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@akkornel
Last active April 16, 2017 22:53
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Bootstrap with RPM package install happening inside the container
# 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 rpm unzip
%setup
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 ${SINGULARITY_ROOTFS}/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
%post
echo 'Unpacking and moving workflow software...'
mkdir /workflow
unzip /tmp/quake-bufferbox-workflow.zip
mv quake-bufferbox-workflow-release*/* /workflow/
echo 'Installing bcl2fastq'
rpm -i bcl2fastq.rpm
echo 'Cleaning up'
rm bcl2fastq.rpm
rmdir quake-bufferbox-workflow-release*
rm /tmp/quake-bufferbox-workflow.zip
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