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/
install.sh
executable file
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/
install.sh
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#!/bin/bash
#
# Install all the programs required for the install of the program.
#
ORIG_DIR=`pwd`
# Argument to build each function
# $1 program name
# $2 folder
change_folder(){
cd $1
}
check_success(){
"$@"
status=$?
if [ $status -ne 0 ]; then
echo "error with $1"
exit 1
fi
return $status
}
orig_dir(){
cd $ORIG_DIR
}
mkdir -p bin
mkdir -p lib/perl5
echo "Installing Dependencies"
echo "Install Zlib"
tar xzf src/zlib-1.2.8.tar.gz
prefix_zlib=${ORIG_DIR}
change_folder zlib-1.2.8
echo $PWD
check_success ./configure --prefix=${ORIG_DIR}
check_success make install
orig_dir
rm -Rf zlib-1.2.8
echo "Installing VCF tools"
tar xzf src/vcftools.tar.gz
LIB_VAR="-lz -L${ORIG_DIR}/lib -I${ORIG_DIR}/include"
change_folder vcftools_0.1.11
check_success make LIB="${LIB_VAR}"
orig_dir
cp vcftools_0.1.11/bin/* bin/
cp vcftools_0.1.11/perl/*pm lib/perl5/
rm -Rf vcftools_0.1.11
echo "Installing VCFlib"
unzip src/vcflib.zip
cp vcflib-master/bin/vcfsnps bin/
chmod 755 bin/vcfsnps
rm -Rf vcflib-master
echo "Installing QCTool"
if [ `uname` = "Darwin" ]; then
tar xzf src/qctool_v1.4-osx.tgz
mv qctool_v1.4-osx/qctool bin/
rm -Rf qctool_v1.4-osx
else
tar xzf src/qctool_v1.4-linux-x86_64.tgz
mv qctool_v1.4-linux-x86_64/qctool bin/
rm -Rf qctool_v1.4-linux-x86_64
fi
echo "Installing Shapeit"
if [ `uname` = "Darwin" ]; then
wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r790.MacOSX.tgz
tar xzf shapeit.v2.r790.MacOSX.tgz
rm shapeit.v2.r790.MacOSX.tgz
mv shapeit bin/
rm -Rf shapeit.v2.r790.MacOSX.tgz
else
echo `uname`
http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/old_versions/shapeit.v2.r790.Ubuntu_12.04.4.static.tar.gz
#wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r790.Ubuntu_12.04.4.static.tar.gz
tar xzf shapeit.v2.r790.Ubuntu_12.04.4.static.tar.gz
rm shapeit.v2.r790.Ubuntu_12.04.4.static.tar.gz
mv shapeit bin/
rm -Rf shapeit.v2.r790.Ubuntu_12.04.4.static.tar.gz
fi
rm -Rf example
rm -f LICENCE
echo "Installing PLINK"
if [ `uname` = "Darwin" ]; then
unzip src/plink-1.07-mac-intel.zip
cp plink-1.07-mac-intel/plink bin/
rm -Rf plink-1.07-mac-intel
else
unzip src/plink-1.07-x86_64.zip
cp plink-1.07-x86_64/plink bin/
rm -Rf plink-1.07-x86_64
fi
echo "Installing Impute2"
if [ `uname` = "Darwin" ]; then
tar xzf src/impute_v2.3.1_MacOSX_Intel.tgz
mv impute_v2.3.1_MacOSX_Intel/impute2 bin/
rm -Rf impute_v2.3.1_MacOSX_Intel
else
tar xzf src/impute_v2.3.1_x86_64_static.tgz
mv impute_v2.3.1_x86_64_static/impute2 bin/
rm -Rf impute_v2.3.1_x86_64_static/
fi
chmod 755 bin/impute2
echo "Installing Tabix"
tar -xjf src/tabix.tar.bz2
change_folder tabix-0.2.6
check_success make LIBPATH="${LIB_VAR}"
orig_dir
cp tabix-0.2.6/bgzip bin/
cp tabix-0.2.6/tabix bin/
rm -Rf tabix-0.2.6
echo "Installing Variscan"
if [ `uname` = "Darwin" ]; then
echo "Cannot install on OSX"
else
tar -xzf src/variscan-2.0.3.tar.gz
(cd variscan-2.0.3/src/ && rm *o)
change_folder variscan-2.0.3
check_success bash autogen.sh && make
orig_dir
mv variscan-2.0.3/src/variscan bin/
rm -Rf variscan-2.0.3
fi
echo "Installing Beagle"
cp src/beagle.jar bin/
echo "Installing getopt"
check_success Rscript src/R_dependencies.R 'getopt'
echo "Installing old rehh"
check_success Rscript src/R_dependencies.R 'rehh'
echo "Install rehh"
check_success R CMD INSTALL src/rehh_1.11.tar.gz
echo "Updating submodules"
git submodule init
git submodule update
echo "Generating Default Config File"
# Because PWD contains slashes (/) need to use # as substitution
sed 's#!SELECT_PIPELINE!#'"${PWD}"'#g' src/defaults.cfg > defaults.cfg
if [[ $EUID -eq 0 ]]; then
echo "Installing PyFasta"
change_folder pyfasta
check_success python setup.py install
orig_dir
echo "Installing PyVCF"
change_folder PyVCF
check_success python setup.py install
orig_dir
echo "Installing selection_pipeline"
check_success python setup.py install
else
echo "Installing PyFasta"
change_folder pyfasta
check_success python setup.py install --user
orig_dir
change_folder PyVCF
echo "Install PyVCF"
check_success python setup.py install --user
orig_dir
echo "Installing selection_pipeline"
check_success python setup.py install --user
fi