Added python 3.9 packages installation up until the end of the CNV section in full_wes v.2.10.0

python_3.9.def

@@ -17,6 +17,8 @@ mkdir ${SINGULARITY_ROOTFS}/data
 /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
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
@@ -30,12 +32,16 @@ dnf remove -y python3 && dnf autoremove
 # by safety but useless, "python3" not found. The python3 present in /usr/bin in final image is created with python3.9 install, so it is only a dependency ? python3 --version is 3.9.6 alright.
 dnf install -y python39
 
-# copy non-pip python packages
-cp /data/GeneralTools.py /usr/lib/python3.9/site-packages/
-cp /data/LabkeyTools.py /usr/lib/python3.9/site-packages/
+# 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 with python2
-cp /data/InterTools.py /usr/lib/python3.9/site-packages/
+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/
+rmdir /data/
 
 # install python pip packages
 pip3.9 install -t /usr/lib/python3.9/site-packages/ labkey
 pip3.9 install -t /usr/lib/python3.9/site-packages/ numpy
+pip3.9 install -t /usr/lib/python3.9/site-packages/ matplotlib
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