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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
AUTOTOOLS_AUTORECONF=yes
inherit autotools-utils eutils flag-o-matic fortran-2 multilib
DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
HOMEPAGE="http://sourceforge.net/projects/staden/"
SRC_URI="
http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz
http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
LICENSE="staden"
SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE="curl debug fortran png tcl tk X zlib"
# either g77 or gfortran must be available
# edit src/mk/linux.mk accordingly
#
# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
#
#
#
DEPEND="
app-arch/xz-utils
dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
sci-biology/samtools
>=sci-libs/io_lib-1.12.2
sys-libs/zlib"
RDEPEND="${DEPEND}
>=dev-tcltk/iwidgets-4.0
tcl? ( >=dev-tcltk/itcl-3.2 )
tk? ( >=dev-tcltk/itk-3.2 )"
S="${WORKDIR}"/staden-${PV/_beta/b}-src
AUTOTOOLS_IN_SOURCE_BUILD=1
PATCHES=(
"${FILESDIR}"/${P}-ldflags.patch
"${FILESDIR}"/${P}-libpng-1.5.patch
"${FILESDIR}"/${P}-zlib.patch )
src_prepare() {
sed \
-e 's:svnversion:false:' \
-i configure.in || die
AT_M4DIR=ac_stubs autotools-utils_src_prepare
}
src_configure(){
local myeconfargs=()
use X && myeconfargs+=( --with-x )
myeconfargs+=(
--with-tklib=/usr/$(get_libdir)/tklib
)
use amd64 && myeconfargs+=( --enable-64bit )
use debug && append-cflags "-DCACHE_REF_DEBUG"
autotools-utils_src_configure
}
src_install() {
autotools-utils_src_install
# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
#cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src || die "failed to cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src"
#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
# subsequently, apps linked against /usr/lib/staden can be run because
# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
# somehow for gap2caf, for example
cat >> "${T}"/99staden <<- EOF
STADENROOT="${EPREFIX}"/usr/share/staden
LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
EOF
doenvd "${T}"/99staden
}
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