Re: [galaxy-dev] RPy and R installation problems
Sorry, that's all I have. Le-Shin On Jul 15, 2012, at 4:41 AM, Morris Chukhman wrote: Yes! That seems to have worked! Thank you very much, Le-Shin! Are there any more of these dependencies that require these little patches to build and install properly? Morris On 7/14/2012 8:16 PM, Le-Shin Wu wrote: I forgot to mention the most important part. You have to modify line 100 in rpy_tools.py that is under the rpy package as version = re.search( +([0-9]+\.[0-9][0-9]+\.[0-9]+), output) Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/
Re: [galaxy-dev] RPy and R installation problems
To build R, you need readline, readline_devel, and gfortran have been installed already. Then, ./configure --enable-R-shlib --prefix=/YOUR_PATH_TO_WHERE_R_WILL_BE_INSTALLED/R make make install To build rpy, you need to first, add R/lib to $LD_LIBRARY_PATH and R/bin to $PATH; sencond, comment out RPY_DOWNLOAD_DIR/src/Rpy.h line 77 as #include Rdevices.h. Then, python setup.py install --prefix=/PATH_TO_WHERE_RPY_WILL_BE_INSTALLED hope this will help. Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/
Re: [galaxy-dev] RPy and R installation problems
I forgot to mention the most important part. You have to modify line 100 in rpy_tools.py that is under the rpy package as version = re.search( +([0-9]+\.[0-9][0-9]+\.[0-9]+), output) Le-Shin On Jul 14, 2012, at 7:15 PM, Chukhman, Morris wrote: When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the following error about the version number being unobtainable from R --version. python setup.py install --prefix=/path/to/shared/python RHOMES= [] DEBUG= True Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R'] Traceback (most recent call last): File setup.py, line 109, in module RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) File /argus/app/src/rpy-1.0.3/rpy_tools.py, line 103, in get_R_VERSION raise RuntimeError(Couldn't obtain version number from output\n RuntimeError: Couldn't obtain version number from output of `R --version'. This is the R --version output: galaxy[rpy-1.0.3]$ R --version R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/. Although rpy2 builds and installs successfully the linear_regression.py module can't seem to use it. It is looking for the rpy module not the rpy2 module. If I ln -s rpy2 rpy, it appears to run but gives an name not defined error in a line like dat= r.list(... What is the proper procedure for installing the R and rpy dependencies? What versions are recommended with the current galaxy on mercurial? On Thu, June 28, 2012 3:51 pm, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan@epa.gov___ 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/ ___ 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/
[galaxy-dev] send data error
Hi, We just installed a galaxy server and are doing the tools testing right now. When we were testing the Send Data tool, we encountered an error as below. Error executing tool: 302 Found The resource was found at /tool_runner/redirect?redirect_url=http%3A%2F%2Fepigraph.mpi-inf.mpg.de%2FWebGRAPH_Public_Test%2Ffaces%2FDataImport.jsp%3FDATA_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Fdatasets%2F6%2Fdisplay%26INFO%3D%26GENOME%3Dhg18%26NAME%3DConvert+genome+coordinates+on+data+4+%5B+UNMAPPED+COORDINATES+%5D%26USERNAME%3Dlewu%40indiana.edu%26GALAXY_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Ftool_runner%3Ftool_id%3Depigraph_import Does this mean the redirect URL is wrong or something else? Can someone help us to solve this problem? Thanks a lot. Best LW___ 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/
[galaxy-dev] Galaxy with PBS runner Setting
We are trying to get galaxy to work on our cluster. Unfortunately, there are some questions I still cannot find the answer to and I'm hoping someone here can help me out. We would like to use the unified approach with TPRQUE PBS to support running galaxy tools on a cluster. Our questions are listed as below. (1) How to configure the universe_wsgi.ini file? Based on the galaxy wiki page, we changed the following parameters in universe_wsgi.ini new_file_path = /N/dc/projects/galaxy/new_files # this directory is accessible both to galaxy server and cluster nodes start_job_runners = 'pbs' default_cluster_job_runner = pbs://cluster.hostname.edu/ #cluster.hostname.edu is the hostname for our cluster Also under [galaxy:tool_runners] section, we add a new tool named mytool for testing as below. mytool = pbs://cluster.hostname.edu/ Does this configuration look correct and enough? (2) We created a new python egg for pbs by using LIBTORQUE_DIR=/usr/local/lib/libtorque python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini A new file pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg was then created under eggs. Do we need to do other things or only this operation is enough? (3) We created a new directory named mytool under tools and added a new file named newTool.xml in it. The content of newTool.xml is as below. Note that, the /N/soft/mason/test_tool is a executable binary file at our cluster. tool id=mytool name=Testing tool version=0.12.7 descriptiondo the pbs testing/description command /N/soft/mason/test_tool -p 8 hg18 -f $inputseq $output /command inputs param name=db type=inputseq label=input file / /inputs outputs data format=sam name=output label=result / /outputs tests test param name=inputseq value=a.fa / output name=output file=b.sam / /test /tests help **What it does** This tool uses Bowtie to produce an alignment. .. _Bowtie: http: /help /tool Does this xml file look correct? Do we also need a python wrapper file to somehow invoking PBS support? (4) Add the following text into tool_conf.xml. section name=My Tools id=mt tool file=mytool/newTool.xml / /section (5) After doing the above modification and restarting our galaxy server , we can see My Tools showing on the tools panel of our galaxy web interface. But after we select an input file and click execute button, the job status shows an error Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. We also check the log file, it shows Invalid job runner: pbs. We appreciate very much for your kind help. Le-Shin ___ 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/
