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#!/bin/sh -e
if test -x /usr/bin/dnf; then
echo Installing prerequisites via dnf...
dnf -y install epel-release
dnf -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools
elif test -x /usr/bin/yum; then
if yum -y install epel-release; then
echo Installing prerequisites via yum...
yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools
else
echo Installing non-test prerequisites via yum...
yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel
emulate=yes
fi
elif test -d /etc/dpkg; then
echo Installing prerequisites via apt-get...
apt-get update
apt-get install -y --no-install-recommends --no-install-suggests libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev samtools bcftools tabix
elif test -x /sbin/apk; then
echo Installing non-test prerequisites via apk...
apk update
apk add zlib-dev bzip2-dev xz-dev curl-dev openssl-dev
emulate=yes
elif test -x ${HOMEBREW_PREFIX-/usr/local}/bin/brew; then
echo Installing prerequisites via brew...
HOMEBREW_NO_AUTO_UPDATE=1 brew install -q samtools bcftools
brew unlink xz || true
else
echo No package manager detected
fi
if test -n "$emulate" && test $# -ge 2; then
emulator=$1
bindir=$2
echo Creating symlinks to $emulator in $bindir...
mkdir -p $bindir
ln -s $emulator $bindir/samtools
ln -s $emulator $bindir/bcftools
ln -s $emulator $bindir/bgzip
ln -s $emulator $bindir/tabix
fi
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