Hi Peter and John,

thanks for your comments and thanks for working on the patch John.

> On Thu, Sep 26, 2013 at 10:27 PM, John Chilton <chil...@msi.umn.edu> wrote:
> > My recommendation would be make the tool dependency install work on as
> > many platforms as you can and not try to optimize in such a way that
> > it is not going to work - i.e. favor reproduciblity over performance.
> 
> Reproducibility versus speed is a particular issue with floating point
> libraries - NumPy using ATLAS vs OpenBLAST vs Intel MKL vs
> just plain NumPy will probably all give slightly different answers
> (on some tasks), and at different speed.
> 
> In this case, for simplicity I would advocate plain NumPy, without
> worrying about needing ATLAS. For packages needing NumPy
> with ALTAS, perhaps a new Tool Shed entry could be created,
> package_numpy_1_7_with_atlas or similar (based on the
> current configuration)?

I updated R, numpy, scipy, scikit and removed the atlas dependency. It
seems to work fine for the ChemicalToolBox. I do not remove the lapack
dependency, because I did not get any complains until now. I also
created new repositories *_with_atlas in my galaxytools repository, if
anyone is interested in atlas dependent packages.

Lets concentrate on reproducibility and leave out the speed improvements
for now. I admit it was do ambitious/idealistic.

Have a nice weekend,
Bjoern

> Peter



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