Yup - I messed that up - sorry.

Can you try the fix in this PR (
https://github.com/galaxyproject/galaxy/pull/4208) and comment on the PR to
let me know if they fix the problem?

-John

On Mon, Jun 19, 2017 at 10:24 AM, Nikos Nikoloutsakos <
nikolou...@admin.grnet.gr> wrote:

> Hi Bjoern,
> i'm not setting the <param id="singularity_volumes">
>
> it seems the default_ro is not interpreting the preprocess_volumes in
> class SingularityContainers
>
> volumes_raw = 
> self._expand_volume_str(self.destination_info.get("singularity_volumes",
> "$defaults"))
> volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
> #preprocessed_volumes_str = preprocess_volumes(volumes_raw,
> self.container_type)
> #volumes = docker_util.DockerVolume.volumes_from_str(preprocessed_
> volumes_str)
>
>
>
> Cheers,
> Nikos
>
>
> On 16/06/2017 07:09 μμ, Björn Grüning wrote:
>
> Hi Nikos,
>
> we are discussion various enhancement with the Singularity developers,
> one is to suppress warnings.
>
> Can you try this for the time being? This is working fine for me.
>
> $tool_directory:rw,$working_directory:rw,$default_file_path:rw
>
> Looking more closely to your error message it seems to be that
> Singularity is interpreting the default_ro, which should not happen.
> This should be replace by either ro or rw. Where do you specify this string?
>
> Cheers,
> Bjoern
>
>
>
> hi,
>
> i have question when submitting jobs as real user
>
> defaults = "$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 ?
>
>
> Thanks,
>
>
>
>
> 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 
> Galaxyhttps://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!
>
> -John
>
>
>
> On Tue, May 2, 2017 at 8:51 AM, Nikos Nikoloutsakos
> <nikolou...@admin.grnet.gr <mailto:nikolou...@admin.grnet.gr> 
> <nikolou...@admin.grnet.gr>> wrote:
>
>     Hello,
>
>     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
>
>
>     --
>     Nikos Nikoloutsakos
>     Greek Research and Technology Network (GRNET)
>     ☎ +30 210 7471127 <+30%2021%200747%201127> <tel:%2B30%20210%207471127>
>     ✉ nikolou...@grnet.gr <mailto:nikolou...@grnet.gr> <nikolou...@grnet.gr>
>      hpc.grnet.gr <http://hpc.grnet.gr> <http://hpc.grnet.gr>
>
>     ___________________________________________________________
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>  --
> Nikos Nikoloutsakos
> Greek Research and Technology Network (GRNET)
> ☎ +30 210 7471127 <+30%2021%200747%201127>
> ✉ nikolou...@grnet.gr
>  hpc.grnet.gr
>
>
>
> ___________________________________________________________
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>
> --
> Nikos Nikoloutsakos
> Greek Research and Technology Network (GRNET)
> ☎ +30 210 7471127 <+30%2021%200747%201127>
> ✉ nikolou...@grnet.gr
>  hpc.grnet.gr
>
>
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