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Diffstat (limited to 'sci-biology/mummer/mummer-3.20.ebuild')
-rw-r--r-- | sci-biology/mummer/mummer-3.20.ebuild | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild new file mode 100644 index 000000000000..2f566667ceca --- /dev/null +++ b/sci-biology/mummer/mummer-3.20.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +MY_P="MUMmer${PV}" +DESCRIPTION="A rapid whole genome aligner" +HOMEPAGE="http://mummer.sourceforge.net/" +SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="doc" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/${MY_P}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-gcc43.patch + # Warning: package uses CPPFLAGS on c in addition to cpp, despite the name + sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \ + -e 's/LDFLAGS =$//' "${S}/Makefile" +} + +src_compile() { + emake || die "emake failed" + + sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \ + -e 's|\(set bindir = \).*|\1/usr/bin|' \ + -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \ + -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \ + scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths" + sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh +} + +src_install() { + dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \ + exact-tandems promer repeat-match show-aligns gaps mummer \ + show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die + newbin annotate mummer-annotate || die + + insinto /usr/share/${PN}/scripts + doins scripts/{*.awk,*.csh,*.pl} + insinto /usr/share/${PN}/lib + doins scripts/Foundation.pm || die + + dodoc ACKNOWLEDGEMENTS ChangeLog README + insinto /usr/share/doc/${PF} + use doc && doins -r docs +} |