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Table of Contents

 

Introduction

 

Usage

No Format
module load misc/bibench

 

Installation

 

No Format
module load R/3.34.30
module load python/2.7.10
module load gsl/2.3
module load misc/bbc/bbc
module load misc/cpb/cpb
export OPSM_HOME=/sw/misc/opsm
module load misc/bicat/2.22
module load misc/qubic/1.0
module load misc/sleipnir/sleipnir 
 
pip install numpy rpy2 decorator nose sphinx

wget http://bmi.osu.edu/hpc/software/BiBench-0.2.tar.gz
python setup.py build 2>&1 | tee pythonBuildLog.txt
python setup.py install 2>&1 | tee pythonInstallLog.txt


install.packages('biclustRCurl', dependencies=TRUE, repos='http://cran.rstudio.com/')
install.packages('isa2XML', dependencies=TRUE, repos='http://cran.rstudio.com/')

install.packages('MASSbiclust', dependencies=TRUE, repos='http://cran.rstudio.com/')
install.packages('Bioconductorisa2', dependencies=TRUE, repos='http://cran.rstudio.com/')
install.packages('fabiaMASS', dependencies=TRUE, repos='http://cran.rstudio.com/')

source("https://bioconductor.org/biocLite.R")
biocLite()
install.packages('GEOquery', dependencies=TRUE, repos='

source("https://bioconductor.org/biocLite.R")
biocLite("fabia")




source("http://www.bioconductor.org/biocLite.R")
biocLite("GEOquery")

source("http://cranwww.rstudiobioconductor.com/'org/biocLite.R")
install.packagesbiocLite('"GEOmetadb', dependencies=TRUE, repos='")

source("http://cranwww.rstudiobioconductor.com/'org/biocLite.R")
install.packagesbiocLite('"GOstats', dependencies=TRUE, repos='")

source("http://cranwww.rstudiobioconductor.com/'org/biocLite.R")
install.packagesbiocLite('"GO.db', dependencies=TRUE, repos='")
 

source("http://cranwww.rstudiobioconductor.com/'org/biocLite.R")

install.packages('multtest', dependencies=TRUE, repos='biocLite("multtest")


source("http://cranwww.rstudiobioconductor.com/'org/biocLite.R")
install.packagesbiocLite('pcaMethods', dependencies=TRUE, repos='http://cran.rstudio.com/')


"pcaMethods")

Dependencies

bioconductor

Bioconductor

sleipnir

No Format
wget https://bitbucket.org/libsleipnir/sleipnir/get/sleipnir.tar.gz
tar -zxvf sleipnir.tar.gz
cd /sw/misc/sleipnir/src/libsleipnir-sleipnir-d629287d6273
sh ./gen_auto
./configure --prefix=/sw/misc/sleipnir --with-gsl=/sw/gsl/gsl-2.3 2>&1 | tee configureLog.txt
make 2>&1 | tee makeLog.txt
make install 2>&1 | tee makeInstallLog.txt

 

 

Reference

 

  1. http://bmi.osu.edu/hpc/software/bibench/install.html