Retrieve custom pipeline python packages from remote git clone instead of own's local repository

python_3.9.def

@@ -21,15 +21,9 @@ Other custom GAD packages include GeneralTools, LabkeyTools, InterTools, VcfTool
 SINGULARITY_ROOTFS=$APPTAINER_ROOTFS
 mkdir ${SINGULARITY_ROOTFS}/data
 
-%files
-# import custom python packages from local machine
-/home/valentinv/Documents/GitLab/gadpipeline/common/GeneralTools.py /data/
-/home/valentinv/Documents/GitLab/gadpipeline/common/LabkeyTools.py /data/
-/home/valentinv/Documents/GitLab/gadpipeline/common/InterTools.py /data/
-/home/valentinv/Documents/GitLab/gadpipeline/common/VcfTools.py /data/
-/home/valentinv/Documents/GitLab/gadpipeline/common/CnvTools.py /data/
-
 %post
+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-*
 
@@ -39,18 +33,15 @@ dnf update -y --exclude=filesystem
 # filesystem packages updates poses problems by tempering with /proc, which is supposed to be owned by root, but is not in the .sif image
 
 dnf remove -y python3 && dnf autoremove
-dnf install -y python39
+dnf install -y python39 git-2.27.0-1.el8.x86_64
 
 # install non-pip python packages
-mv /data/GeneralTools.py /usr/lib/python3.9/site-packages/
-mv /data/LabkeyTools.py /usr/lib/python3.9/site-packages/
-# import of LabkeyTools.py in python3 causes error (TabError - indentation). Probably compatibility problem from python2
-mv /data/InterTools.py /usr/lib/python3.9/site-packages/
-mv /data/VcfTools.py /usr/lib/python3.9/site-packages/
-mv /data/CnvTools.py /usr/lib/python3.9/site-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/
 
 # install python pip packages
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ labkey
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ labkey==1.4.0
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ numpy
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ matplotlib
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pandas
@@ -62,13 +53,14 @@ pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pyvcf
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ simplejson
 
 #cleaning
-rmdir /data/
+rm -rf /data/
 
 %test
 echo "python version :"
 python3 -V
 echo "listing installed pip packages :" 
 python3 -m pip list 
+echo "Version of gadpipeline used to create this image: \"${GAD_VERSION}\", to retrieve custom gadpipeline python packages"
 
 %labels 
 Contained_OS_version CentOS_8.5.211