On Thu, Feb 17, 2011 at 5:48 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis <sdav...@mail.nih.gov> wrote:
> > I have a tool that takes a pdb file as input.  The authors of the
> *compiled*
> > code require that the suffix be either ".pdb" or ".ent".  When I upload a
> > .pdb file, the filename that gets fed to the tool now ends in .dat.  What
> is
> > the best way to get the original file extension stored in the file
> database?
> >
> > Thanks,
> > Sean
>
> Once in Galaxy all the data files have the extension .dat on disk, so
> I would try using a wrapper script that creates a symbolic link from the
> input.dat file to something like input.pdb or input.ent (and if that
> doesn't
> work, copy the file) before running the compiled code and then remove
> it afterwards.
>
>
Hi, Peter.  I ended up doing just that.  The hack in all its messiness is
here:

https://gist.github.com/831017



> Separately from this, you may need to extend Galaxy to define pdb
> as a new file format (ideally with a data type sniffer).
>
> This kind of question is better asked on the dev list (CC'dd)
>
>
Thanks.  That is the next step.

Sean
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