On Mon, Sep 23, 2013 at 1:57 PM, John Chilton <chil...@msi.umn.edu> wrote:
> 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.
>

Hi John,

First let me tell you why I think duplicating the biopython install
reduces reproducibility. I have this on my tool setup.py:
    install_requires=[
        "docopt",
        "biopython",
        "python-levenshtein"
    ],

While I could specify versions here(ex. biopython==1.62), I feel that
is not a good thing outside of Galaxy. I think pip should be free to
install the latest version of these packages until I found there is an
issue otherwise. I think this is the most common approach, I might be
wrong thou. This leaves me with the issue that then when Galaxy
installs my tool using virtualenv, it will grab the most up-to-date
version of these packages, hence reducing reproducibility. Did I
explain myself well enough? I'll be happy to debate about any of this.

I agree with you about breaking the original intent of virtualenv, but
as you mention without 'install_pip' or similar, I'm left without the
option of making my life easy by just installing my package with an
approach using pypi.

Thanks,
Carlos

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