Make gad version variable available in a singularity-compatible manner and modify help

python_3.9.def

@@ -2,7 +2,7 @@ Bootstrap: docker
 From: centos:8
 
 %help 
-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.
 Authors : valentin.vautrot@u-bourgogne.fr
 
@@ -14,16 +14,15 @@ 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 v2.10.0 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-*
 
@@ -35,7 +34,7 @@ dnf update -y --exclude=filesystem
 dnf remove -y python3 && dnf autoremove
 dnf install -y python39 git-2.27.0-1.el8.x86_64
 
-# install non-pip python packages
+# install custom gapipeline packages
 git clone --branch ${GAD_VERSION} http://gitlab.gad-bioinfo.org/gad/gadpipeline.git /data/gadpipeline/
 
 mv -v /data/gadpipeline/common/GeneralTools.py /data/gadpipeline/common/LabkeyTools.py /data/gadpipeline/common/InterTools.py /data/gadpipeline/common/VcfTools.py /data/gadpipeline/common/CnvTools.py /usr/lib/python3.9/site-packages/
@@ -56,6 +55,7 @@ pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ simplejson
 rm -rf /data/
 
 %test
+GAD_VERSION=2.11.0
 echo "python version :"
 python3 -V
 echo "listing installed pip packages :"