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Singularity
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Singularity
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Bootstrap: docker
From: centos:latest
%files
./apps_recipes/bwa_v0.7.17_centos7.scif /opt
./apps_recipes/samtools_v1.9_centos7.scif /opt
./apps_recipes/bcftools_v1.9_centos7.scif /opt
%post
echo "Install basic development tools"
yum -y groupinstall "Development Tools"
yum -y update && yum -y install wget curl
echo "Install python2.7 setuptools and pip"
yum -y install python-setuptools
easy_install pip
echo "Installing SCI-F"
pip install scif
echo "Installing bwa app"
scif install /opt/bwa_v0.7.17_centos7.scif
# Executables must be exported for nextflow, if you use their singularity native integration.
# It will be cool to use $SCIF_APPBIN_bwa variable, but it must be set after PATH variable, because I tried to use it here and in %environment without success.
echo 'export PATH=${PATH}:/scif/apps/bwa/bin' >> $SINGULARITY_ENVIRONMENT
echo "Installing samtools app"
scif install /opt/samtools_v1.9_centos7.scif
echo 'export PATH=${PATH}:/scif/apps/samtools/bin' >> $SINGULARITY_ENVIRONMENT
echo "Installing bcftools app"
scif install /opt/bcftools_v1.9_centos7.scif
echo 'export PATH=${PATH}:/scif/apps/bcftools/bin' >> $SINGULARITY_ENVIRONMENT
%runscript
exec scif "$@"