Add HPCtools.py in singularity and use 2.11.0 branch from gadpipeline to clone tools

python_3.9.def

@@ -21,7 +21,7 @@ SINGULARITY_ROOTFS=$APPTAINER_ROOTFS
 
 %post
 mkdir /data
-export GAD_VERSION=2.11.0_python3
+export GAD_VERSION=2.11.0
 echo "export GAD_VERSION=${GAD_VERSION}" >> ${SINGULARITY_ENVIRONMENT}
 
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
@@ -37,7 +37,7 @@ dnf install -y python39 git-2.27.0-1.el8.x86_64 compat-openssl10.x86_64
 # 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/
+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 /data/gadpipeline/common/HPCTools.py /usr/lib/python3.9/site-packages/
 
 printf "labkey==1.4.0\nnumpy==2.0.2\nmatplotlib==3.9.4\npandas==2.2.3\nchart-studio==1.1.0\nscipy==1.13.1\npyvcf==0.6.8\nsimplejson==3.19.3\nmodified-thompson-tau-test==0.1.3\n" > constraints.txt
 
@@ -65,5 +65,5 @@ 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
+Contained_OS_version CentOS_8.5.2110
 Contained_python_version 3.9.6
\ No newline at end of file