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 < nikoloutsa@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 <nikoloutsa@admin.grnet.gr <mailto:nikoloutsa@admin.grnet.gr> <nikoloutsa@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> ✉ nikoloutsa@grnet.gr <mailto:nikoloutsa@grnet.gr> <nikoloutsa@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> ✉ nikoloutsa@grnet.gr hpc.grnet.gr