GISTIC-Installation.md

1. Install the required linux library

apt-get install libxmu-dev

2. Install matlab component runtime

From the directory ([MCR dir]) with instal script run:

 ./install -mode silent -agreeToLicense yes

3. Update environment variables

On the target computer, append the following to your LD_LIBRARY_PATH environment variable:

/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64

Next, set the XAPPLRESDIR environment variable to the following value:

/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/X11/app-defaults

export LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/sys/java/jre/glnxa64/jre/lib/amd64

export XAPPLRESDIR=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v80/X11/app-defaults

4. Example run of gistic

From [GISTIC dir]:

basedir=/Users/Noushin/Dropbox/clonal-evolution/mouse-2014/src/GISTIC/example_results
thisdir=$(pwd)
export segfile=$thisdir/examplefiles/segmentationfile.txt
export cnvfile=$thisdir/examplefiles/cnvfile.txt
export markersfile=$thisdir/examplefiles/markersfile.txt
export alf=$thisdir/examplefiles/arraylistfile.txt
export refgenefile=$thisdir/refgenefiles/hg16.mat
./gp_gistic2_from_seg -b $basedir -seg $segfile -mk $markersfile -refgene $refgenefile -alf $alf -cnv $cnvfile -genegistic 1 -smallmem 1 -broad 1 -brlen 0.5 -conf 0.90 -armpeel 1 -savegene 1 -gcm extreme

5. Specilized data objeccts (Mouse Genome):

ftp://ftp.broadinstitute.org/pub/GISTIC2.0/refgenes/mm9_v0.2_refgene.tgz