[galaxy-dev] Using Singularity images to resolve dependences in Galaxy 18.05

[Peter van Heusden]

Hi there

Is it possible to use Singularity images to resolve dependencies in Galaxy
18.05? If so is there documentation somewhere?

I have a Galaxy server where for at least some of the dependencies conda
will not be a good option so I would like to be able to use singularity if
at all possible.

Thanks!
Peter

[Björn Grüning]

Hi Peter,

yes this is working :)
Usegalaxy.eu is using it for a few tools.

Documentation is here ;)
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L484

Also the Docker compose image is can also use Singularity if you want to
reverse engineer it :)

Ciao,
Bjoern

Post by Peter van Heusden
Hi there
Is it possible to use Singularity images to resolve dependencies in
Galaxy 18.05? If so is there documentation somewhere?
I have a Galaxy server where for at least some of the dependencies conda
will not be a good option so I would like to be able to use singularity
if at all possible.
Thanks!
Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
https://lists.galaxyproject.org/
http://galaxyproject.org/search/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.

[Peter van Heusden]

Thanks Björn!

So it is a job_conf thing rather than a dependency manager config thing?

From the job_conf.xml example I am not clear how it expects to find the
container images? How is the search path configured, what naming scheme is
used for containers? And does it "pull" containers automatically (like the
conda dependency manager does) or should I pre-populate the system with
container images?

Thanks,
Peter

Post by Björn Grüning
Hi Peter,
yes this is working :)
Usegalaxy.eu is using it for a few tools.
Documentation is here ;)
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L484
Also the Docker compose image is can also use Singularity if you want to
reverse engineer it :)
Ciao,
Bjoern

Post by Peter van Heusden
Hi there
Is it possible to use Singularity images to resolve dependencies in
Galaxy 18.05? If so is there documentation somewhere?
I have a Galaxy server where for at least some of the dependencies conda
will not be a good option so I would like to be able to use singularity
if at all possible.
Thanks!
Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
https://lists.galaxyproject.org/
http://galaxyproject.org/search/