Commit 61c38963 authored by Valentin Vautrot's avatar Valentin Vautrot

Added python 3.9 packages installation up until the end of the mito pipeline in full_wes v.2.10.0

parent 19b5fe24
...@@ -6,6 +6,17 @@ From: centos:8 ...@@ -6,6 +6,17 @@ From: centos:8
This is a singularity container packing a python 3.9 (only version) environment with all the packages necessary to execute all the python scripts present in the version 2.10.0 of the gad pipeline. This is a singularity container packing a python 3.9 (only version) environment with all the packages necessary to execute all the python scripts present in the version 2.10.0 of the gad pipeline.
Python 3.9 is the latest available version in CentOS 8 used for this build. Python 3.9 is the latest available version in CentOS 8 used for this build.
Authors : valentin.vautrot@u-bourgogne.fr Authors : valentin.vautrot@u-bourgogne.fr
Creation date : 2023-09-13
%setup
SINGULARITY_ROOTFS=$APPTAINER_ROOTFS
mkdir ${SINGULARITY_ROOTFS}/data
%files
# import custom python packages from local machine
/home/valentinv/Documents/GitLab/gadpipeline/common/GeneralTools.py /data/
/home/valentinv/Documents/GitLab/gadpipeline/common/LabkeyTools.py /data/
/home/valentinv/Documents/GitLab/gadpipeline/common/InterTools.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-*
...@@ -13,18 +24,18 @@ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' / ...@@ -13,18 +24,18 @@ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /
dnf install -y epel-release dnf install -y epel-release
dnf update -y --exclude=filesystem 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 install -y python39
dnf remove -y python3 && dnf autoremove dnf remove -y python3 && dnf autoremove
# by safety but useless, "python3" not found. The python3 present in /usr/bin 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
# install python packages
# pip3.9 install -t /usr/lib/python3.9/site-packages/
%files # copy non-pip python packages
# import custom python packages from ccub. TO MODIFY FOR LOCAL MACHINE cp /data/GeneralTools.py /usr/lib/python3.9/site-packages/
/work/gad/shared/pipeline/2.10.0/common/GeneralTools.py /usr/lib/python3.9/site-packages cp /data/LabkeyTools.py /usr/lib/python3.9/site-packages/
# 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/
# %environment # install python pip packages
# export PYTHONPATH="/usr/lib/python3.9:/usr/lib/python3.9/site-packages/" pip3.9 install -t /usr/lib/python3.9/site-packages/ labkey
# export PYTHON="usr/bin/python3.9" pip3.9 install -t /usr/lib/python3.9/site-packages/ numpy
\ No newline at end of file
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