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Last active April 16, 2017 22:49
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Bootstrap file with RPM package install
# vim: ts=4 sw=4 noet
# Stanford Quake Lab bufferbox workflow container bootstrap
BootStrap: yum
OSVersion: 7
Include: perl unzip
TMPDIR=`mktemp -d`
echo 'Downloading the workflow software...'
curl -o ${SINGULARITY_ROOTFS}/tmp/ ''
echo 'Downloading bcl2fastq package...'
curl -o ${TMPDIR}/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm '' || exit 1
echo 'Installing bcl2fastq...'
rpm --root=${SINGULARITY_ROOTFS} -i ${TMPDIR}/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm
rm ${TMPDIR}/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm
rmdir ${TMPDIR}
echo 'Unpacking and moving workflow software...'
mkdir /workflow
unzip /tmp/
mv quake-bufferbox-workflow-release*/* /workflow/
echo 'Removing workflow archive...'
rmdir quake-bufferbox-workflow-release*
rm /tmp/
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