On Thu, Feb 17, 2011 at 5:48 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis <sdavis2@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