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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