Installation Instruction

Installation Instruction

NOT stable enough for open test yet due to current ongoing infrastructure change and updates.

Introduction

First, I want to thank you that you are interested in this project. Current visnab is not released to BioC yet, this package is built on R 2.14 and BioC 2.9. It should be stable in next release cycle of R and BioC. For now, it's still under frequently update, we cannot guarantee it provide accurate processing and visualization for experimental data, since a data validation stage is not conducted yet. It's not easy to install now, since visnab depends on several packages which are not released yet.

For those who still want to play with this package, here is a general instruction for installing this package.

Dependencies

There are two ways to install developmental version packages in Bioconductor. You can download those package here http://www.bioconductor.org/packages/devel/bioc/ , or you can install developmental R which is 2.14 currently, then run

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

then it's automatically installing the package in devel repos of BioC.

• Install system dependency , Qt 4.6+
• Install package qtbase/qtpaint/plumbr/objectSignals under https://github.com/ggobi
• Install package scales in https://github.com/hadley
• Install all depended package in bioconductor developmental repos 2.9. such as IRanges, GenomicGRanges
• Install rtracklayer, Rsamtools(bioc 2.9) if you want to run some examples
• Install package MutableRanges in the svn repos of bioconductor. Please check out the package.

svn co --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MutableRanges/

Install Visnab

Please run R CMD INSTALL directly on visnab without checking this package.