release cmd test spell check | 02 December 2015, 19:19:59 UTC |
5095ed3 | Eddie Belter | 02 December 2015, 18:55:11 UTC | AnP: clean up adn update release test | 02 December 2015, 18:57:18 UTC |
a599536 | Eddie Belter | 02 December 2015, 18:54:55 UTC | AnP: add status message to release command | 02 December 2015, 18:54:55 UTC |
dee1ceb | Thomas Mooney | 02 December 2015, 18:31:47 UTC | Whitespace. | 02 December 2015, 18:31:47 UTC |
82f8c13 | Susanna Kiwala | 02 December 2015, 17:01:38 UTC | Merge pull request #846 from susannasiebert/qc_config_management Set up a QC configuration management system | 02 December 2015, 17:01:38 UTC |
83004bc | Susanna Kiwala | 02 December 2015, 16:39:13 UTC | Merge branch 'master' of https://github.com/genome/genome into qc_config_management Conflicts: lib/perl/Genome/Qc/Tool/VerifyBamId.t | 02 December 2015, 16:39:13 UTC |
5a6b97e | Susanna Kiwala | 02 December 2015, 16:30:25 UTC | Merge pull request #1133 from susannasiebert/qc_framework_verify_bam_id_vcf Add optional property to VerifyBamId QC tool to set default genotype vcf file | 02 December 2015, 16:30:25 UTC |
6be04a2 | APipe Tester | 02 December 2015, 13:16:48 UTC | Updated `genome` tab completion. | 02 December 2015, 13:16:48 UTC |
5fb6dee | APipe Tester | 02 December 2015, 13:15:09 UTC | Updated class browser cache. | 02 December 2015, 13:15:09 UTC |
090802b | Eddie Belter | 02 December 2015, 02:44:52 UTC | Merge pull request #1135 from ebelter/instdata-import-wf-builder InstData Import: Convert to use WF Builder | 02 December 2015, 02:44:52 UTC |
a1255c1 | Eddie Belter | 02 December 2015, 01:49:46 UTC | InstData Import: do not pass downsample ratio if unused | 02 December 2015, 01:49:46 UTC |
2dc88c5 | Eddie Belter | 02 December 2015, 01:44:33 UTC | InstData Import: Remove library/sample name from inputs | 02 December 2015, 01:44:37 UTC |
3375b42 | Eddie Belter | 02 December 2015, 01:42:44 UTC | InstData Import Merge Cleanup: use factory to create inputs | 02 December 2015, 01:42:44 UTC |
3264a5a | Eddie Belter | 02 December 2015, 01:34:59 UTC | Merge remote-tracking branch 'origin/master' into instdata-import-wf-builder Conflicts: lib/perl/Genome/InstrumentData/Command/Import/WorkFlow/ArchiveToFastqs.t lib/perl/Genome/InstrumentData/Command/Import/WorkFlow/Inputs.pm lib/perl/Genome/InstrumentData/Command/Import/WorkFlow/Inputs.t lib/perl/Genome/InstrumentData/Command/Import/WorkFlow/Run.pm | 02 December 2015, 01:34:59 UTC |
b1d2b5d | Eddie Belter | 01 December 2015, 21:13:40 UTC | Merge pull request #1112 from ebelter/instdata-inputs2 InstData Import Inputs | 01 December 2015, 21:13:40 UTC |
872f95a | Susanna Kiwala | 01 December 2015, 17:54:55 UTC | Merge pull request #1136 from susannasiebert/qc_framework_verify_bam_id_vcf_part3 Bugfixes for ImportGenotypeVcfFile command | 01 December 2015, 17:54:55 UTC |
fa0fb80 | Chris Miller | 01 December 2015, 17:00:45 UTC | updating path to bam-window cmd in help | 01 December 2015, 17:00:45 UTC |
9037c98 | David Morton | 01 December 2015, 16:46:47 UTC | Merge pull request #1137 from davidlmorton/ptero_cancel_builds Model::Build->stop() now cancels PTero workflows | 01 December 2015, 16:46:47 UTC |
ae16c33 | David Morton | 01 December 2015, 16:46:39 UTC | Merge pull request #1131 from davidlmorton/ptero_lsf_stuffs PTero LSF Stuff | 01 December 2015, 16:46:39 UTC |
56b0c19 | David Morton | 01 December 2015, 14:47:42 UTC | Model::Build->stop() now cancels PTero workflows | 01 December 2015, 14:47:42 UTC |
b133ecd | David Morton | 01 December 2015, 14:20:01 UTC | Use Genome::Config::set_env | 01 December 2015, 14:20:01 UTC |
80f3a61 | APipe Tester | 30 November 2015, 21:46:49 UTC | updated ur submodule to 0346c3e | 30 November 2015, 21:46:49 UTC |
0a3c60b | Susanna Kiwala | 30 November 2015, 16:15:25 UTC | Output the correct id | 30 November 2015, 16:15:25 UTC |
939d1b3 | Susanna Kiwala | 30 November 2015, 16:15:08 UTC | Add reference sequence build to G::Qc::C::ImportGenotypeVcfFile to use as requestor | 30 November 2015, 16:15:08 UTC |
97cd34f | Susanna Kiwala | 30 November 2015, 15:02:16 UTC | Merge pull request #1079 from susannasiebert/epitope_prediction_parser Refactor of epitope prediction NetMHC parser | 30 November 2015, 15:02:16 UTC |
5775399 | Susanna Kiwala | 30 November 2015, 15:01:42 UTC | Fix typo | 30 November 2015, 15:01:42 UTC |
12d953f | APipe Tester | 26 November 2015, 13:16:26 UTC | Updated `genome` tab completion. | 26 November 2015, 13:16:26 UTC |
0517f2b | Eddie Belter | 26 November 2015, 01:14:05 UTC | InstData Import: update builder XML as it differs from WF produced XML. | 26 November 2015, 01:14:05 UTC |
99f869c | Eddie Belter | 26 November 2015, 01:00:18 UTC | InstData Import: convert fastq to use wf builder | 26 November 2015, 01:00:18 UTC |
9ec0c24 | Eddie Belter | 26 November 2015, 00:44:01 UTC | InstData Import: convert downsample bam op addition to use builder | 26 November 2015, 00:44:01 UTC |
232d90e | Eddie Belter | 26 November 2015, 00:39:26 UTC | InstData Import: do not pass downsample ratio through if not defined | 26 November 2015, 00:39:26 UTC |
141dfad | Eddie Belter | 26 November 2015, 00:38:39 UTC | InstData Import: complete conversion of SRA wf to use builder | 26 November 2015, 00:38:39 UTC |
bbd8784 | Eddie Belter | 26 November 2015, 00:37:45 UTC | InstData Import: make wf op class for name accessible by calling from $self | 26 November 2015, 00:37:45 UTC |
15f5fd3 | Eddie Belter | 25 November 2015, 23:06:19 UTC | InstData Import: man command expects dag instead of workflow | 25 November 2015, 23:06:19 UTC |
6580479 | Eddie Belter | 25 November 2015, 23:05:24 UTC | InstData Import: verify not imported source_path is also output | 25 November 2015, 23:05:24 UTC |
f469d67 | Eddie Belter | 25 November 2015, 23:03:02 UTC | InstData Import: use library to get names in fastqs to bam | 25 November 2015, 23:04:35 UTC |
99afd48 | Eddie Belter | 25 November 2015, 22:50:20 UTC | InstData Import: convert to workflow builder | 25 November 2015, 22:50:20 UTC |
b781ce8 | Eddie Belter | 25 November 2015, 22:21:35 UTC | InstData Import: revert inputs factory to ur obect | 25 November 2015, 22:21:44 UTC |
0536797 | Feiyu Du | 25 November 2015, 21:08:12 UTC | Merge pull request #1134 from dufeiyu/lsf_resource_dv2_dispatcher Increase memory limit of lsf_resource_dv2_dispatcher | 25 November 2015, 21:08:12 UTC |
137ee74 | Feiyu Du | 25 November 2015, 20:38:55 UTC | increase mem limit to prevent more build failures | 25 November 2015, 20:38:55 UTC |
306f161 | David Morton | 25 November 2015, 20:14:11 UTC | Add validator for ptero_lsf_polling_interval | 25 November 2015, 20:14:11 UTC |
c00477b | David Morton | 25 November 2015, 20:12:25 UTC | Update test data | 25 November 2015, 20:12:25 UTC |
6da0970 | Susanna Kiwala | 25 November 2015, 20:08:02 UTC | Make default_genotype_vcf_file a G::SR::StageableSimple::SingleFile | 25 November 2015, 20:08:02 UTC |
2103386 | Susanna Kiwala | 25 November 2015, 19:08:19 UTC | Add optional property to VerifyBamId QC tool to set default genotype vcf file This file would be used if no qc_genotype_vcf_file is specified in the build | 25 November 2015, 19:08:19 UTC |
8db4e56 | Thomas B. Mooney | 25 November 2015, 19:06:09 UTC | Merge pull request #1132 from tmooney/bsub_and_wait_completion Add missing word "for" in method name. | 25 November 2015, 19:06:09 UTC |
a469278 | Thomas Mooney | 25 November 2015, 18:21:13 UTC | Add missing word "for" in method name. | 25 November 2015, 18:21:13 UTC |
11e9b33 | Susanna Kiwala | 25 November 2015, 18:09:58 UTC | Merge pull request #1130 from susannasiebert/qc_framework_verify_bam_id_vcf Make QC genotype VCF file an input to the SSG pipeline and use in verifyBamId | 25 November 2015, 18:09:58 UTC |
b0de8e9 | mkiwala | 25 November 2015, 15:53:25 UTC | Merge pull request #1129 from mkiwala/ptero-lsf-parameters Set queue and projectName when getting ptero lsf params | 25 November 2015, 15:53:25 UTC |
ef99a04 | APipe Tester | 25 November 2015, 13:16:39 UTC | Updated `genome` tab completion. | 25 November 2015, 13:16:39 UTC |
1dc02d8 | APipe Tester | 25 November 2015, 13:15:05 UTC | Updated class browser cache. | 25 November 2015, 13:15:05 UTC |
45954b9 | David Morton | 25 November 2015, 06:29:45 UTC | Ensure all lsf jobs for build have projectName set | 25 November 2015, 06:29:45 UTC |
e0bef5e | Thomas B. Mooney | 24 November 2015, 22:26:57 UTC | Merge pull request #1091 from tmooney/unarchive_requires_analysis_project Unarchiving now requires an AnP instead of a lab. | 24 November 2015, 22:26:57 UTC |
7818afb | Thomas B. Mooney | 24 November 2015, 20:58:01 UTC | Merge pull request #1126 from tmooney/haplotype_caller_reserves_lsf_resource Set a default resource request for the BucketIterator. | 24 November 2015, 20:58:01 UTC |
7e274c2 | Susanna Kiwala | 24 November 2015, 20:57:54 UTC | Inputs should be obtained from the build, not the model | 24 November 2015, 20:57:54 UTC |
bb2bb49 | Michael J. Kiwala | 24 November 2015, 20:46:33 UTC | Options in the lsf resource string take precedence | 24 November 2015, 20:46:33 UTC |
f1dd13d | David Morton | 24 November 2015, 20:44:50 UTC | Add ability to set lsf_project_name on ptero lsf jobs | 24 November 2015, 20:44:50 UTC |
94838ac | David Morton | 24 November 2015, 20:35:08 UTC | Ensure polling_interval is number like | 24 November 2015, 20:35:08 UTC |
a2020ea | David Morton | 24 November 2015, 19:49:07 UTC | configurable polling interval for ptero lsf jobs | 24 November 2015, 20:13:04 UTC |
eec8d47 | David Morton | 24 November 2015, 18:56:51 UTC | Merge pull request #1108 from davidlmorton/ptero_integration_tests_command Convert Ptero/IntegrationTest.pl into a Command | 24 November 2015, 18:56:51 UTC |
d1b7b1e | Michael J. Kiwala | 24 November 2015, 17:09:04 UTC | Set queue and projectName when getting ptero lsf params | 24 November 2015, 17:09:04 UTC |
da5e483 | Susanna Kiwala | 24 November 2015, 16:20:42 UTC | Update docs | 24 November 2015, 16:48:22 UTC |
e29383c | Susanna Kiwala | 24 November 2015, 16:07:09 UTC | Test new genotype_vcf_file subroutine for VerifyBamId | 24 November 2015, 16:48:22 UTC |
bdb53f2 | Susanna Kiwala | 24 November 2015, 16:06:32 UTC | New subroutine on VerifyBamID QC tool to use qc_genotype_vcf_file | 24 November 2015, 16:48:22 UTC |
be10d97 | Susanna Kiwala | 24 November 2015, 16:05:54 UTC | Test qc_genotype_vcf_file handling in the SSG QC step | 24 November 2015, 16:48:22 UTC |
7fe7f44 | Susanna Kiwala | 24 November 2015, 16:05:01 UTC | Make qc_genotype_vcf_file an input to the SSG pipeline and pass along to the QC step | 24 November 2015, 16:48:22 UTC |