Nate, 

could we go to the beginning of the issue:

where is the galaxy env set?  I've seen a few post but I can only gather 
partial info.

- it is NOT set from the galaxy user .bashrc or .profile
- if it is indeed partially set from /etc/profile - using a Rocks cluster 
leaves you with many entries there to ponder
- if it is using ld.so.conf.d as well - it will read /usr/lib64 entries etc... 
- is there a precise way to see what env is used for galaxy? The log script 
gives you a nice read on the python path but is there a way to see all envs? 
Looking at envs as the user "galaxy" does not equate what galaxy ends up using.

multiple issues on the CentOS install:

I found the setting or non-setting  leading to the missing rpy module by 
looking at the runner log script - 
while it was loading python2.6.6 it was also loading the site-packages and 
other python parts from /usr/lib64...python2.4 

Once I edited run.sh to use the correct python and correct R path and added the 
RHOME to the rpy dependent scripts - this problem went away seemingly only to 
produce an env looking issue: sh rm command not found when running rpy 
dependent applications. Did somehow the edit destroy the /bin and usr/bin path? 
Would these be set in run.sh as well?   

To your question: 
where do you set RHOME in the env? 

We'd prefer to set all path options in run.sh in case all above is true that 
you cannot set it in ~/.bash* 

best,
joe
________________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, September 02, 2011 1:40 PM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rpy - No module named rpy CentoOs install

Joseph Hargitai wrote:
> additional info:
>
> it is possible on the same node to run manually
>
> ./gsummary.py
>
> with the header:
>
> #!/usr/bin/env python
>
> import sys, re, tempfile
> from rpy_options import set_options
> set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R')
> from rpy import *
>
> Where else can there be an env setting to prevent this app not finding the 
> mod from within galaxy?

Hi Joe,

If you set RHOME in the environment and then run gsummary.py without the
additions, does it work?

--nate

>
> j
>
>
> ________________________________
> From: Joseph Hargitai
> Sent: Thursday, September 01, 2011 12:28 PM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: rpy - No module named rpy CentoOs install
>
> Hi,
>
> On our Ubuntu install stat packages and all that require rpy work fine.
>
> On our CentOs install seeing this stubborn error that I did see from previous 
> post to be difficult to fix.
>
> At first suspected the SGE issue - environment not transferring to  compute 
> nodes. After changing the app to run local had the same issue.
>
> CentOs: 2.6.18-92.1.13.el5
>
> rpy module is in:
>
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages
>
> _rpy2122.so
> _rpy2131.so
>
> version:
> [galaxy@compute-0-65 galaxy-dist]$ python -c "import rpy; print 
> rpy.__version__"
> 1.5.1
>
> path:
>
> python -c 'import sys; print "\n".join( sys.path )'
>
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg
> /apps1/python/2.6.6/intel/lib/python26.zip
> /apps1/python/2.6.6/intel/lib/python2.6
> /apps1/python/2.6.6/intel/lib/python2.6/plat-linux2
> /apps1/python/2.6.6/intel/lib/python2.6/lib-tk
> /apps1/python/2.6.6/intel/lib/python2.6/lib-old
> /apps1/python/2.6.6/intel/lib/python2.6/lib-dynload
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL
>
>
> compiled against /R/2.13.1
>
>
> env:
>
> export PATH=.:\
> /apps1/R/2.13.1/intel/bin:\
> /apps1/python/2.6.6/intel/bin:\
> /apps1/pipe/bowtie/0.12.7/intel:\
> /apps1/pipe/bwa/0.5.9/intel:\
> /apps1/samtools/0.1.13/intel/bin:\
> /apps1/fastx_toolkit/0.0.13/intel/bin:\
> /apps1/maq/maq-0.7.1:\
> /apps1/maq/maq-0.7.1/scripts:\
> /apps1/bfast/bfast-0.6.5a/butil:\
> /apps1/bfast/bfast-0.6.5a/scripts:\
> /apps1/abyss/1.2.7/intel/bin:\
> /apps1/velvet/velvet_1.0.12:\
> /apps1/pipe/tophat/1.3.0/intel/bin:\
> /apps1/pipe/cufflinks/1.0.3/intel/bin:\
> /apps1/blast/2.2.25/gnu/bin:\
> /apps1/blast+/2.2.5/gnu/bin:\
> /apps1/sputnik/intel/bin:\
> /apps1/taxonomy/intel/bin:\
> /apps1/add_scores/add_scores:\
> /apps1/emboss/6.4.0/intel/bin:\
> /apps1/hyphy/hyphy/HYPHY:\
> /apps1/lastz/1.02.00:\
> /apps1/perm/0.3.6/intel/bin:\
> /apps1/beam2/intel/bin:\
> /apps1/pass2/intel/bin:\
> /apps1/plink/1.07/intel/bin:\
> /apps1/fbat/2.0.3/bin:\
> /apps1/eigensoft/3.0/intel/bin:\
> /apps1/mosaik/Mosaik-1.1.0021-Linux-x64/bin:\
> /apps1/freebayes/freebayes.git/bin:\
> $PATH
>
> export LD_LIBRARY_PATH=.:\
> /apps1/python/2.6.6/intel/lib:\
> /apps1/libgtextutils/0.6/intel/lib:\
> /apps1/emboss/6.4.0/intel/lib:\
> /apps1/intel/lib/intel64:\
> /apps1/intel/mkl/lib/em64t:\
> /apps1/tcltk/8.5.9/intel/lib:\
> /apps1/zlib/1.2.5/intel/lib:\
> /apps1/graphviz/2.26.3/intel/lib:\
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simtk/chem/openmm/OpenMM:\
> /apps1/python/2.6.6/intel/lib/python2.6/site-packages:\
> /apps1/libpng/1.5.0/intel/lib:\
> /apps1/R/2.13.1/intel/lib64/R/lib:\
> $LD_LIBRARY_PATH
>
> export PKG_CONFIG_PATH=.:\
> /apps1/R/2.13.1/intel/lib64/pkgconfig:\
> /apps1/libgtextutils/0.6/intel/lib/pkgconfig:\
> /apps1/sparsehash/1.11/intel/lib/pkgconfig:\
> $PKG_CONFIG_PATH
>
> export CLASSPATH=.:\
> /apps1/gatk/gatk-git/dist:\
> /apps1/gatk/gatk-git/lib:\
> /apps1/srma/srma-0.1.13:\
> /apps1/haploview/4.2:\
> /apps1/picard/picard-tools-1.50:\
> /apps1/fastqc/fastqc-0.9.5:\
> $CLASSPATH
>
>
> best,
> joe
>
>

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