Thanks a lot for these explantions,

I have downloded refactored tools (rpy2 is more suited to our R version).
Unfortunatly, galaxy still do not import rpy2 ..

Traceback (most recent call last):
 File "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py", line 
6, in <module>
   import rpy2.robjects as robjects
ImportError: No module named rpy2.robjects


Moreover our rpy2 module is avalaible and listed in our python. Maybe a problem with Python ?

Thanks in advance,
Sarah

Hans-Rudolf Hotz a écrit :
Hi Sarah

you need to install the rpy module:

http://rpy.sourceforge.net/rpy.html


As a warning: we have been struggling to get rpy to work with newer versions of R. In or experience in only works with R version 2.9 and older. Thanks to a recent effort of our sysadmin, we can now use it with 2.15 - which is good, but not great, as our default version of R is now 3.0

Although we haven't started to us it, I recommend using rpy2:

http://rpy.sourceforge.net/rpy2.html

Most tools have been refactored by John Chilton

see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html


Regards, Hans-Rudolf




On 06/05/2013 10:19 AM, Sarah Maman wrote:
Hello,

Some Galaxy tools failed to import rpy module and displays the following
message:

Traceback (most recent call last):
  File
"/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py",
line 5, in <module>
    from rpy import *
ImportError: No module named rpy


For instance, the tool "Regrouping" (tools/stats/grouping.py) have been
refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this
tool runs on my local instance of Galaxy.
But I would like to be able use rpy module instead of refactor the
others tools.

Could you, please, help me to understand why the eggs ' import does not
allow the use of rpy module? How to debug these tools?

Thnaks in advance,
Sarah




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