yunzhengluoyi / mutect Goto Github PK

# make a new source directory (e.g. mutect-src)
mkdir mutect-src
cd mutect-src

# get MuTect source
git clone [email protected]:broadinstitute/mutect.git

# get the GATK source and set to the latest tested version
git clone [email protected]:broadgsa/gatk-protected.git
cd gatk-protected
git reset --hard 3.1 

# build the GATK first and install it to the local mvn repo.  Once GATK publishes to a public repo this will be much simpler
mvn -Ddisable.queue install

# build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)
cd ../mutect
mvn verify

# run integration tests, if you like
./run_regression.pl
./tieout_regression.pl