On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> 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 disagree strongly. This is not a good idea. My thought is if you are
using a virtualenv, you shouldn't be trying to compose it with other
python dependencies - to me the whole point of virtualenv is that it
creates isolated little environments. I am not sure why duplicating
the biopython install reduces reproduciblity.

If you want to use individual Python packages using Galaxy's
dependency mechanism, I think you should then package them up one at a
time and hand modify PYTHONPATH and PATH - the way biopython is done.

Galaxy should have a separate action to make this easy, say
install_pip or something like that, as outlined by James Taylor at
some point.

-John

>
>> 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
>>
>> Thanks,
>> Carlos
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>
>
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