diff --git a/containers/Singularity.simple b/containers/Singularity.simple new file mode 100644 index 0000000000000000000000000000000000000000..869c738c3b664fe6161a7867112e168cb605ecb3 --- /dev/null +++ b/containers/Singularity.simple @@ -0,0 +1,51 @@ +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 diff --git a/Singularity b/tuto-singularity similarity index 100% rename from Singularity rename to tuto-singularity