Core modules used by the GMS
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alignment_summary @ 8932081 adding submodule alignment_summary Aug 31, 2012
bam-readcount @ c044123 adding submodule bam-readcount Aug 31, 2012
bam-window @ 572bfaf reset bam-window submodule to origin/master Feb 11, 2013
bassovac @ 41b7bc4 adding submodule bassovac Aug 31, 2012
bin Remove "Workflow" from comments and output for version check. Mar 28, 2017
bmm @ 311e4d9 sciClone bmm and vendor/r-cran-normt3 update Jul 24, 2013
breakdancer @ 8f07f3d advance breakdancer Nov 22, 2012
configuration-manager @ f719544 updated configuration-manager submodule to f719544 Mar 4, 2013
copyCat @ 78b25a7 set copyCat pointer to master, old one was broken Apr 22, 2013
cron @ 584bc07 remove die condition in vcf Backfill Mar 6, 2014
etc/genome/spec Remove obsolete spec for "model_root". Mar 28, 2018
fqgrep @ fe0206d adding submodule fqgrep Aug 31, 2012
genome-db-cosmic @ bdec904 adding submodule genome-db-cosmic Aug 31, 2012
genome-db-omim @ d9b949a adding submodule genome-db-omim Aug 31, 2012
genome-db-pfam @ e5acfb0 adding submodule genome-db-pfam Aug 31, 2012
genome-env-tests Update tests to stop testing for workflow options. Dec 5, 2016
genome-music-testdata @ 860ea75 adding submodule genome-music-testdata Aug 31, 2012
genome-music/gmt-web pruning history to eliminate protected data from branch Aug 31, 2012
genome-snapshot-deps @ 7d13e9e update genome-snapshot-deps Sep 5, 2014
genome-snapshot-testdata @ 72c0ded adding submodule genome-snapshot-testdata Aug 31, 2012
genome-sys-user pruning history to eliminate protected data from branch Aug 31, 2012
genome-webserver Remove "dev_mode" configuration. Sep 6, 2016
genome-www change `env` prefixes to XGENOME_ May 18, 2015
getopt-complete @ 2dc69f2 updated getopt-complete submodule to 2dc69f2 Jun 26, 2014
gms-config @ 6ccaa62 updated gms-config submodule to 6ccaa62 Mar 4, 2013
gmt-sys-vmbuilder change `env` prefixes to XGENOME_ May 18, 2015
graphite @ 705afc6 updated graphite submodule to 705afc6 Mar 6, 2017
hooks hard code to /usr/bin/perl Dec 31, 2013
init pruning history to eliminate protected data from branch Aug 31, 2012
jenkins @ 80b7ba2 updated jenkins submodule to 80b7ba2 Mar 6, 2017
joinx @ e83e763 submodules -> latest Sep 14, 2012
lib Remove DeNovoAssembly UploadToDacc command. Oct 4, 2018
pairoscope @ 5fdcd27 update pairoscope submodule to latest version Jul 3, 2013
sciClone @ 723cadc sciClone bmm and vendor/r-cran-normt3 update Jul 24, 2013
scripts moved to jenkins repo Dec 3, 2012
sff2fastq @ b815f97 adding submodule sff2fastq Aug 31, 2012
somatic-sniper @ b83aab3 point to latest version and docs Jul 5, 2013
sqitch updated sqitch/genome submodule to 734c786 Oct 28, 2015
tgi-etc @ 08ba1a6 adding submodule tgi-etc Aug 31, 2012
tigra @ 6fe6b74 adding submodule tigra Aug 31, 2012
tigra-sv @ 715dda8 update submodule pointers Oct 16, 2012
ur @ b63a182 updated ur submodule to b63a182 Aug 22, 2016
varscan @ 83ae9d8 adding submodule varscan Aug 31, 2012
vendor add vendor/star to submodules Apr 29, 2014
workflow @ c0f1230 updated workflow submodule to c0f1230 Oct 15, 2015
.gitignore cleanup and changes to .gitignore Jun 17, 2013
.gitmodules move sqitch/gms to submodule sqitch/genome Feb 9, 2015
.mailmap add .mailmap Feb 19, 2013
.test-tracker.conf Update lsf_log_dir for test-tracker configuration. Sep 26, 2018
LICENSE pruning history to eliminate protected data from branch Aug 31, 2012
README one less so Sep 30, 2014
WHERE_TO_PUT_CODE pruning history to eliminate protected data from branch Aug 31, 2012
create-c-project.sh pruning history to eliminate protected data from branch Aug 31, 2012
create-project pruning history to eliminate protected data from branch Aug 31, 2012
test-data-relocate-me update symlink so it used current GENOME_TEST_INPUTS Dec 12, 2014

README

# Genome

Genome analysis software from The Genome Institute at Washington University
School of Medicine, funded by the National Human Genome Research Institute.

## Testing

Running tests currently depends on many TGI resources so testing cannot be
performed outside TGI at this time.  Within TGI you can run tests by doing,

    genome-test-env test-tracker prove --lsf --git

This chains the `genome-test-env` and `test-tracker` commands together.  See
`test-tracker prove --help` for its usage.  For example, you may need to pass a
value to the `--git` option if your branch is not setup to track
`origin/master`.