Hi Carlos!
Hi,
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[1] dependent of package_biopython_1_62.
[1]http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_6
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): <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.
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?
Yes!
Full ool_dependencies.xml: <?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="setup_virtualenv">ngs-tools==0.1.6</action> </actions> </install> </package> </tool_dependency>
Contents of site-packages in my tool install dir: $ ls -1 shed_tools_dependencies.central/ngs-tools/0.1.6/cjav/package_ngs_tools_0_1_6/3c646b8328bb/venv/lib/python2.7/site-packages/ Bio biopython-1.62-py2.7.egg-info BioSQL docopt-0.6.1-py2.7.egg-info docopt.py docopt.pyc easy-install.pth Levenshtein.so ngs ngs_tools-0.1.6-py2.7.egg-info pip-1.3.1-py2.7.egg python_Levenshtein-0.10.2-py2.7.egg-info setuptools-0.6c11-py2.7.egg setuptools.pth
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