Question: Filename Extension In New Tool
gravatar for Sean Davis
7.8 years ago by
Sean Davis220
Sean Davis220 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
ADD COMMENTlink modified 7.8 years ago by Peter Cock1.4k • written 7.8 years ago by Sean Davis220
gravatar for Peter Cock
7.8 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
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. 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) Peter
ADD COMMENTlink written 7.8 years ago by Peter Cock1.4k
Hi, Peter. I ended up doing just that. The hack in all its messiness is here: Thanks. That is the next step. Sean
ADD REPLYlink written 7.8 years ago by Sean Davis220
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