On Thu, Feb 17, 2011 at 12:37 PM, Sean Davis wrote:
>
> On Thu, Feb 17, 2011 at 5:48 AM, Peter 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.
>>
>
> Hi, Peter.  I ended up doing just that.  The hack in all its messiness is
> here:
> https://gist.github.com/831017

I would be wary of using ${input.name} like that - test with things
like renaming the dataset in Galaxy, and pasting in a PBD file
rather than uploading one. Also I suspect you can get filenames
with spaces in them which will probably cause trouble. You'll
notice that Galaxy generates its own *.dat filename which avoid
spaces.

Personally I would generate the *.pdb or *.ent filename within
the wrapper script based on the input file name (*.dat). Try:

os.symlink(fname,fname+".pdb")
...
symdcmd = "SymD %s.pdb" % fname


>>
>> 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.

I haven't done this myself yet (but I may well need to before long).

Peter

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