Commit 1c716329 authored by Valentin Vautrot's avatar Valentin Vautrot

Added python 3.9 packages installation up until the end of the CNV section in full_wes v.2.10.0

parent 61c38963
...@@ -17,6 +17,8 @@ mkdir ${SINGULARITY_ROOTFS}/data ...@@ -17,6 +17,8 @@ mkdir ${SINGULARITY_ROOTFS}/data
/home/valentinv/Documents/GitLab/gadpipeline/common/GeneralTools.py /data/ /home/valentinv/Documents/GitLab/gadpipeline/common/GeneralTools.py /data/
/home/valentinv/Documents/GitLab/gadpipeline/common/LabkeyTools.py /data/ /home/valentinv/Documents/GitLab/gadpipeline/common/LabkeyTools.py /data/
/home/valentinv/Documents/GitLab/gadpipeline/common/InterTools.py /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/
%post %post
sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-* sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
...@@ -30,12 +32,16 @@ dnf remove -y python3 && dnf autoremove ...@@ -30,12 +32,16 @@ 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. 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 dnf install -y python39
# copy non-pip python packages # install non-pip python packages
cp /data/GeneralTools.py /usr/lib/python3.9/site-packages/ mv /data/GeneralTools.py /usr/lib/python3.9/site-packages/
cp /data/LabkeyTools.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 with python2
cp /data/InterTools.py /usr/lib/python3.9/site-packages/ 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 # 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/ labkey
pip3.9 install -t /usr/lib/python3.9/site-packages/ numpy pip3.9 install -t /usr/lib/python3.9/site-packages/ numpy
pip3.9 install -t /usr/lib/python3.9/site-packages/ matplotlib
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment