On Mon, Sep 23, 2013 at 1:51 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>> 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.

Hi Björn,

No luck with this recommendation. See my full tool_dependencies.xml
below in case I miss read you. Biopython still gets installed into
this repository install 'venv'. I will try to move to what biopython
is doing. Hopefully and probably better, as John mentioned something
like 'install_pip' will come around in the future with support for
automatically modifying PYTHONPATH accordingly based on the repository
dependencies.

<?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">
            <action type="set_environment_for_install">
                <repository name="package_biopython_1_62" owner="biopython">
                    <package name="biopython" version="1.62" />
                </repository>
            </action>
            <actions>
                <action type="setup_virtualenv">ngs-tools==0.1.6</action>
            </actions>
        </install>
    </package>
</tool_dependency>

Thanks,
Carlos

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