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Commit b20afeed authored by Amandine  PERRIN's avatar Amandine PERRIN
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Add simplified singularity file for PanACoTA

parent 3812564e
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Bootstrap: docker
From:python:3.7-stretch
%post
# Update apt-get packages
apt-get update &&\
apt-get -y upgrade
# To use the "local" python, not the system one.
export PATH="/usr/local/bin":$PATH
# To avoid using python things installed in the HOME of root
# (that will be mounted during singularity build)
export PYTHONNOUSERSITE=1
# Install packages needed
apt-get install -y wget
# apt-get install -y \
# wget \
# python3 \
# python3-pip
# Upgrade pip
pip3 install --upgrade pip
# For manually-installed programs
mkdir -p /opt/src
# Install PanACoTA
cd /opt/src
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
cd /opt/src/pipeline_annotation
git checkout dev &&\
./make
%environment
export LC_ALL=C
# To use the "local" python, not the system one.
export PATH="/usr/local/bin":$PATH
# To avoid using python things installed in the HOME of the user
# (that will be mounted during container execution)
export PYTHONNOUSERSITE=1
%runscript
if [ "$*" ]
then
exec /usr/local/bin/PanACoTA "$@"
else
exec /usr/local/bin/PanACoTA -h
fi
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