On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster firstname.lastname@example.org 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.
(I think I was originally on the wrong track by assuming I should be using the tool-data folder, which is complicated by not knowing where that will existing on disk).
I think your request is still valid though and we will add this enhancement for the Galaxy tool component to handle $REPOSITORY_INSTALL_DIR in tool configs. In the meantime, it looks like you can work around this missing feature. Please let me know if you bump into issues.
I can still see potential uses for $REPOSITORY_INSTALL_DIR both in the tool XML language, and as an environment variable - but I don't need that for the time being.
Thanks Greg, all sorted for now,