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Name

APPS/STATISTIS/R-3.0.2

Description

R statistics program

Status

Production

Last update

2013-12-11

Usage example

Here is a simple test case for the runtime environment.

Download the example job here

The job description file R.xrsl:

&(executable=R.sh)
(jobname=R_test)
(stdout=std.out)
(stderr=std.err)
(cputime=60)
(memory=2000)
(runtimeenvironment="APPS/STATISTICS/R")
(inputfiles=
 ("sort.R" "sort.R" )
)

 

Corresponding execution script R.sh

#!/bin/sh
echo "Hello R"
R --vanilla < sort.R
exitcode=$?
exit $exitcode
Commands to submit the sample job in linux and MacOSX machines

Download and unpack the sample job:

Set up grid environment and submit the job

arcproxy
arcsub R.xrsl

 

Follow the progress of the job and retrieve the result when the job is finished,

arcstat job_id
arcget job_id

 

In the commands above, job_id should be replaced with the job identifier given by the the arcsub command

for example:

 

arcstat gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366
arcget gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366

 

The arcget command will store the results of the job to a new directory named according to the job ID number.

Interface definition

The runtime environment sets the following environment variables:

  • $R_DIR is set so that it points to the directory containing the R executables
  • PATH is set so that the $R_DIR is included in the path

System administrator guide for installing the RE

R executables

R pacage was downloaded from the R site:

wget http://cran.r-project.org/src/base/R-3/R-3.0.2.tar.gz
gunzip R-3.0.2.tar.gz
tar xvf R-3.0.2.tar
mkdir 3.0.2
cd R-3.0.2
./configure --prefix=/home/export/software/R/3.0.2 --with-x=no
make
make install
cd ../3.0.2/
 ./R --vanilla < install_packages.R

 

R libraries

When the R installation was ready, extra libraries were installed with R commands. (Note that not all the libraries listed below were successfully installed).

 

source("/opt/chipster/comp/modules/admin/R-2.14/smip.R")
install.packages(repos="http://ftp.sunet.se/pub/lang/CRAN", dependencies=TRUE, pkgs="locfit")
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("affy", ask=FALSE) # Methods for Affymetrix Oligonucleotide Arrays
biocLite("affyQCReport")
biocLite("altcdfenvs", ask=FALSE)
biocLite("AmpAffyExample", ask=FALSE)
# biocLite("AnnotationDbi") # Annotation Database Interface
biocLite("ape", ask=FALSE) # circular hclust dendrograms etc
biocLite("ArrayExpress")
biocLite("ArrayExpress", ask=FALSE)
biocLite("ash")
biocLite("beadarray")
biocLite("beadarraySNP")
biocLite("Biobase", ask=FALSE)
biocLite("biomaRt", ask=FALSE) # Requires RCurl
biocLite("Biostrings", ask=FALSE)
biocLite("BSgenome.Hsapiens.UCSC.hg19")
biocLite("CGHbase")
biocLite("CGHcall", ask=FALSE)
biocLite("CGHregions", ask=FALSE)
biocLite(c("GOstats","goTools","topGO"), ask=FALSE)
biocLite("ChIPpeakAnno")
biocLite("chipseq")
biocLite("cMAP", ask=FALSE)
biocLite("cosmo")
biocLite(c("Resourcerer","XML"), ask=FALSE)
biocLite(c("Rgraphviz","Ruuid"), ask=FALSE) # graphviz and its dependencies; did not install for R-2.11
biocLite("ctc")
#biocLite("CustomCDF")
biocLite("DBI", ask=FALSE) #RMySQL is a dependency?, AnnBuilder
biocLite('DESeq', ask=FALSE)
biocLite("DNAcopy")
biocLite("DPpackage", ask=FALSE)          # Dirichlet Processes / topic models etc
biocLite("drosgenome1.db", ask=FALSE)
biocLite("edgeR")
biocLite('edgeR', ask=FALSE)
biocLite("GeneCycle")
biocLite("GeneNet")
biocLite("geneplotter")
biocLite("GenomeGraphs")
biocLite("GenomicFeatures", ask=FALSE)
biocLite('GenomicRanges', ask=FALSE)
biocLite("GEOquery")
biocLite("ggbio", ask=FALSE)
biocLite("glmnet", ask=FALSE)             # Lasso, elastic net, regularized generalized linear models
biocLite("GlobalAncova")
biocLite("globaltest")
biocLite("GOstats")
biocLite("graph")
biocLite("graph", ask=FALSE)
biocLite("GSA", ask=FALSE)
biocLite("Heatplus", ask=FALSE) #annotated heatmaps
biocLite("hgu133a.db", ask=FALSE)
biocLite("hgu133aprobe", ask=FALSE)
biocLite("hgu133plus2cdf", ask=FALSE)
biocLite("hgu133plus2.db", ask=FALSE)
biocLite("hgu133plus2probe", ask=FALSE)
biocLite("hgu95a.db", ask=FALSE)
biocLite("hom.Hs.inp.db", ask=FALSE)
biocLite("idiogram")
biocLite("IlluminaHumanMethylation27k.db")
biocLite("impute")
biocLite('IRanges', ask=FALSE)
biocLite("KEGG.db", ask=FALSE) # A set of annotation maps for KEGGSOAP
biocLite("KEGGSOAP", ask=FALSE)
biocLite("kohonen", ask=FALSE) # better than 'som' package
biocLite("ks")
biocLite("limma", ask=FALSE) # Linear Models for Microarray Data
biocLite("locfit")
biocLite("LPE")
biocLite("lumi")
biocLite('lumi', ask=FALSE)
biocLite("lumiHumanIDMapping")
biocLite("lumiMouseIDMapping")
biocLite("lumiRatIDMapping")
biocLite("Matrix", ask=FALSE)  # boosting matrix calculations
biocLite("MEDIPS")
biocLite("mgu74a.db", ask=FALSE)
biocLite("microRNA", ask=FALSE)
biocLite("miRNApath", ask=FALSE)
biocLite("mixOmics", ask=FALSE) #http
biocLite("MLInterfaces")
biocLite("MotIV")
biocLite("oligo")
biocLite("oligoClasses")
biocLite("org.Hs.eg.db", ask=FALSE)
#biocLite("org.HsMm.ortholog.db")
biocLite("org.Mm.eg.db", ask=FALSE)
biocLite("pamr", ask=FALSE)
biocLite("PAnnBuilder")
#biocLite("pgfSweave")
biocLite("PICS")
biocLite("pint", ask=FALSE) # Pairwise INTegration of functional genomics data
biocLite("plier")
biocLite("PMA", ask=FALSE) #http
biocLite("prada")
biocLite('puma', ask=FALSE)
biocLite("qvalue")
biocLite("qvalue", ask=FALSE)
biocLite("RbcBook1", ask=FALSE)
biocLite('RBGL', ask=FALSE)
biocLite("RCurl", ask=FALSE)                                        
biocLite("rGADEM")
biocLite("RmiR")
biocLite("RmiR", ask=FALSE)
biocLite("RmiR.Hs.miRNA", ask=FALSE)
#biocLite("Rredland")
biocLite("Rsamtools")
biocLite("RSQLite", ask=FALSE)
biocLite("RSVGTipsDevice", ask=FALSE)  
biocLite("rtracklayer")
biocLite("rtracklayer", ask=FALSE)
biocLite("Ruuid")
biocLite("safe")
biocLite("seqLogo")
biocLite("ShortRead")
biocLite("ShortRead", ask=FALSE)
biocLite("siggenes")
biocLite("SIM", ask=FALSE) #http
biocLite("simpleaffy")
biocLite("snapCGH", ask=FALSE)
biocLite("SPIA", ask=FALSE)
biocLite("ssize")
biocLite("statmod")
biocLite('tigre', ask=FALSE)
biocLite("tikzDevice", ask=FALSE)
biocLite("TxDb.Mmusculus.UCSC.mm10.ensGene", ask=FALSE)
biocLite("vegan")


 

Modify the scripts as needed and save the main script in your ARC runtime directory as APPS/STATISTIS/R-3.0.2wget http://cran.r-project.org/src/base/R-3/R-3.0.2.tar.gz
  1004    10:49    gunzip R-3.0.2.tar.gz
  1005    10:49    tar xvf R-3.0.2.tar
  1007    10:49    mkdir 3.0.2
  1008    10:50    cd R-3.0.2
  1009    10:50    ./configure --prefix=/ (
  1010    10:50    pwd
  1011    10:50    ./configure --prefix=/home/export/software/R/3.0.2
  1012    10:52    ./configure --prefix=/home/export/software/R/3.0.2 --with-x=no
  1014    11:55    make install
  1017    12:01    3.0.2/
  1024    12:55    ./R < install_packages.R
  1026    12:57    nano install_packages.R
  1027    12:58    ./R --vanilla < install_packages.R

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