> 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 dependent of package_biopython_1_62.
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):
<repository name="package_biopython_1_62" owner="biopython">
<package name="biopython" version="1.62" />
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?
> Full ool_dependencies.xml:
> <?xml version="1.0"?>
> <package name="biopython" version="1.62">
> <repository changeset_revision="ac9cc2992b69"
> name="package_biopython_1_62" owner="biopython"
> toolshed="http://testtoolshed.g2.bx.psu.edu" />
> <package name="ngs-tools" version="0.1.6">
> <install version="1.0">
> <action type="setup_virtualenv">ngs-tools==0.1.6</action>
> Contents of site-packages in my tool install dir:
> $ ls -1
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