Commit 01ba0654 authored by Valentin Vautrot's avatar Valentin Vautrot

Modify setup and gad_version variable provision (here 2.11.0_python3) in python3.9 def file

parent 1eb92924
......@@ -14,15 +14,16 @@ singularity exec -e /path/to/this/sif/image python3 -m pip list installed
or
singularity test /path/to/this/sif/image
Other custom GAD packages include GeneralTools, LabkeyTools, InterTools, VcfTools, CnvTools from v2.11.0 of the gadpipeline.
Other custom GAD packages include GeneralTools, LabkeyTools, InterTools, VcfTools, CnvTools from a specific version of the gadpipeline (see test section)
%setup
SINGULARITY_ROOTFS=$APPTAINER_ROOTFS
mkdir ${SINGULARITY_ROOTFS}/data
%post
# since singularity is not compatible with the %arguments sections, GAD_VERSION has to be redifined in %post and %test section if changed, not to mention adaptation of the %help section
GAD_VERSION=2.11.0
mkdir /data
export GAD_VERSION=2.11.0_python3
echo "export GAD_VERSION=${GAD_VERSION}" >> ${SINGULARITY_ENVIRONMENT}
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-*
......@@ -56,7 +57,6 @@ pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ modified-thompson-
rm -rf /data/
%test
GAD_VERSION=2.11.0
echo "python version :"
python3 -V
echo "listing installed pip packages :"
......
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