On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning
<bjoern.gruen...@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,


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:

To search Galaxy mailing lists use the unified search at:

Reply via email to