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Bootstrap with RPM package install happening inside the container
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# 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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