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Introduction
Usage
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module load misc/bibench |
Installation
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module load R/3.4.0 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/') ###installinstall.packages('Bioconductorisa2', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('fabiaMASS', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('GEOquery', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('GEOmetadb', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('GOstats', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('GO.db', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('multtest', dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages('pcaMethods', dependencies=TRUE, repos='http://cran.rstudio.com/') |
Dependencies
...
source("https://bioconductor.org/biocLite.R")
biocLite()
source("https://bioconductor.org/biocLite.R")
biocLite("fabia")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GEOquery")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GEOmetadb")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GOstats")
source("http://www.bioconductor.org/biocLite.R")
biocLite("GO.db")
source("http://www.bioconductor.org/biocLite.R")
biocLite("multtest")
source("http://www.bioconductor.org/biocLite.R")
biocLite("pcaMethods")
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Dependencies
bioconductor
sleipnir
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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