Added all python packages needed to run full_wes.sh, full_wgs.sh and…

python_3.9.def

@@ -26,18 +26,19 @@ 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-*
 
 dnf install -y epel-release
+dnf update -y libmodulemd
 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
-# by safety but useless, "python3" not found, just librairies (for dnf ?). 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
 
-# install rMATS environment
+# install rMATS & required packages
 dnf --enablerepo=powertools -y install lapack-devel
-dnf --enablerepo=powertools -y install -y blas-devel
+dnf --enablerepo=powertools -y install blas-devel
 dnf install -y gsl-devel.x86_64
 dnf install -y gcc-gfortran
+mkdir /usr/bin/rMATS4.2.0/
 mv /data/rMATS-turbo-Linux-UCS4 /usr/bin/rMATS4.2.0/rMATS-turbo-Linux-UCS4
 # causes error (parenthesis). rMATS written in python2.7.x so probably compatibility problem with python3
 
@@ -50,12 +51,38 @@ mv /data/VcfTools.py /usr/lib/python3.9/site-packages/
 mv /data/CnvTools.py /usr/lib/python3.9/site-packages/
 
 # install python pip packages
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ wheel
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ labkey
 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
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ plotly
+# pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ plotly
 # is causing an error due to plotly.plotly module being deprecated in python3.9. chart-studio package (with the chart_studio.plotly module) is to be used in replacement.
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ chart-studio
 pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ scipy
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pyvcf
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ simplejson
 
+# install packages required by lumpy (pysam)
+# dnf install -y make
+# dnf install -y zlib-devel
+# dnf install -y bzip2-devel
+# dnf install -y xz-devel
+# dnf install -y libcurl-devel
+# pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ cython
+
+# let pip install htslib may not be a good idea, unless configuring with, eg :
+# export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
+# pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pysam
+
+#clean
 rmdir /data/
+
+%test
+printf "\n\ntest phase ################\n\n"
+echo "python version :"
+python3 -V
+echo "listing installed pip packages :" 
+python3 -m pip list 
+echo "checking if there is any outdated or unrequired packages :"
+python3 -m pip list -o --not-required
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