i have question when submitting jobs as real user

defaults = "$galaxy_root:default_ro,$tool_directory:default_ro"

singularity gives a WARNING since the home dir is already mounted "WARNING: Not mounting requested bind point (already mounted in container): default_ro"

can this be avoided ?


On 14/06/2017 07:46 μμ, John Chilton wrote:
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 (https://github.com/galaxyproject/galaxy/pull/4175) - 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 https://github.com/galaxyproject/galaxy/pull/4185 and here is the tooling PR (https://github.com/galaxyproject/galaxy-lib/pull/64) and cached container PR (https://github.com/galaxyproject/galaxy/pull/4179) support. 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 <nikoloutsa@admin.grnet.gr> wrote:

Are there any galaxy forks using Singularity images instead of Docker ?
Is it trivial enough to replace "docker run" with "singularity exec" ?

Thank you,

Nikos Nikoloutsakos
Greek Research and Technology Network (GRNET)
+30 210 7471127

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Nikos Nikoloutsakos
Greek Research and Technology Network (GRNET)
☎ +30 210 7471127
✉ nikoloutsa@grnet.gr