swh:1:snp:5789d5563ae0ff1fac9d4620526a6e02863df326

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Revision Author Date Message Commit Date
03c13ab set config to test config 24 February 2014, 21:48:43 UTC
b0c1b0f Merge branch 'master' of ssh://git/srv/git/genome 24 February 2014, 20:37:45 UTC
651352e bug fixed 24 February 2014, 20:37:16 UTC
a3d1fc4 Merge branch 'updated' into gb_master 24 February 2014, 20:32:31 UTC
6cf9e49 Remove trailing tabs introduced by intersectBed 24 February 2014, 20:30:46 UTC
7a5b51f Add -v intersect type 24 February 2014, 20:30:45 UTC
bd97a5b Add option to keep header in bed/vcf file 24 February 2014, 20:30:45 UTC
42b7625 Remove trailing whitespace. 24 February 2014, 18:45:58 UTC
7e5dd38 Fixing an edge case where indel readcounts can be reported incorrectly when there are multiple alleles at a single position 22 February 2014, 23:46:55 UTC
2cdf01b Updated `gmt` tab completion. 22 February 2014, 13:17:59 UTC
f71bac1 Updated `genome` tab completion. 22 February 2014, 13:17:15 UTC
92dd197 add samtools vcf file support 21 February 2014, 22:20:14 UTC
77bb9e3 Fix message typo 21 February 2014, 19:27:45 UTC
212225b bugfix: Genome::Model::Tools::FastTier::AddTiers expects a anno file, not bed file delete annoFileToBedFile conversion before calling Genome::Model::Tools::FastTier::AddTiers because the anno file format is correct delete bedFileToAnnoFile after addTiering because the file is already in anno format 21 February 2014, 19:09:00 UTC
426c15e Sort VEP output after annotating sometimes VEP puts out unsorted data. 21 February 2014, 18:40:16 UTC
502a0a8 updated workflow submodule to a98122e 21 February 2014, 16:06:22 UTC
dc11ee1 Updated `gmt` tab completion. 21 February 2014, 13:17:40 UTC
1e1eb32 Updated `genome` tab completion. 21 February 2014, 13:16:52 UTC
79576e5 change clia to cle 20 February 2014, 22:58:10 UTC
3abd50f Update all tools with a joinx_version parameter to have no default and instead ask G:M:T::Joinx for its current default value. This is not ideal because of the copypasted _resolve_joinx_version duplication. But at least the default version is centralized now. 20 February 2014, 22:10:15 UTC
fd3e880 removing stupid header 20 February 2014, 19:42:45 UTC
1f1b84e Updated `genome` tab completion. 20 February 2014, 13:16:56 UTC
6ef656a Fix clinseq module definition to address warnings in Command/Services/WebApp/Core.t 19 February 2014, 22:49:58 UTC
74cb597 updated graphite submodule to ac4c603 19 February 2014, 22:45:32 UTC
b070eea clin-seq - add check for cancer_annotation_db method on rna-seq models before attempting to use 19 February 2014, 22:19:29 UTC
a8dc0e7 add test case for ro intermediate dir 19 February 2014, 21:17:40 UTC
f33e73b preserve errno to prevent an bug if an intermediate system call gets added 19 February 2014, 21:17:40 UTC
f269d80 Disconnect from DB before running workflow. 19 February 2014, 20:37:50 UTC
aeca638 clin-seq - minor update to analysis plan 19 February 2014, 20:17:28 UTC
8f3c3aa add description to the correct analysis menu item table 19 February 2014, 19:15:20 UTC
6bed63c Remove extra quotation marks. Previously Genome::Sys->bsub_and_wait was putting this into ``s, so the quotation marks were necessary. Now it's using IPC::System::Simple, so each string is already a single token in the array of parameters. (This fix is similar to commit 2fa2de5dcd3b9cf470461c7124f7accfd35686a7dd) 19 February 2014, 17:29:33 UTC
2fa2de5 Remove extra quotation marks. Previously Genome::Sys->bsub_and_wait was putting this into ``s, so the quotation marks were necessary. Now it's using IPC::System::Simple, so each string is already a single token in the array of parameters. 19 February 2014, 17:14:38 UTC
bc2da62 Merge branch 'my_annotation' into gb_master 19 February 2014, 17:00:11 UTC
764f139 Update docs 19 February 2014, 16:59:54 UTC
6b30685 Add custom annotation option for vep 19 February 2014, 16:59:53 UTC
1cab51b add description to Analysis menu items 19 February 2014, 16:54:13 UTC
21856e8 Updated `gmt` tab completion. 19 February 2014, 13:18:58 UTC
d301024 Updated `genome` tab completion. 19 February 2014, 13:18:16 UTC
e58a1f1 Updated class browser cache. 19 February 2014, 13:16:44 UTC
b2e5ee0 clin-seq - add variant filter option to snv-indel-report 19 February 2014, 03:33:02 UTC
a4afa7b remove useless command 18 February 2014, 22:14:52 UTC
9ce3064 More robustly tolerate special characters in protein names. 18 February 2014, 21:36:32 UTC
c6e3787 set never rerunnable on build workflow job 18 February 2014, 21:33:54 UTC
fa4f87a add option for rerunnable and never_rerunnable 18 February 2014, 21:33:53 UTC
f2f2555 remove clia column now that it is unused 18 February 2014, 21:32:13 UTC
5c715dd change user_name to run_as in config profile 18 February 2014, 20:30:18 UTC
42f85d9 add a backfill option for adding a menu item to an analysis project 18 February 2014, 20:28:34 UTC
499b1f9 This partially reverts commit 77e03be534ab4b424140bc95879dd9d6d5041b4c. But only the stupid parts that I didn't mean to commit in the first part. Conflicts: lib/perl/Genome/Model/Tools/Analysis/Coverage/AddReadcounts.pm 18 February 2014, 19:38:46 UTC
33f2e00 actually pass the min_quality_score option to BamReadcount.pm 18 February 2014, 19:28:03 UTC
a56d3a7 remove counting with varscan as an option 18 February 2014, 19:03:02 UTC
e0f27b4 fix regex which could identify the wrong indel allele if there were multiple indels that could match the allele string 18 February 2014, 19:03:02 UTC
03ef2f4 add support for launching builds as the run_as user 18 February 2014, 17:31:10 UTC
8caf4ec support launching builds as the run_as user 18 February 2014, 17:31:02 UTC
c7e2a8e remove space between option and value We need to keep the option, e.g. `-g`, connected to the value, e.g. `/apipe-builder`, so that the wrapper that we use to sudo can allow us to securely run commands like: sudo -i bsub [options] annotate-log \ genome model services build run [options] 18 February 2014, 17:31:01 UTC
0f3549b _capture already lazy loads IPC::System::Simple 18 February 2014, 17:31:01 UTC
0ce9c15 support passing in the bsub executable We need to be able to pass in `sudo bsub` so we can't hard-code the executable as `bsub`. 18 February 2014, 17:31:00 UTC
d983c46 refactor to use Genome::Sys::LSF::bsub 18 February 2014, 17:30:59 UTC
c3fe6e7 extract _job_group 18 February 2014, 17:30:59 UTC
aec9d1b Renaming pairing to mapping. 18 February 2014, 17:09:52 UTC
12892a1 updating docs to be more clear on version number 18 February 2014, 14:38:56 UTC
1adcd5f Updated `genome` tab completion. 18 February 2014, 13:16:54 UTC
db7b25e Updated class browser cache. 18 February 2014, 13:15:27 UTC
35afe69 Make the following changes to BreakDancer DetectVariants module: * no longer die if fastqs are empty, but instead throw a warning * add test producing no ctx output 18 February 2014, 06:34:40 UTC
beb7406 tagged deploy 18 February 2014, 00:45:40 UTC
15c5a3b drop m_m_id_user_name_build_requested_index 18 February 2014, 00:42:08 UTC
d85056a drop uniq_m_m_idun index 18 February 2014, 00:42:07 UTC
8b2a595 add index to created_by column 18 February 2014, 00:42:06 UTC
954fcb3 add index to run_as column 18 February 2014, 00:42:05 UTC
7e6e826 remove hostname so password is not required on gms-postgres 18 February 2014, 00:42:03 UTC
9197564 begin migration of Model's user_name to created_by and run_as CHANGELOG: Model now has created_by and run_as properties to distinguish the different use cases user_name was being used for. At this stage of the migration user_name is still functional but it is now deprecated and may be removed in the near future. You should review any scripts you have that might be getting Models with the user_name property and update them to use created_by or run_as instead. 18 February 2014, 00:09:23 UTC
0e02e29 assume run_as is a better replacement than created_by 18 February 2014, 00:09:22 UTC
f187d02 assume run_as is better replacement than created_by 18 February 2014, 00:09:20 UTC
c771f93 assume default alignments care more about run_as than created_by 18 February 2014, 00:09:19 UTC
81e86e8 switch to created_by and run_as in TGI project XML view 18 February 2014, 00:09:17 UTC
b9971f0 switch to using created_by when updating project models 18 February 2014, 00:09:16 UTC
9cdb0fe switch to created_by and run_as in population group XML view 18 February 2014, 00:09:15 UTC
8e93292 switch to created_by and run_as in model Solr view 18 February 2014, 00:09:13 UTC
6f1317d switch to created_by and run_as in model set XML view 18 February 2014, 00:09:12 UTC
767a8e9 switch to created_by and run_by in GoldSnpComparison XML view 18 February 2014, 00:09:11 UTC
6638808 override created_by and run_as in 'export metadata' test 18 February 2014, 00:09:10 UTC
fc809f2 switch "fast" build XML view to use created_by and run_as 18 February 2014, 00:09:08 UTC
1e44005 switch build set XML view to use created_by and run_as 18 February 2014, 00:09:07 UTC
46130ff both created_by and run_as are "affected_users" 18 February 2014, 00:09:05 UTC
ea2d1e8 switch genome model search result view to user created_by and run_as 18 February 2014, 00:09:04 UTC
2134395 switch genome model view to user created_by and run_as 18 February 2014, 00:09:03 UTC
ff9050b ensure defining a model sets run_as and created_by 18 February 2014, 00:09:02 UTC
8112748 add run_as and created_by (to disambiguate user_name) 18 February 2014, 00:09:00 UTC
7f2ebd6 comment out nonsensical test for now 18 February 2014, 00:06:34 UTC
dfc09f9 update CQID to utilize new subject_mapping entities 17 February 2014, 23:58:18 UTC
4e8ce20 Restore clobbered tag. 17 February 2014, 23:52:25 UTC
233e365 Remove SubjectPairings in favor of SubjectMappings 17 February 2014, 23:32:02 UTC
dc6971a Tag the move from pairings to mappings. 17 February 2014, 23:28:45 UTC
7ac86bf Replace subject pairings with subject mappings. This will facilitate running SomVal and other pipelines in more circumstances. 17 February 2014, 23:28:17 UTC
24949b0 rename clia to cle in apconfig 17 February 2014, 21:45:19 UTC
c2cbcd7 add CLE column to analysis projects 17 February 2014, 21:44:26 UTC
2022347 remove unnecessary user_name specifications 17 February 2014, 20:21:54 UTC
fabe186 remove unused feature Method was not called with model argument anywhere. 17 February 2014, 19:41:33 UTC
ad6f606 remove mysterious block of data at end of file 17 February 2014, 19:31:27 UTC
c661e42 updated workflow submodule to a4dfa59 17 February 2014, 19:27:21 UTC
9e7ed41 Resolve race condition in make_path 15 February 2014, 21:45:25 UTC
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