Re: Running Debian Med through Singularity.

[Olivier Sallou <olivier.sallou@irisa.fr>]

----- Mail original -----
> De: "Charles Plessy" <plessy@debian.org>
> À: "debian-med" <debian-med@lists.debian.org>
> Envoyé: Vendredi 10 Janvier 2020 07:36:12
> Objet: Running Debian Med through Singularity.

> Hi all,
> 
> long time no post,
> 
> happy new year !
> 
> At work, our cluster is running CentOS... but it has Singularity
> installed.
> 
> I just updated the Debian wiki to add instructions on how to create an
> image with Blends metapackages such as med-cloud:
> 
> https://wiki.debian.org/singularity#Example_3:_Build_a_larger_image_from_scratch
> 
> Next step is perhaps to find an easy way to make stable images with
> all the backports of the Debian Med bioinformatics tools installed...

Hi,
there is the biocontainers [0] initiative (which I am part of...) , that takes debianmed tools (among other tools) to create Docker and singularity images (though singularity accept docker images). Docker images are hosted on DockerHub.

I regularly take debian stable with backports to inject tools in biocontainers github repo [1] , and it automatically create images for those (with other non debian ones).
For example https://biocontainers.pro/#/tools/abacas , image has tag v1.3.1-5-deb.
All *-deb* tags are created from debianmed.
Singularity images are available here: https://containers.biocontainers.pro/s3/SingImgsRepo/ (when not too long to answer)


[0] https://biocontainers.pro/#/registry
[1] https://github.com/biocontainers/containers


Olivier
> 
> Have a nice day,
> 
> Charles
> 
> --
> Charles Plessy                              Akano, Uruma, Okinawa, Japan
> Debian Med packaging team         http://www.debian.org/devel/debian-med
> Tooting from work,           https://mastodon.technology/@charles_plessy
> Tooting from home,                 https://framapiaf.org/@charles_plessy