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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit python-r1
DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds"
HOMEPAGE="
http://sourceforge.net/projects/scaffold-b
http://edwards.sdsu.edu/scaffold_builder"
SRC_URI="
http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
#http://www.scfbm.org/content/8/1/23
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
sci-biology/mummer"
DEPEND="${RDEPEND}"
S="${WORKDIR}"
src_install(){
echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
cat scaffold_builder.py >> scaffold_builder.pyy || die
mv scaffold_builder.pyy scaffold_builder.py || die
python_foreach_impl python_doscript scaffold_builder.py
dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
newdoc "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf
}
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