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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/