This project allows to use singularity containers transparently on HPCs, so that an application inside the container can be used without adjusting any scripts or pipelines (e.g. nipype).

Important: add bind points to .bashrc before executing this script

This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.:

export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data"

This gives you a list of all tested images available in neurodesk:

https://github.com/NeuroDesk/neurodesk/blob/master/neurodesk/apps.json

curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/neurodesk/apps.json

Clone repo into a folder with the intented image name

git clone https://github.com/NeuroDesk/transparent-singularity convert3d_1.0.0_20200701

Install

This will create scripts for every binary in the container located in the $DEPLOY_PATH inside the container. It will also create activate and deactivate scripts and module files for lmod (https://lmod.readthedocs.io/en/latest/)

cd convert3d_1.0.0_20200701
./run_transparent_singularity.sh --container convert3d_1.0.0_20200701.sif

Use in module system LMOD

Add the module folder path to $MODULEPATH

Manual activation and deactivation (in case module system is not available). This will add the paths to the .bashrc

Activate

source activate_convert3d_1.0.0_20200701.sif.sh

Deactivate

source deactivate_convert3d_1.0.0_20200701.sif.sh

Uninstall container and cleanup

./ts_uninstall.sh