On Mon, Sep 23, 2013 at 1:51 PM, Björn Grüning <bjoern.gruening@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