It's seems like you got me ! yey ! :D  I was already working on my fork for singularity ,
since we don't need any sudo rights for the galaxy user "setup manually by the admin and the paths hard-coded for each tool "

I will test it out and let you know !

Best regards from Greece,

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

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

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