Submit Singularity job in VRE Workbench Tool

Last modified by publicadmin on 2025/12/16 13:04

VRE users are able to run singularity container in VRE workbench tool of VM connected through Guacamole.

1. VRE Workbench Tool of Gucamole VM

Apache Guacamole is a clientless remote desktop gateway that supports standard protocols like VNC, RDP, and SSH. Guacamole has been integrated into the VRE using a Single Sign-On Protocol and is configured on a per-project basis. For more details on

What is Guacamole VM workbench tool?
How to request access to my project's Guacamole VM workbench tool?
How to access into Guacamole VM and launch terminal?

Please visit this page: VRE User Guide/Analyzing Data/Gucamole

2. Submit Singularity Job

Users can run singularity container in Guacamole VM by running following scripts in the terminal:

singularity help [pull|build|run|exec|shell]
singularity run <library://, docker://, and shub:// URIs or imageFileName>

$ singularity run docker://busybox$ singularity run library://sylabsed/examples/lolcow

singularity pull <library://, docker://, and shub:// URIs>

$ singularity pull library://sylabsed/examples/lolcow$ lslolcow_latest.sif

singularity build

$ singularity build lolcow-for-chance.sif library://sylabsed/examples/lolcow$ lslolcow-for-chance.sif

singularity exec <library://, docker://, and shub:// URIs or imageFileName>

$ singularity exec lolcow_latest.sif cowsay moo

Notes: exec also works with the library://, docker://, and shub:// URIs. This creates an ephemeral container that executes a command and disappears.$ singularity exec library://sylabsed/examples/lolcow cowsay "Fresh from the library!"

singularity shell <library://, docker://, and shub:// URIs or imageFileName>

$ singularity shell lolcow_latest.sif

For more detailed, please refer to the official website.