1 files changed, 51 insertions, 0 deletions
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
new file mode 100644
index 000000000000..bbddc6bdc8ad
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="A eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+src_unpack() {
+	unpack ${A}
+	mv GlimmerHMM ${P}
+}
+
+src_prepare() {
+	sed \
+		-e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
+		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
+		-i "${S}/train/trainGlimmerHMM" || die
+
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	tc-export CC CXX
+}
+
+src_compile() {
+	emake -C "${S}/sources"
+	emake -C "${S}/train"
+}
+
+src_install() {
+	dobin sources/glimmerhmm train/trainGlimmerHMM
+
+	insinto /usr/share/${PN}/lib
+	doins train/*.pm
+	insinto /usr/share/${PN}/models
+	doins -r trained_dir/*
+	exeinto /usr/libexec/${PN}/training_utils
+	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+	dodoc README.first train/readme.train
+}