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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
