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
Hi Bjoern,
i'm not setting the
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 =
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,$default_file_path:rw
Looking more closely to your error message it seems to
hi,
i have question when submitting jobs as real user
defaults = "$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
Hi,
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,
Nikos
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
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
✉ nikolou...@grnet.gr
hpc.grnet.gr
