CpG-Islander

This script is designed for makeCGI package installation and execution.

The papers about CGI search using HMM can be found here:
http://www.ncbi.nlm.nih.gov/pubmed/20212320
http://www.ncbi.nlm.nih.gov/pubmed/19777308

Installation process

1. Install "BSgenome" and "Biostrings" Bioconductor packages (if you are in trouble see the instructions below)

2. Download and install makeCGI from the following page: http://rafalab.jhsph.edu/CGI/

You can install it via Tools/Install packages menu of RStudio or run the following commands

makecgi_directory="changeme"
setwd(makecgi_directory)
install.packages("makeCGI_1.2.tar.gz", repos = NULL, type = "source")

Installing Bioconductor packages

IF YOUR INTERNET CONNECTION USES PROXY

Replace username, password, proxy ip and port and run following in the terminal:

export http_proxy=http://username:password@proxy_address:proxy_port/
export HTTP_PROXY=http://username:password@proxy_address:proxy_port/

If you are using RStudio then restart it

Set proxy and check it

Sys.setenv(http_proxy="http://username:password@proxy_address:proxy_port/")

Check that proxy set up succeed

Sys.getenv("http_proxy")

INSTALL BIOCONDUCTOR PACKAGES

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

Install makeCGI dependencies

biocLite("BSgenome")
biocLite("Biostrings")