Hello Marshall,

Apologies for the delay in reply, we have been restructuring our community shared tool area and wanted to have that going before we sent you instructions.


The first step in submitting a new tool/set of tools would be to create a wrapped version and adding it to the Tool Shed (if you have not done this already). If you have some of these tools running in your own instance already, we encourage you to consider this option so others can start using the alternate tools right away:

http://wiki.g2.bx.psu.edu/Tool%20Shed
(Brand new wiki! Content is being worked on, for now just click through to the new Tool Shed itself).

Next, if you want, please open an enhancement request using our ticketing system at bitbucket. Your comments about the advantages of the Sage version are certainly worth considering as Galaxy evolves.
http://bitbucket.org/galaxy/galaxy-central/issues

Of course not all new tools/enhancements are incorporated into the core Galaxy build, but this will place your suggestion into the queue for the team to review and provide feedback. Even if we do not end up including this in galaxy-central, having your option in the Tool Shed is a great way to offer the Galaxy community another analysis option.

Thank you for the nice comments! We are very glad to have you as part of our development community,

Best,

Jen
Galaxy team



On 3/29/11 3:22 PM, Marshall Hampton wrote:
I've just started seriously looking at Galaxy, and I already have a
suggestion (everyone's a critic...): switch from using rpy or even
rpy2 to scipy/numpy/matplotlib for basic statistics and plots.  I
wrestled a bit with getting rpy to work on my local setup and decided
it would be quicker to write my own plotting tool extensions, which
indeed turned out to be the case.  Since you already require python it
seems much more natural to use python-native tools.

To give some positive feedback, learning to write an extension was
surprisingly easy and encourages me to work on more.

I use currently use Sage (http://www.sagemath.org/) to both analyze
next-generation sequence data (454 and Illumina) and create
interactive tools for the biologists I collaborate with.  The Sage
project involves many of the same issues and challenges facing Galaxy.
  Sage is based on python, but includes R.  I realize that there are
many things you would want to do with R that aren't included in
scipy/biopython, so it might be worthwhile to look at how Sage wraps
R.  Its far from perfect, but I prefer it to rpy2.  In the Sage source
tree the interface is at:  $SAGE_ROOT/devel/sage/sage/interfaces/r.py.
  (Ugly online copy at:
http://hg.sagemath.org/sage-main/file/361a4ad7d52c/sage/interfaces/r.py).

-Marshall Hampton
Department of Mathematics and Statistics and the Integrated Biosciences Program
University of Minnesota Duluth
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