Commit 9067d85d authored by Holger Brandl's avatar Holger Brandl

updated samtools to 1.5

parent 60a50030
......@@ -4,14 +4,18 @@
## define common binaries
if [ $(hostname) == "bioinformatics-srv1" ]; then
export BIO_BIN_BASE="/local/home/brandl/bin"
elif [[ $(hostname) == *-mac* ]]; then
export BIO_BIN_BASE=~/bin
else
export BIO_BIN_BASE="/projects/bioinfo/holger/bin"
if [ -z ${BIO_BIN_BASE} ]; then echo "BIO_BIN_BASE is not set"; exit 1; fi
fi
export PATH=${BIO_BIN_BASE}/bowtie2-2.2.5:$PATH
export PATH=${BIO_BIN_BASE}/FastQC_0.11.2:$PATH
export PATH=${BIO_BIN_BASE}/bedtools2-2.25.0/bin/:$PATH
export PATH=${BIO_BIN_BASE}/samtools-1.3:$PATH
export PATH=${BIO_BIN_BASE}/samtools-1.5:$PATH
export PATH=${BIO_BIN_BASE}/STAR-2.5.2b/source:$PATH
export PATH=${BIO_BIN_BASE}/ucsc:$PATH # for wigToBigWig
......
......@@ -58,11 +58,15 @@ cd bedtools2-2.25.0
make
samtools
## samtools
cd ~/bin
wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
tar xvf samtools-1.3.1.tar.bz2
cd samtools-1.3.1
wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
tar xvf samtools-1.5.tar.bz2
cd samtools-1.5
make
#on mac
./configure --disable-lzma
make
......
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