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