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Re: Should we offer Debian Med workflow-containers?



Dear Olivier, dear Yaroslav, dear Alex,

Thank you all for your kind and constructive replies - as expected :o)

Am 18.01.21 um 12:30 schrieb olivier sallou:
> On Sun, 2021-01-17 at 16:42 +0100, Steffen Möller wrote:
>> Hello,
>>
>> Our HPC environment does not offer Docker, but Singularity
>> (
>> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177459
>> )
>> is supported. I thought I should give it a shot. Is anybody using
>> this
>> already on this list?
> we propose singularity in our hcp env too. There is no issue to run
> *docker* images as images follow a standard managed by all *docker*
> like tools.

I already mentioned you during Sunday's video meeting because of your
work for BioContainers. And I also want to get some directions from
Hervé and Matúš who can also be helpful to have these containers found.

> For info, you mat have a look too at podman. Like singularity it
> supports root-less env.

http://docs.podman.io/en/latest/index.html

Many thanks. Yes, this is nice. I do not yet fully grasp what system can
work with what other system's containers with how much overhead.

https://github.com/containers/podman is golang again  - but for some
magic we already have it https://tracker.debian.org/pkg/libpod . THANKS!

> Singularity cons is non-root env , but for most of our users this is
> fine as long as they do not need to modify container content.
>
> May be an issue for *some* tools writing in /var/lib|cache etc.. but
> most will be fine.

I am a bit shocked that you all seem to be already using containers with
Debian when I just silently used conda [and felt just a bit bad about
it]. I sketched containers as a possible theme for our Sprint only
because of the "recommends" vs "suggests" exchange on the Debian Med
task lists and Charles' pointer to the effect on containers. Are there
other "we should have done that years ago" themes for our Sprints that I
am not aware of / prioritising enough? Thanks to Mo we have machine
learning and GPU support. Data management.

Best,

Steffen




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