Sorry for the late response - but earlier this week Björn Grüning and I
added various support to Galaxy's development branch for Singularity.
The following pull request added Singularity support in job running (
) - here job destinations
may describe the paths to Singularity containers. It may also work with
Singularity 2.3 to just specify Docker containers and let it auto-convert -
I haven't tested that.
For "best practice" tools - these are tools that have only requirements
that can resolve via Conda in the best practice Conda channels we can do
even more - we can build Singularity containers and use them automatically
- either ahead of time or build on the demand during job execution.
Here is the PR that added the on-demand building support for such
Singularity containers to Galaxy
and here is the tooling
) and cached
container PR (https://github.com/galaxyproject/galaxy/pull/4179
If you or anyone has a chance to try it out and beta test - let the list
know how it goes. I plan to talk a little about this work and related
Docker and Conda work at the GCC so I hope to see you there!
On Tue, May 2, 2017 at 8:51 AM, Nikos Nikoloutsakos <
Are there any galaxy forks using Singularity images instead of Docker ?
Is it trivial enough to replace "docker run" with "singularity exec"
Greek Research and Technology Network (GRNET)
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