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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit flag-o-matic fortran-2
DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
HOMEPAGE="https://sourceforge.net/projects/staden"
SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
LICENSE="staden"
SLOT="0"
KEYWORDS="~amd64"
IUSE="debug doc fortran png tcl tk X zlib"
# either g77 or gfortran must be available
# edit src/mk/linux.mk accordingly
#
# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
#
#
#
DEPEND="
app-arch/xz-utils
dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
sci-biology/samtools:0
>=sci-libs/io_lib-1.13.8
sys-libs/zlib"
RDEPEND="${DEPEND}
>=dev-tcltk/iwidgets-4.0
tcl? ( >=dev-tcltk/itcl-3.2 )
tk? ( >=dev-tcltk/itk-3.2 )
net-misc/curl
doc? ( sci-biology/staden_doc )"
S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
PATCHES=(
"${FILESDIR}/${P}-ldflags.patch"
)
src_prepare() {
default
sed \
-e 's:svnversion:false:' \
-i configure.in || die
}
src_configure(){
use debug && append-cflags "-DCACHE_REF_DEBUG"
econf \
$(use_enable X x) \
$(use_enable amd64 64bit) \
--with-tklib="/usr/$(get_libdir)/tklib"
}
src_install() {
default
# 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
}
pkg_postinst(){
einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
}
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