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
<richard.schaefer(a)ibvt.uni-stuttgart.de> 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/