Bootstrap file with RPM package install

bootstrap.def

# vim: ts=4 sw=4 noet
# Stanford Quake Lab bufferbox workflow container bootstrap

BootStrap: yum
OSVersion: 7
MirrorURL: http://yum.stanford.edu/mrepo/centos%{OSVERSION}-x86_64/RPMS.all/
GPG: https://www.centos.org/keys/RPM-GPG-KEY-CentOS-7
Include: perl unzip

%setup
	TMPDIR=`mktemp -d`
	echo 'Downloading the workflow software...'
	curl -o ${SINGULARITY_ROOTFS}/tmp/quake-bufferbox-workflow.zip 'https://code.stanford.edu/research-computing-public/quake-bufferbox-workflow/repository/archive.zip?ref=release%2F1'
	echo 'Downloading bcl2fastq package...'
	curl -o ${TMPDIR}/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm 'https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm' || exit 1
	echo 'Installing bcl2fastq...'
	rpm --root=${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}

%post
	echo 'Unpacking and moving workflow software...'
	mkdir /workflow
	unzip /tmp/quake-bufferbox-workflow.zip
	mv quake-bufferbox-workflow-release*/* /workflow/
	echo 'Removing workflow archive...'
	rmdir quake-bufferbox-workflow-release*
	rm /tmp/quake-bufferbox-workflow.zip