PLINK

PLINK is a program from the Shaun Purcell er al. at the Center for Human Genetic Research, Massachusetts General Hospital.

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. It intigrates with haploview and a graphical interface gPlink to aid in the visualisation an anotation of results. PLINK also integrates with R to facilitate analysis.

Key features of PLINK include

• Excellent data handling capabilities (multiple formats supported).
• IBD/IBS non-parametric linkage analysis.
• Association tests for loci, hapoltypes, quantitative traits, epistasis and much more.
• Monte-Carlo simulations for validation of results.
• Handling of Population Stratification.
• Analysis of Copy Number Variants (CNVs).

The ebuild is shown below

# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
 
DESCRIPTION="PLINK is a set of tools for the statistical analysis of Whole Genom
e Association Studies."
HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"
 
# License of the package.  This must match the name of file(s) in
# /usr/portage/licenses/.  For complex license combination see the developer
# docs on gentoo.org for details.
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~x86"
IUSE="R"
 
S="${WORKDIR}/${P}-src"
 
DEPEND="
        virtual/libc
        virtual/jdk"
RDEPEND="${DEPEND}
        virtual/jre
        R? ( dev-lang/R )"
 
src_install() {
        mkdir ${D}usr
        dobin ${PN} gPLINK.jar || die "Install failed"
}

plink-1.03.ebuild

Create a directory in your /usr/local/portage overlay, grab the ebuild, digest it and emerge it

# mkdir -p /usr/local/portage/sci-biology/plink
# cd /usr/local/portage/sci-biology/plink
# wget http://kimura.no-ip.org/dokuwiki/lib/exe/fetch.php?id=plink&cache=cache&media=plink-1.03.ebuild.bz2
# bunzip2 plink-1.03.ebuild.bz2
# ebuild plink-1.03.ebuild digest
# emerge -av plink

• Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81 PubMedfull article

• PLINK homepage
• Plink Tutorial
• Shaun Purcell
• Center for Human Genetic Research, Massachusetts General Hospital