Re: [galaxy-dev] Repository tool dependencies and virtualenv install

23 Sep 2013

      On Mon, Sep 23, 2013 at 2:24 PM, Carlos Borroto
<carlos.borroto@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