Using Singularity images to resolve dependences in Galaxy 18.05

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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

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Re: Using Singularity images to resolve dependences in Galaxy 18.05

Björn Grüning-3
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

Am 19.09.2018 um 10:12 schrieb 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
> 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.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.org/search/
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Re: Using Singularity images to resolve dependences in Galaxy 18.05

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

On Wed, 19 Sep 2018 at 10:15 Björn Grüning <[hidden email]> wrote:
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

Am 19.09.2018 um 10:12 schrieb 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
> 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.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.org/search/