On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster <greg@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