Added python 3.9 packages installation up until the end of the mito pipeline in full_wes v.2.10.0

python_3.9.def

@@ -6,6 +6,17 @@ From: centos:8
 This is a singularity container packing a python 3.9 (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.
 Python 3.9 is the latest available version in CentOS 8 used for this build.
 Authors : valentin.vautrot@u-bourgogne.fr
+Creation date : 2023-09-13
+
+%setup
+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/
 
 %post
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
@@ -13,18 +24,18 @@ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /
 
 dnf install -y epel-release
 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 install -y python39
 dnf remove -y python3 && dnf autoremove
-# by safety but useless, "python3" not found. The python3 present in /usr/bin is created with python3.9 install, so it is only a dependency ? python3 --version is 3.9.6 alright.
-
-# install python packages
-# pip3.9 install -t /usr/lib/python3.9/site-packages/ 
+# 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
 
-%files
-# import custom python packages from ccub. TO MODIFY FOR LOCAL MACHINE
-/work/gad/shared/pipeline/2.10.0/common/GeneralTools.py /usr/lib/python3.9/site-packages
+# 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/
+# 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/
 
-# %environment
-# export PYTHONPATH="/usr/lib/python3.9:/usr/lib/python3.9/site-packages/"
-# export PYTHON="usr/bin/python3.9"
\ No newline at end of file
+# 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