/
install_deps.sh
executable file
·38 lines (35 loc) · 1.04 KB
/
install_deps.sh
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#!/bin/bash
set -e
TOPLEVEL_DIR=$PWD
mkdir -p deps
############################################
## zlib
wget -c http://zlib.net/zlib-1.2.13.tar.gz
tar xvzf zlib-1.2.13.tar.gz
pushd zlib-1.2.13
./configure --prefix `pwd`/..
make
make install
popd
#############################################
#
if [ ! -e deps/samtools-0.1.19.tar.bz2 ]; then
wget -c https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download -O deps/samtools-0.1.19.tar.bz2
fi
tar jxvf deps/samtools-0.1.19.tar.bz2
pushd samtools-0.1.19
make
make razip
popd
###############################################
# Downloads were failing often so keep a local copy to speedup the installation
echo "Installing samtools 1.x"
if [ ! -e deps/samtools-1.9.tar.bz2 ] ; then
wget -c https://sourceforge.net/projects/samtools/files/samtools/1.9/samtools-1.9.tar.bz2/download -O deps/samtools-1.9.tar.bz2
fi
tar xvjf deps/samtools-1.9.tar.bz2
pushd samtools-1.9
./configure prefix=$TOPLEVEL_DIR
make -j $J
#prefix=$TOPLEVEL_DIR
make install prefix:=$TOPLEVEL_DIR