Hi Carlos!

> 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

Cool thanks! I think that is best practise!

> 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.

Can you try to insert that (maybe adopt, its not checked):

  <action type="set_environment_for_install">
     <repository name="package_biopython_1_62" owner="biopython">
          <package name="biopython" version="1.62" />
     </repository>
  </action>

Only with that the PYTHONPATH is populated.

> 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?

Yes!

> 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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