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install.sh
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install.sh
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#!/usr/bin/env sh
rm -rf bin/;
mkdir bin/;
cd include
echo 'building zlib'
cd zlib-*/;
make clean;
./configure --prefix=`pwd`
make;
cd ..;
echo 'building samtools'
cd samtools-*/;
make clean;
make;
cd ..;
cd ..;
cd src/;
echo 'building ATCGmapMerge'
g++ ATCGmapMerge.cpp -o ../bin/ATCGmapMerge -lz -L ../include/zlib-1.2.8
echo 'building CGmapSelectByRegion'
g++ CGmapSelectByRegion.cpp -o ../bin/CGmapSelectByRegion
echo 'building CGmapMethInBed'
g++ CGmapMethInBed.cpp -o ../bin/CGmapMethInBed
echo 'building CGmapMethInFragReg'
g++ CGmapMethInFragReg.cpp -o ../bin/CGmapMethInFragReg
echo 'building CGmapFromBAM'
gcc -o ../bin/CGmapFromBAM CGmapFromBAM.c -lz -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18;
echo 'building CGmapToCGbz'
gcc -o ../bin/CGmapToCGbz CGmapToCGbz.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
echo 'building CGbzToCGmap'
gcc -o ../bin/CGbzToCGmap CGbzToCGmap.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
echo 'building ATCGmapToATCGbz'
gcc -o ../bin/ATCGmapToATCGbz ATCGmapToATCGbz.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
echo 'building ATCGbzToATCGmap'
gcc -o ../bin/ATCGbzToATCGmap ATCGbzToATCGmap.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
echo 'building CGbzFetchRegion'
gcc -o ../bin/CGbzFetchRegion CGbzFetchRegion.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
echo 'building ATCGbzFetchRegion'
gcc -o ../bin/ATCGbzFetchRegion ATCGbzFetchRegion.c -L ../include/zlib-1.2.8 -lbam -L ../include/samtools-0.1.18 -lz
cd ..
cd bin
for pr in ../src/*.py ../src/*.pl ../src/*.R; do
pn=`basename $pr | cut -d"." -f1`
echo 'building '`basename $pn`
ln -s $pr $pn
chmod +x $pn
done
cd ..