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.3E_tag_set

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
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