[galaxy-dev] Restore Account
Hello, My Galaxy account leonyum...@gmail.com has been marked deleted. Would you please restore it for me? Thank you very much. Best, Leon ___ 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] Restore Account
Hello Leon, The Galaxy Main server is a public resource and we implemented quotas to grant everyone fair access. We found that you had 3 accounts. This exceeds per user account published quotas: http://main.g2.bx.psu.edu/static/terms.html http://wiki.g2.bx.psu.edu/Main We very much appreciate that you find Galaxy useful. But, when the system is overloaded by users subverting quotas, no one ends up accomplishing very much work successfully, as many users and perhaps you yourself may have noticed this prior week. Using a single account going forward is required for continued access to the public server. Please contact our system administrator Nate using galaxy-b...@bx.psu.edu to discuss this privately. Galaxy has always been open source and is designed to be easy to deploy on your own resources, or on the cloud. Your usage needs might be better suited to one of these alternatives. For more information, please see: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices Best, Jen Galaxy team On 7/14/12 4:07 AM, Ming Yu wrote: Hello, My Galaxy account leonyum...@gmail.com mailto:leonyum...@gmail.com has been marked deleted. Would you please restore it for me? Thank you very much. Best, Leon ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] RPy and R installation problems
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/
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/
