See https://github.com/NeuroDesk/transparent-singularity for updates
https://github.com/NeuroDesk/transparent-singularity
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).
This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.:
export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data"
https://github.com/NeuroDesk/neurodesk/blob/master/cvmfs/log.txt
curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/cvmfs/log.txt
git clone https://github.com/NeuroDesk/transparent-singularity convert3d_1.0.0_20210104
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_20210104
./run_transparent_singularity.sh --container convert3d_1.0.0_20210104
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
source activate_convert3d_1.0.0_20210104.sh
source deactivate_convert3d_1.0.0_20210104.sif.sh
./ts_uninstall.sh