On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Peter and John,
thanks for your comments and thanks for working on the patch John.
Peter wrote:
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.
Great. Hopefully all my tools with a NumPy dependency via Biopython will pickup this change automatically when the next nightly Tool Shed tests are run. (That's what I hope will happen, otherwise I'll need to bump the dependency revision in the Biopython package & all the tools calling that).
I also created new repositories *_with_atlas in my galaxytools repository, if anyone is interested in atlas dependent packages.
Sounds good :)
Lets concentrate on reproducibility and leave out the speed improvements for now. I admit it was do ambitious/idealistic.
It is nice to aim high, but I think here practicality wins.
Have a nice weekend, Bjoern
You too, Peter