cleaning unecessary command lines for previous installations attempts (rmats, lumpy)

python_3.9.def

@@ -19,7 +19,6 @@ mkdir ${SINGULARITY_ROOTFS}/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/
-/home/valentinv/Documents/projet_apptainer/rMATS.4.0.2/rMATS-turbo-Linux-UCS4 /data/
 
 %post
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
@@ -33,15 +32,6 @@ dnf update -y --exclude=filesystem
 dnf remove -y python3 && dnf autoremove
 dnf install -y python39
 
-# install rMATS & required packages
-dnf --enablerepo=powertools -y install lapack-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
-
 # 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/
@@ -63,18 +53,6 @@ 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/
 
@@ -83,6 +61,4 @@ 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-echo "checking if there is any outdated or unrequired packages :"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
\ No newline at end of file
+python3 -m pip list 
\ No newline at end of file