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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