1 files changed, 57 insertions, 0 deletions
diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r3.ebuild
new file mode 100644
index 000000000000..68af0d66acb4
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r3.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
+
+MY_P=${PN}.${PV}
+
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+RDEPEND="java? ( >=virtual/jre-1.5 )"
+DEPEND="java? ( >=virtual/jdk-1.5 )"
+
+S=${WORKDIR}/${PN}-align
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-includes.patch
+)
+
+src_prepare() {
+	default
+	java-pkg-opt-2_src_prepare
+}
+
+src_compile() {
+	emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}"
+
+	if use java; then
+		pushd display >/dev/null || die
+		eant -Ddisplay all || die
+		popd >/dev/null || die
+	fi
+}
+
+src_install() {
+	dobin align/${PN}
+
+	dodoc align/{README,PROBCONS.README}
+
+	insinto /usr/share/${PN}/examples
+	doins -r examples/.
+
+	if use java; then
+		java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar
+		java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
+	fi
+}