update Singularity and rebuild the container

[bgruening]

Singularity is now available in EPEL and ansible-roles/CyVerse-Ansible.singularity can probably be dropped. We do need a version >3 as the sing-images that we are building requires it.

[hexylena]

🎉🎉🎉

[bgruening]

Something which we can add later this year if we have time. Singularity and GPUs: http://gpucomputing.shef.ac.uk/education/creating_gpu_singularity/

[bgruening]

blocking issue to get Singularity working on pulsar:

• tool_script is not passed through (embedded) pulsar and container usage galaxyproject/pulsar#188

  • We can work around this by @gmauro patch, but this means we can only use very simple tools (e.g. tool without; or quotes)

• latest master version of pulsar has this bug: AttributeError: 'ToolRequirement' object has no attribute 'get' with latest master galaxyproject/pulsar#204

• this issues, we need Singularity installed in the latest version

• pulsar is not able to rewrite the Singularity path, this means we need to have the Singularity images in the same location on the Galaxy head-node and pulsar servers, currently this is /data/0/singularity/mulled/

  • non-blocking issue is that we need Singularity images on CVMFS, this will also fix the path-rewrite ob Singularity images
    • we currently rebuild all images and @simonbray is setting up a bot to keep them up-to-date
    • bot is available and converts everything from Docker to Singularity: https://github.com/BioContainers/singularity-build-bot

• necessary configuration to make this work on EU is here: activate Singularity container resolver infrastructure-playbook#94

[natefoo]

@jmchilton Is your work going to bring tool_script.sh to Pulsar, or only if you run the k8s setup?

[jmchilton]

I've got some WIP on bringing the whole tool script to Pulsar... I'm not sure it is the right approach but it is an approach. I think pushing the container information to Pulsar and having it build what is needed is probably better and should also be implemented... I don't know why I've been so slow to make progress on this but I'm trying. galaxyproject/pulsar#202

[gmauro]

4800332 makes available Singularity's version 3.2.1

[bgruening]

Updated the list to reflect John's latest fixes.