Ryan Golhar wrote:
> In my local instance of Galaxy, I'm trying to download the BAM and
> BAI file from the tool SAM-to-BAM.  I see the links for downloading
> the Dataset and bam_index.
> 
> BTW - I'm running Safari on Mac OS X.
> 
> When I download the Dataset, I get the BAM file.  When I download
> the bam_index, it gets renamed to
> Galaxy13-[SAM-to-BAM_on...].bam_index.html
> 
> The error is the extension, .bam_index.html.  This should be
> .bam.bai. The BAM file gets saved correctly with .bam.

Well, I got rid of the .html in the most recent changeset,
5615:8d5850e45538.  bam_index is an artifact of the metadata filetype
and will less simple to force to bai on download, so I've opened an
issue here:

  https://bitbucket.org/galaxy/galaxy-central/issue/566/

--nate

> 
> I check the sam-to-bam XML wrapper but can't determine where this
> filename comes from or how to fix it.  Has anyone else run into
> this?
> 
> 
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