====== Fugue ======
Fugue is a program from the [[http://www.sph.umich.edu/csg/abecasis|Abecassis Lab]] at the Center for Statistical Genetics, University of Michigan.

Its used to reconstruct haplotypes from high density human genetic data derived from platforms such as Affymetrix SNPchip or Illumina Bead Array, and is capable of handling population based data (i.e. unrelated individuals) or family based data (i.e. related individuals) and as such was used to derive the haplotype maps of human chromosomes 19 and 22

===== Ebuild =====
The ebuild is shown below
<code python>
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

DESCRIPTION="Haplotype reconstruction and association testing in individuals.\
 and families."
HOMEPAGE="http://www.sph.umich.edu/csg/abecasis/fugue/"
SRC_URI="http://www.sph.umich.edu/csg/abecasis/fugue/${P}.tar.gz"
SLOT="0"

# 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=""

KEYWORDS="~x86"

src_install() {
        mkdir ${D}usr #For some reason this is needed
        make install INSTALLDIR=${D}usr/bin || die
}

</code>

{{:fugue-0.2.3.ebuild.bz2|fugue-0.2.3.ebuild}}

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

<code bash>
# mkdir -p /usr/local/portage/sci-biology/fugue
# cd /usr/local/portage/sci-biology/fugue
# wget http://kimura.no-ip.org/dokuwiki/lib/exe/fetch.php?id=fugue&cache=cache&media=fugue-0.2.3.ebuild.bz2
# ebuild fugue-0.2.3.ebuild digest
# emerge -av fugue
</code>

===== References ======

  * Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA //et al.// (2002) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. //Nature Genetics// **33**:382-387 [[http://www.ncbi.nlm.nih.gov/pubmed/12590262|PubMed]][[http://www.sph.umich.edu/csg/abecasis/publications/pdf/Nat.Genet.vol.33-pp.382.pdf|full article]]
  * Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM //et al.// (2002) A first-generation linkage disequilibrium map of human chromosome 22.//Nature// **418**:544-548 [[http://www.ncbi.nlm.nih.gov/pubmed/12110843|PubMed]][[http://www.sph.umich.edu/csg/abecasis/publications/pdf/Nature.vol.418-pp.544.pdf|full article]]

===== Links =====
  * [[http://www.sph.umich.edu/csg/abecasis/fugue/|Fugue homepage]]
  * [[http://www.sph.umich.edu/csg/abecasis/|Abecasis Lab]]
  * [[http://www.sph.umich.edu/csg/|Ceneter for Statistical Genetics, University of Michigan]]