On Mon, Sep 23, 2013 at 2:24 PM, Carlos Borroto
<carlos.borr...@gmail.com> wrote:
>> 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>

I made a mistake here. After fixing it still didn't work. I placed
action "set_environment_for_install" outside of actions. It should be:

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

Testing now John's recommendations of specifying versions in
setup_virtualenv, which means I won't be using package_biopython_1_62
and its dependencies. It would be nice to see how package_biopython_*
could be used in my case. It would also be nice to know if the
consensus is to keep everything(dependencies included) inside the
toolshed or not.

Thanks,
Carlos

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