Thanks, Dan! This will be a huge help. :)
On Thu, May 21, 2015 at 2:41 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi brian,
> I’ve enhanced Galaxy’s external display application framework to support
> accessing files in the extra files path in a pull request here:
> To enable access you need to set allow_extra_files_access="True" for the
> display parameter. To access the files, you append the relative path of the
> extra file to the end of the URL generated for the parameter.
> If you want to try this feature before it is merged into the codebase, you
> can apply it as a patch (
> Please let us know if you encounter any issues using this new feature.
> Thanks for using Galaxy,
> On May 20, 2015, at 11:10 PM, Brian Haas <bh...@broadinstitute.org> wrote:
> 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:
> primary data set:
> and extra associated files:
> 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 to work.
> 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.
> many thanks,
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Brian J. Haas
The Broad Institute
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