Hi all,
Galaxy has long had two very simple (but largely unused) dependency mechanisms in a tool's XML (pre-dating the tool shed), for binaries and Python modules, e.g.
<requirements> <requirement type="python-module">numpy</requirement> <requirement type="binary">taxBuilder</requirement> </requirements>
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirement.3...
This has since been supplemented by the Tool Shed centric package requirement mechanism.
How can a tool declare a Python dependency, and have it installed automatically via the Tool Shed? Presumably it would have to end up as an egg in the Galaxy eggs folder, and not be installed under the default Python's PYTHONPATH?
There is nothing about Python modules mentioned here: http://wiki.galaxyproject.org/ToolShedToolFeatures
What I would suggest is that the the existing <requirement type="python-module"> is compared to the curated modules on http://eggs.g2.bx.psu.edu/ and if available the relevant egg be download from there. In which was, I have a request for additional eggs to be hosted there ;)
Regards,
Peter