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&gt; 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/