Technical prerequisites for Bioinformatics research in R, RStudio and Ubuntu 14.04 LTS or Windows (64-bit versions)

Posted: 2014/10/18 in Data Science, Ubuntu
Tags: , , , ,

Purpose of these lists is to clarify which applications and R packages need to be installed on your PC to be able to perform bioinformatics research in Ubuntu 14.04 LTS or Windows (64-bit versions)


Order of installation of applications in Windows, Mac OS X or GNU/Linux before installing packages in R 3.1.1 or newer:

* libxml2-devel in Fedora 20 (=GNU/Linux distribution)
* gcc gcc47-c++ gcc-fortran in OpenSuse (=GNU/Linux distribution)
* gcc g++ gfortran xmlsec1 libxml2-dev libcurl4-openssl-dev r-cran-rcurl curl in Ubuntu 14.04 LTS 32-bit or 64-bit (=GNU/Linux distribution)
* R 3.1.1 or newer
* Windows 64-bit users should run the following .cmd script as administrator:

https://courses.edx.org/courses/KIx/KIexploRx/3T2014/discussion/forum/i4x-kiX-KIexploRx-course-2014_Practicalities/threads/5451f72635c79c749c000906

The previous .cmd script takes care of installing curl,R,RStudio and other applications in Windows. Or you can download curl here:

https://mark911.wordpress.com/2015/09/27/how-to-compile-and-install-newest-version-of-curl-from-github-in-ubuntu-14-04-lts-64-bit/

https://courses.edx.org/courses/KIx/KIexploRx/3T2014/discussion/forum/4ba16c478c9948cca206bf240bcd185d/threads/541873c00579cf8ead0005db

http://stackoverflow.com/questions/23198204/curl-is-not-recognized-as-an-internal-or-external-command

* Google Chrome browser or any other browser that uses the newest version of Adobe Flash in Windows, Mac OS X and GNU/Linux: https://www.google.com/chrome/browser/
* RStudio is optional, but recommended: http://www.rstudio.com/products/rstudio/download/
* I recommend avoiding RKWard (as R extension), as it seems to have issues with R 3.1.1 in combination with BioConductor packages.


Order of installation of R packages in R 3.1.1 (or newer) after installing previous applications in Ubuntu 14.04 LTS or Windows (64-bit versions):

* XML (requires install first of libxml2-dev or libxml2-devel in GNU/Linux)
* RJSONIO (requires install first of gcc and gcc47-c++ in OpenSuse and install of g++ in Ubuntu)
* Rcpp (requires R version >= 3.0.0 !)
* httr (requires R version >= 3.0.0 !)
* maps
* reshape2
* RCurl (requires install first of curl binary on operating system level)
* devtools (is required to install sweSCB R package from Github)
* sweSCB (install from github, requires install first of devtools R package)
* calibrate
* pheatmap
* gplots
* Biobase,BioConductor package, installed through biocLite()
* DESeq2 ,BioConductor package, installed through biocLite()
* biomaRt ,BioConductor package, installed through biocLite()
* org.Hs.eg.db ,BioConductor package, installed through biocLite()
* topGO ,BioConductor package, installed through biocLite()
* for those who want to do the extended, non-mandatory version of the lab: Rsubread is a BioConductor package which is not available on Windows. If you are on Windows, just do the short version of the lab. Rsubread only works on Linux and Mac OS X 32-bit and 64-bit systems.
* Rgraphviz,BioConductor package, installed through biocLite()
* GEOquery,BioConductor package, installed through biocLite()
* limma,BioConductor package, installed through biocLite()

Copy-paste each line below one line at a time into R or RStudio. Hit the ENTER key between each line.

install.packages("XML")
install.packages("RJSONIO")
install.packages("Rcpp", dependencies = TRUE)
install.packages("httr")
install.packages("maps")
install.packages("reshape2")
install.packages("RCurl")
install.packages("devtools", dependencies = TRUE)
devtools::install_github("sweSCB","rOpenGov")
install.packages("calibrate")
install.packages("pheatmap")
install.packages("gplots")

# install bioconductor packages
# warning: compiling DESeq2 may take a long time
# do NOT interrupt the process!

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

# run following biocLite("BiocUpgrade") 
# if you are upgrading from an older Bioconductor version
# to Bioconductor version 3.0 (BiocInstaller 1.16.0)
# The current release of Bioconductor is version 3.0 
# it works with R version 3.1.1
# Users of older R and Bioconductor versions must update their installation
# to take advantage of new features.

biocLite("BiocUpgrade")
biocLite("Biobase",dependencies=TRUE)
biocLite("DESeq2",dependencies=TRUE) 
biocLite("biomaRt")
biocLite("org.Hs.eg.db")
biocLite("topGO",dependencies=TRUE)
biocLite("Rsubread")
biocLite("Rgraphviz")
biocLite("GEOquery")
biocLite("limma")

Here is more info about installing the curl binary:

https://mark911.wordpress.com/2015/09/27/how-to-compile-and-install-newest-version-of-curl-from-github-in-ubuntu-14-04-lts-64-bit/

http://www.confusedbycode.com/curl/

http://www.confusedbycode.com/curl/

https://courses.edx.org/courses/KIx/KIexploRx/3T2014/discussion/forum/4ba16c478c9948cca206bf240bcd185d/threads/541873c00579cf8ead0005db

Source: https://courses.edx.org/courses/KIx/KIexploRx/3T2014/discussion/forum/i4x-kiX-KIexploRx-course-2014_Technical_issues/threads/541fda54f346085445000bc8

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