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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit eutils flag-o-matic base subversion # autotools
DESCRIPTION="A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin)."
HOMEPAGE="http://sourceforge.net/projects/staden"
# https://staden.svn.sourceforge.net/svnroot/staden staden
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk"
#KEYWORDS="~amd64 ~x86"
else
SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz"
#KEYWORDS="~amd64 ~x86"
fi
LICENSE="staden"
SLOT="0"
KEYWORDS=""
IUSE="debug fortran X png curl tcl tk zlib"
# either g77 or gfortran must be available
# edit src/mk/linux.mk accordingly
#
# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
#
#
#
DEPEND="dev-vcs/subversion
>=dev-lang/tk-8.4
>=dev-lang/tcl-8.4
dev-tcltk/tklib
>=sci-libs/io_lib-1.12.2
>=sys-libs/zlib-1.2
>=media-libs/libpng-1.2
sci-biology/samtools
>=app-arch/xz-utils-4.999"
# maybe we should depend on app-arch/lzma or app-arch/xz-utils?
RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
tk? ( >=dev-tcltk/itk-3.2 )
>=dev-tcltk/iwidgets-4.0"
src_unpack() {
if [ "$PV" == "9999" ]; then
subversion_src_unpack
S="${WORKDIR}"/"${P}"/src/ || die
cd "${S}" || die
./bootstrap || die "bootstrap failed"
else
unpack ${A} || die
S="${WORKDIR}"/staden-2.0.0b7-src || die "Cannot cd ${WORKDIR}/staden-2.0.0b7-src"
cd "${S}" || die "Cannot cd ${S}"
./bootstrap || die "bootstrap failed"
fi
}
src_configure() {
local myconf
use X && myconf=" --with-x"
myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK, see http://bugs.gentoo.org/show_bug.cgi?id=311847#c10
use amd64 && myconf="${myconf} --enable-64bit"
use debug && append-cflags "-DCACHE_REF_DEBUG"
use debug && append-cxxflags "-DCACHE_REF_DEBUG"
econf ${myconf} || die "configure failed"
emake || die "emake failed"
}
src_compile() {
emake || die "emake failed"
}
src_install() {
emake install DESTDIR="${D}" || die "make install failed"
echo "STADENROOT="${EPREFIX}"/usr/share/staden" > "${S}"/99staden
doenvd "${S}"/99staden || die
}
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