Hi,

I have created a tool that depends on biopython. I don't like the idea
of having several copies of biopython around and also for best
practice making workflows using my tool reproducible, I chose to make
my package repository[1] dependent of package_biopython_1_62.

[1]http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_6

I'm installing my package using the virtualenv option. As you can see
below I marked biopython as prior_installation_required="True".
However, I can see that virtualenv is installing a copy of biopython
in 'venv' under my tool install(see below). This doesn't sound right.
I was expecting that by making my repository dependent of biopython's
one that source would be used in my tool.

My plan is to create any non-existing "Tool dependency definition"
repository for every package my tool requires. This way you can always
count the same version of any of these packages is being used. I
thought that was the point, right?


Full ool_dependencies.xml:
<?xml version="1.0"?>
<tool_dependency>
    <package name="biopython" version="1.62">
        <repository changeset_revision="ac9cc2992b69"
name="package_biopython_1_62" owner="biopython"
prior_installation_required="True"
toolshed="http://testtoolshed.g2.bx.psu.edu"; />
    </package>
    <package name="ngs-tools" version="0.1.6">
        <install version="1.0">
            <actions>
                <action type="setup_virtualenv">ngs-tools==0.1.6</action>
            </actions>
        </install>
    </package>
</tool_dependency>

Contents of site-packages in my tool install dir:
$ ls -1 
shed_tools_dependencies.central/ngs-tools/0.1.6/cjav/package_ngs_tools_0_1_6/3c646b8328bb/venv/lib/python2.7/site-packages/
Bio
biopython-1.62-py2.7.egg-info
BioSQL
docopt-0.6.1-py2.7.egg-info
docopt.py
docopt.pyc
easy-install.pth
Levenshtein.so
ngs
ngs_tools-0.1.6-py2.7.egg-info
pip-1.3.1-py2.7.egg
python_Levenshtein-0.10.2-py2.7.egg-info
setuptools-0.6c11-py2.7.egg
setuptools.pth

Thanks,
Carlos
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