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 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!
-John
On Tue, May 2, 2017 at 8:51 AM, Nikos Nikoloutsakos
<nikolou...@admin.grnet.gr <mailto: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 <tel:%2B30%20210%207471127>
✉ nikolou...@grnet.gr <mailto:nikolou...@grnet.gr>
hpc.grnet.gr <http://hpc.grnet.gr>
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Nikos Nikoloutsakos
Greek Research and Technology Network (GRNET)
☎ +30 210 7471127
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hpc.grnet.gr
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--
Nikos Nikoloutsakos
Greek Research and Technology Network (GRNET)
☎ +30 210 7471127
✉ nikolou...@grnet.gr
hpc.grnet.gr
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