1 files changed, 55 insertions, 0 deletions
diff --git a/sci-biology/amap/amap-2.2-r6.ebuild b/sci-biology/amap/amap-2.2-r6.ebuild
new file mode 100644
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--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r6.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-opt-2 java-pkg-simple toolchain-funcs
+
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
+SRC_URI="http://baboon.math.berkeley.edu/amap/download/${P/-/.}.tar.gz"
+S="${WORKDIR}/amap-align"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+DEPEND="java? ( >=virtual/jdk-1.8:* )"
+RDEPEND="java? ( >=virtual/jre-1.8:* )"
+
+DOCS=( align/{README,PROBCONS.README} )
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-includes.patch
+)
+
+src_prepare() {
+	default
+	use java && java-pkg-opt-2_src_prepare && java-pkg_clean
+}
+
+src_configure() {
+	tc-export CXX
+}
+
+src_compile() {
+	emake -C align
+	if use java; then
+		JAVA_JAR_FILENAME="amapdisplay.jar"
+		JAVA_SRC_DIR="display/src"
+		java-pkg-simple_src_compile
+	fi
+}
+
+src_install() {
+	dobin align/${PN}
+
+	insinto /usr/share/${PN}
+	doins -r examples
+
+	use java && java-pkg-simple_src_install
+}