Hi Peter,  see below...

On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:

> On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Peter,
>> Thanks for your thoughts on this.  I've created the following Trello card 
>> for this enhancement.
>> https://trello.com/card/galaxy-tool-enhancement-to-accommodate-repository-install-dir/506338ce32ae458f6d15e4b3/636
>> The priority for the tool shed in the area of tool dependencies like this 
>> has been
>> the implementation of features that enable sharing a single dependency across
>> multiple tools in separate repositories, so your scenario is not yet 
>> supported.
>> This enhancement would actually be as much (or perhaps more) on the Galaxy
>> end than the tool shed, I think, so there may be more resources available to 
>> get
>> to it sooner than I can right now.  Of course, someone wil get to it as soon 
>> as
>> possible.
>> Thanks again for all of your feedback and insight on this.
>> Greg Von Kuster
> Hi Greg,
> I've read http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
> which is targeted at Galaxy administrators rather than tools authors.
> It explains how a revision specific folder is assigned to each installed
> tool, but what (if anything) of the Tool's folder structure is preserved?

The installation process uses the mercurial API, so the process to install a 
specific repository changeset_revision ultimately includes the following 2 hg 

hg clone <repository_clone_url>
hg update -r changeset_revision

This results in the structure of the installed repository being exactly the 
same of the specific revision from which the repository was cloned.

> e.g. One of the paths given is:
> .../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml
> The prefix is the revision specific path for that tool for that Tool Shed,
> .../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/
> Within that, it seems to preserve the emboss_datatypes folders. i.e.
> goto http://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes
> and click browse repository tip files from the top left actions menu,
> it has just one file: emboss_datatypes/datatypes_conf.xml

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.  

> (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.

> Thanks,
> Peter

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