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 [[email protected]] Sent: Friday, September 02, 2011 1:40 PM To: Joseph Hargitai Cc: [email protected] 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: [email protected] > 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/
