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The cl-submit-container is a new tool to submit requests for installing a Singularity container on the O2 cluster. An image source is used as an argument to generate an install request, which will build and deploy a Singularity container to an authorized container directory.

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Once a container is submitted and successfully created, it will be available under a user-specific directory, i.e. /n/app/singularity/containers/<HMSID>. The user has read and execute permissions on this folder, but cannot modify any of its contents. For more information on running Singularity containers in o2, see Running Singularity Containers in O2.

Common Examples

1. Create a Singularity image called nginx with the nginx container pulled from Docker Hub URI:

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container docker://nginx:latest

2. Create a Singularity container called genomics from a Dockerfile (note:-n genomics is used to name the image genomics instead of genomics_workflow)

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container -n genomics ~/CONTAINERS/working_dir/genomics_workflow.dockerfile

3. Create a Singularity container from a Singularity definition file:

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container ~/ollama.def