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Allow use of Singularity instead of Docker #98

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jpdna opened this Issue Feb 1, 2018 · 3 comments

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jpdna commented Feb 1, 2018

The HPC I have access to does not, and will not in foreseeable future allow Docker for security reasons, however I can create and use Singularity containers, such can be created from Docker images.
http://singularity.lbl.gov/docs-docker

I'm going to work on doing that, just wanted to get any comment.

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akmorrow13 commented Feb 1, 2018

I believe this is a useful problem in general for bdg (we cannot run docker on the cluster in cluster mode). Would this fix that issue as well?

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heuermh commented Feb 1, 2018

+1, this should happen in step with changes for #34, which should follow from #69. As you mentioned, the same Docker images can be used when making the call via Singularity. The Nextflow user community has a lot of experience with this.

@heuermh heuermh self-assigned this Feb 5, 2018

@heuermh heuermh added this to the 0.2.0 milestone Feb 20, 2018

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heuermh commented Feb 20, 2018

@jpdna Could you take a look at the Singularity command line that is created by #107? This test method provides an example.

A few questions remain:

  • Mount syntax is --bind source:target, do you know why those wouldn't work for you?
  • Does running Singularity via sudo make sense?
  • If the image is a local file (e.g. foo.img), do we need to create an absolute path for that? or perhaps copy to all nodes via files mechanism?

@heuermh heuermh closed this in #107 Mar 22, 2018

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