This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for readDepth version v0.9.8.4 2012/06/01

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Prerequisites

"Make sure all R package dependencies are installed (methods, foreach, doMC, IRanges, DNAcopy). Some of these are found in the Bioconductor repositories."

• $ sudo R
• > install.packages("doMC")
• > source("http://bioconductor.org/biocLite.R")
• > biocLite("DNAcopy")
• > quit()

Installation

1. $ cd /programinstallers/
2. $ wget -N http://readdepth.googlecode.com/files/readDepth_0.9.8.4.tar.gz
3. $ sudo R CMD INSTALL readDepth_0.9.8.4.tar.gz
4. Programs to make annotation files
   $ wget -N http://readdepth.googlecode.com/files/createCustomAnnotations.v1.tar.gz
5. $ tar -zxvf createCustomAnnotations.v1.tar.gz
   

   createCustomAnnotations.v1/
   createCustomAnnotations.v1/runEachChr.sh
   createCustomAnnotations.v1/allSeq.pl
   createCustomAnnotations.v1/mapAndGc.pl
   createCustomAnnotations.v1/README

6. Install
   $ cd createCustomAnnotations.v1
7. $ cp -puv runEachChr.sh allSeq.pl mapAndGc.pl /usr/local/bin/
8. Copy README file for web documentation
   $ mkdir /U:/simonlabweb/bioinformatics/programs/readdepth
9. $ cp -puv README /U:/simonlabweb/bioinformatics/programs/readdepth/ccaREADME.txt