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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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