gastic 安装

所有文件下载地址：

ftp://ftp.broadinstitute.org/pub/GISTIC2.0/

cd /home/software/

tar zxf GISTIC_2_0_22.tar.gz

cd GISTIC_2_0_22

#安装MCR环境

./MCRInstaller.bin（安装到当前文件夹中的MATLAB Component Runtime文件夹中）

然后按照 run_gistric_example文件设置环境变量

因为实例文件是csh，我将其改为bash，改动如下：

#!/bin/bash
thisdir=/home/software/gistic/GISTIC_2_0_22
# --- SET UP ENVIRONMENT VARIABLES ---
echo --- setting up environment variables ---
# presumed location of MATLAB Component Runtime (MCR) v7.14
# if the MCR is in a different location, edit the line below
export MCR_HOME=/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime

export LD_LIBRARY_PATH=/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/runtime/glnxa64:/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/sys/os/glnxa64:/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64
export XAPPLRESDIR=/home/software/gistic/GISTIC_2_0_22/MATLAB_Component_Runtime/v714/X11/app-defaults
# 此步的变量写错的话，会报错如下：

./gp_gistic2_from_seg: error while loading shared libraries: libmwmclmcrrt.so: cannot open shared object file: No such file or directory

# --- RUN GISTIC 2.0 ---
echo --- creating output directory ---
basedir=$thisdir/example_results
mkdir -p $basedir

echo --- running GISTIC ---
segfile=$thisdir/examplefiles/segmentationfile.txt
markersfile=$thisdir/examplefiles/markersfile.txt
refgenefile=$thisdir/refgenefiles/hg16.mat
alf=$thisdir/examplefiles/arraylistfile.txt
cnvfile=$thisdir/examplefiles/cnvfile.txt
echo $LD_LIBIARARY_PATH

./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

#文件准备完成后运行

./run_gistric_example

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