Complete bootstrap definition file, with runscript

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

%setup
	TMPDIR=`mktemp -d`
	echo "(Files being downloaded to ${TMPDIR})"

	echo 'Downloading and unpacking the workflow software...'
	curl -o ${TMPDIR}/quake-bufferbox-workflow.zip 'https://code.stanford.edu/research-computing-public/quake-bufferbox-workflow/repository/archive.zip?ref=release%2F1'
	unzip ${TMPDIR}/quake-bufferbox-workflow.zip -d ${TMPDIR}
	mkdir ${SINGULARITY_ROOTFS}/workflow
	mv ${TMPDIR}/quake-bufferbox-workflow-release*/* ${SINGULARITY_ROOTFS}/workflow/

	echo 'Downloading and installing bcl2fastq package...'
	curl -o ${TMPDIR}/bcl2fastq.rpm 'https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2.19.0.316-Linux-x86_64.rpm' || exit 1
	rpm --root ${SINGULARITY_ROOTFS} -i ${TMPDIR}/bcl2fastq.rpm

	echo 'Downloading and installing EPEL key and release package...'
	curl -o ${TMPDIR}/epel-key.gpg 'https://getfedora.org/static/352C64E5.txt'
	curl -o ${TMPDIR}/epel-release.rpm -L 'https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm'
	rpm --root ${SINGULARITY_ROOTFS} --import ${TMPDIR}/epel-key.gpg
	rpm --root ${SINGULARITY_ROOTFS} -i ${TMPDIR}/epel-release.rpm

	echo 'Installing EPEL-based packages'
	yum --installroot ${SINGULARITY_ROOTFS} -y install perl-Email-MIME perl-Email-Send

	echo 'Cleaning up'
	rmdir ${TMPDIR}/quake-bufferbox-workflow-release*
	rm ${TMPDIR}/quake-bufferbox-workflow.zip
	rm ${TMPDIR}/bcl2fastq.rpm
	rm ${TMPDIR}/epel-key.gpg ${TMPDIR}/epel-release.rpm
	rmdir ${TMPDIR}

%runscript
	#!/bin/bash
	if [ $# -eq 0 ]; then
		echo 'Hello!  This is the Mr. Workflow runscript.'
		echo 'Please run this again, with either "NextSeq" or "MiSeq" as the next parameter.'
		echo 'That will run either the NextSeq workflow script, or the MiSeq workflow script.'
		echo 'For example (if the container is called "container.img"):'
		echo '    ./container.img nextseq scan path/to/runfolders'
		echo '    ./container.img miseq deliver path/to/a/runfolder'
		exit 0
	fi
	case "${1,,}" in
	miseq)
		shift
		exec /workflow/bbox-workflow-miseq $*
		;;
	nextseq)
		shift
		exec /workflow/bbox-workflow-nextseq $*
		;;
	*)
		echo "I'm sorry; I didn't recognize what you want me to do."
		echo "Please make 'nextseq' or 'miseq' the first argument, before anything else (like 'run' or 'scan')."
		echo 'Thanks!'
		exit 1
	;;
	esac
	# Nothing should ever reach here!