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: 
https://github.com/galaxyproject/galaxy/pull/284

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 (https://github.com/galaxyproject/galaxy/pull/284.patch).

Please let us know if you encounter any issues using this new feature.


Thanks for using Galaxy,

Dan


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:
> galaxy/database/files/000/dataset_1.dat
> and extra associated files:
> galaxy/database/files/000/dataset_1_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,
> 
> ~brian
> 
> 
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