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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