On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
>>
>> Yes, the complete directory hierarchy and content of the original
>> repository revision is preserved when it installed into Galaxy.
>>
>>> Based on a sample of one, it seems the installation process just
>>> unpacks the tool shed files (well, probably using hg rather than
>>> unpacking a tar-ball), and preserves their relative path structure.
>>> If so, I can just use relative paths to find a data file from the tool
>>> executable's own location on disk. (This is what I was hoping
>>> would be the case - I'm looking for explicit confirmation).
>>
>> This is correct, hg clone provides this behavior.
>>
>>> i.e. For the example use case, if motif.py and motif.dat are in the
>>> same folder in the Tool Shed upload, they will be in the same folder
>>> as each other once installed. That way motif.py can easily locate the
>>> data file motif.dat by looking in the same folder as it itself is located.
>>> This is actually very simple (provided I can assume the local folder
>>> structure is maintained).
>>
>> Yes, this is correct.
>
> Excellent - that solves this use-case nicely.
>

The tool I was talking about is actually a re-implementation of
predictNLS from the Rost Lab, which uses regular expressions
to look for Nuclear Localization Signals (NLS):
https://rostlab.org/owiki/index.php/PredictNLS

My Galaxy version is now available here:
http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls

Touch wood that will automatically install (and comes with
a minimal test case too).

Thanks,

Peter
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