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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