This is a singularity container packing a python 3.9.6 (only version) environment with all the packages necessary to execute all the python scripts present in the version 2.10.0 of the gad pipeline.
This is a singularity container packing a python 3.9.6 (only version) environment with all the packages necessary to execute all the python scripts present in the version 2.11.0 of the gad pipeline.
Python v3.9.6 is the latest available version in CentOS v8.5.211 used for this build.
Other custom GAD packages include GeneralTools, LabkeyTools, InterTools, VcfTools, CnvTools from v2.10.0 of the gadpipeline, modified to work with python3.9
(= from the 2.11.0_python3 branch)
Other custom GAD packages include GeneralTools, LabkeyTools, InterTools, VcfTools, CnvTools from v2.11.0 of the gadpipeline.
%setup
SINGULARITY_ROOTFS=$APPTAINER_ROOTFS
mkdir ${SINGULARITY_ROOTFS}/data
%post
# since singularity is not compatible with the %arguments sections, GAD_VERSION has to be redifined in %post and %test section if changed, not to mention adaptation of the %help section
GAD_VERSION=2.11.0
sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*