Here's a quick update on my adventure in
galaxy-dev. First - a quick review. I have a composite data
type where files are stored as:
I want to link this up to a display application (web app
running on the same server via apache) such that galaxy
provides a URL that will enable read access to these files.
From what I could gather, there's no straightforward way
to get a stable URL from galaxy that points to the
extra_files in the composite data set, such as getting links
to a bunch of bam files and indexes placed there.
Assigning each of the extra files as metadata items (ie.
similar to a bam.bai file as a metadata file for a single
bam file) could have been an option, but I couldn't get that
For now, since my Galaxy instance and my web app are
running on the same machine with access to the same file
system, I'll just have my web app read the files directly
from the galaxy database directory via symlinks set up by my
galaxy tool during the run. It's a clunky way of doing
things but should suffice for now given my setup.
If others have better solutions, I'm definitely
interested in hearing them.