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R is a free software environment for statistical computing and graphics. | |||
==SGE module files== | |||
The following Modules files should be loaded for this package: | |||
<pre> | |||
module load R/R-2.7.2 | |||
</pre> | |||
For other versions, simply replace the version number | |||
<pre> | |||
module load R/R-2.11.1 | |||
</pre> | |||
The following libraries are available | |||
* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/library | |||
** The default libraries that come with R | |||
** Rmpi | |||
** Snow | |||
* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/bioc | |||
** BioConductor libraries (default package set using getBioC) | |||
Additional libraries should be installed by the user under ~/R_exlibs or follow these instructions: | |||
**Make a directory on your home page to install packages/libraries to (DEST_DIR) | |||
**Make a .Rprofile document in your home space (~/) with the following content, i.e. run the following command on your terminal | |||
<pre> | |||
cat > $HOME/.Rprofile <<\EOF | |||
.libPaths(“~/DEST_DIR") | |||
cat(".Rprofile: Setting UK repositoryn") | |||
r = getOption("repos") # hard code the UK repo for CRAN | |||
r["CRAN"] = "http://cran.uk.r-project.org" | |||
options(repos = r) | |||
rm(r) | |||
EOF | |||
NOTE:Change DEST_DIR to the name of the directory you created. | |||
</pre> | |||
**Load R module and open it. | |||
**Run install.packages(“Package_Name”) at the prompt. | |||
**This would install Package_Name to DEST_DIR. To use it just use library(Package_Name) | |||
'''NOTE''': If you install a package with one version of R, it might not be compatible with another version. So it would be advisable to pick one version of R and go with it, so that you don’t have to install multiple versions of the same package. | |||
==SGE Job script == | |||
'''Sample R Grid Engine Job Script''' | |||
This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM | |||
<pre> | |||
#!/bin/bash | |||
#$ -S /bin/bash | |||
#$ -cwd | |||
# | |||
#$ -j y | |||
#$ -N rtestjob | |||
# Use '#$ -m n' instead to disable all email for this job | |||
#$ -m eas | |||
#$ -M YOUR_EMAIL_ADDRESS | |||
#$ -l h_rt=2:00:00,s_rt=1:55:00 | |||
#$ -l vf=256M | |||
. /etc/profile.d/modules.sh | |||
module load R/R-2.7.2 | |||
#$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD | |||
R CMD BATCH rscript.R | |||
</pre> | |||
[[Category:Software]][[Category:Bio-statistics]] | |||
Revision as of 19:03, 5 February 2016
This page is a Generic stub.
You can help by expanding this page..
R is a free software environment for statistical computing and graphics.
SGE module files
The following Modules files should be loaded for this package:
module load R/R-2.7.2
For other versions, simply replace the version number
module load R/R-2.11.1
The following libraries are available
- /share/apps/R/R-X.X.X/gnu/lib/R/library
- The default libraries that come with R
- Rmpi
- Snow
- /share/apps/R/R-X.X.X/gnu/lib/R/bioc
- BioConductor libraries (default package set using getBioC)
Additional libraries should be installed by the user under ~/R_exlibs or follow these instructions:
- Make a directory on your home page to install packages/libraries to (DEST_DIR)
- Make a .Rprofile document in your home space (~/) with the following content, i.e. run the following command on your terminal
cat > $HOME/.Rprofile <<\EOF
.libPaths(“~/DEST_DIR")
cat(".Rprofile: Setting UK repositoryn")
r = getOption("repos") # hard code the UK repo for CRAN
r["CRAN"] = "http://cran.uk.r-project.org"
options(repos = r)
rm(r)
EOF
NOTE:Change DEST_DIR to the name of the directory you created.
- Load R module and open it.
- Run install.packages(“Package_Name”) at the prompt.
- This would install Package_Name to DEST_DIR. To use it just use library(Package_Name)
NOTE: If you install a package with one version of R, it might not be compatible with another version. So it would be advisable to pick one version of R and go with it, so that you don’t have to install multiple versions of the same package.
SGE Job script
Sample R Grid Engine Job Script This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM
#!/bin/bash #$ -S /bin/bash #$ -cwd # #$ -j y #$ -N rtestjob # Use '#$ -m n' instead to disable all email for this job #$ -m eas #$ -M YOUR_EMAIL_ADDRESS #$ -l h_rt=2:00:00,s_rt=1:55:00 #$ -l vf=256M . /etc/profile.d/modules.sh module load R/R-2.7.2 #$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD R CMD BATCH rscript.R