The proliferation of individual python package install definitions has
continued and it has spread to some MSI managed tools. I worry about
the tedium I will have to endure in the future if that becomes an
established best practice :) so I have implemented the python version
of what I had described in this thread:

As patch:
https://github.com/jmchilton/galaxy-central/commit/161d3b288016077a99fb7196b6e08fe7d690f34b.patch
Pretty version:
https://github.com/jmchilton/galaxy-central/commit/161d3b288016077a99fb7196b6e08fe7d690f34b

I understand that there are going to be differing opinions as to
whether this is the best way forward but I thought I would give my
position a better chance of succeeding by providing an implementation.

Thanks for your consideration,
-John


On Wed, Apr 17, 2013 at 3:56 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Apr 16, 2013 at 2:46 PM, John Chilton <chil...@msi.umn.edu> wrote:
>> Stepping back a little, is the right way to address Python
>> dependencies?
>
> Looks like I missed this thread, hence:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014169.html
>
>> I was a big advocate for inter-repository dependencies,
>> but I think taking it to the level of individual python packages might
>> be going too far - my thought was they were needed for big 100Mb
>> programs and stuff like that.
>
> It should work but it is a lot of boilerplate for something which
> should be more automated.
>
>> At the Java jar/Python library/Ruby gem
>> level I think using some of the platform specific packaging stuff to
>> creating isolated environments for each program might be a better way
>> to go.
>
> I agree, the best way forward isn't obvious here, and it may make
> sense to have tailored solutions for Python, Perl, Java, R, Ruby,
> etc packages rather than the current Tool Shed package solution.
>
> I've like to be able to just continue to write this kind of thing in my
> tool XML files and have it actually taken care of (rather than ignored):
>
> <requirements>
>      <requirement type="python-module">numpy</requirement>
>      <requirement type="python-module">Bio</requirement>
> </requirements>
>
> Adding a version key would be sensible, handling min/max etc
> as per Python packaging norms.
>
> Peter
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