INSTALL

Installation Instructions for GetGeo Galaxy Tool
December 16, 2012
Aryeh Hillman

This tool requires a relatively up-to-date installation
of Galaxy, requires a relatively recent version of R
with the packages Biobase and GEOquery, and requires
a relatively recent version of Python and packages
httlib2 and json. I recommend installing httlib2
and json with pip (i.e. sudo pip install httplib2).

When and if dependencies are met a folder should be
created within the Galaxy distribution at the path
tools, call it "aryeh" or some other name of your
choice. Place the files "getGeo.py" and "getGeo.xml"
in that directory. Next, we need to make Galaxy
aware of the tool. To do that, edit tool_conf.xml,
which is in the root directory of Galaxy. Create a new
tool section or add it to an existing section. Suppose
we would like to create a new tool section, add the following:

<section name="Aryeh's Tools" id="aryeh">
   <tool file="aryeh/getGeo.xml"/>
</section>

Restart Galaxy and the tool should be available.