Share Docker Volumes when integrating Containers in Galaxy

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Share Docker Volumes when integrating Containers in Galaxy

Schäfer, Richard
Hello,

I want to integrate a Docker container as a tool in Galaxy. This works great. However,
I need the forward a Volume to the container (at least that how it works outside of Galaxy).
In particular, this would be the BLAST database.

This means, I would want to share the location specified in blastdb.loc and forward it to the
container. Is there a way to do this?

I see that there is an option to expose volumes to containers by specifying it in the job.conf.xml

<param id="docker_volumes">$defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro</param>

However, I guess this will then be done for all containers? And how do I integrate blastdb.loc in that command?
For that, my tool config looks like this:

<param name="database" type="select" display="radio" label="NCBI-nt database">
               <options from_file="blastdb.loc">
                   <column name="name" index="1"/>
                   <column name="value" index="2"/>
               </options>
</param>

I simply want to access the path inside of the container and therefore shared it with the container.

Thanks for any help

Cheers
Rich
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Re: Share Docker Volumes when integrating Containers in Galaxy

Galaxy Development List Archive mailing list
I don't have any advise from the BLAST DB side, but I would
expect the same solution to work with any *.loc file and the
file system it points at.

Peter

On Mon, May 20, 2019 at 10:50 AM Schäfer, Richard
<[hidden email]> wrote:

>
> Hello,
>
> I want to integrate a Docker container as a tool in Galaxy. This works great. However,
> I need the forward a Volume to the container (at least that how it works outside of Galaxy).
> In particular, this would be the BLAST database.
>
> This means, I would want to share the location specified in blastdb.loc and forward it to the
> container. Is there a way to do this?
>
> I see that there is an option to expose volumes to containers by specifying it in the job.conf.xml
>
> <param id="docker_volumes">$defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro</param>
>
> However, I guess this will then be done for all containers? And how do I integrate blastdb.loc in that command?
> For that, my tool config looks like this:
>
> <param name="database" type="select" display="radio" label="NCBI-nt database">
>                <options from_file="blastdb.loc">
>                    <column name="name" index="1"/>
>                    <column name="value" index="2"/>
>                </options>
> </param>
>
> I simply want to access the path inside of the container and therefore shared it with the container.
>
> Thanks for any help
>
> Cheers
> Rich
> ___________________________________________________________
> 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:
>   %(web_page_url)s
>
> 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:
  %(web_page_url)s

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