Transparent Singularity

For more advanced users who wish to use Transparent Singularity directly

Transparent singularity is here

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:

curl -s

Clone repo into a folder with the intented image name

git clone 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 (

cd convert3d_1.0.0_20210104
./ convert3d_1.0.0_20210104

Options for Transparent singularity:

  • --storage - this option can be used to force a download from docker, e.g.: --storage docker
  • --container - this option can be used to explicitly define the container name to be downloaded
  • --unpack - this will unpack the singularity container so it can be used on systems that do not allow to open simg / sif files for security reasons, e.g.: --unpack true
  • --singularity-opts - this will be passed on to the singularity call, e.g.: --singularity-opts '--bind /cvmfs'

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





Uninstall container and cleanup