Added rMATS installation and required environment for full_rna.sh

python_3.9.def

@@ -19,6 +19,7 @@ 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-*
@@ -29,17 +30,24 @@ 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. 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.
+# 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
+dnf --enablerepo=powertools -y install lapack-devel
+dnf --enablerepo=powertools -y install -y blas-devel
+dnf install -y gsl-devel.x86_64
+dnf install -y gcc-gfortran
+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/
-# import of LabkeyTools.py in python3 causes error (TabError - indentation). Probably compatibility problem with python2
+# import of LabkeyTools.py in python3 causes error (TabError - indentation). Probably compatibility problem from python2
 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 --upgrade -t /usr/lib/python3.9/site-packages/ labkey
@@ -47,4 +55,7 @@ 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/ scipy
\ No newline at end of file
+# 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/ scipy
+
+rmdir /data/