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.

>> (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,

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