gentoo auto-resync : 27:08:2024 - 12:00:02

3 files changed, 56 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 15208c4ebe35..621896d2b335 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index c97246215a2f..269b2ea31c9d 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -2,4 +2,5 @@ AUX amap-2.2-includes.patch 1088 BLAKE2B 3b870c229f3efb9819d9f176b59b014ad4bae30
 AUX amap-2.2-makefile.patch 1089 BLAKE2B 5ed09060ebc9c0c5748d1bdd1517bc6d5e7989d8125db1dff13a221f13e69e717508ac30410ae0c38a4e126f490179ac68ee7e501f7c7d61888993c850f6fbf8 SHA512 cd08a7a71eb85521c60e522d3a8ea0b2bbe4dfb93c0f4d6f0e2e4c35787a0836f23f51f50c4c9344eeda6533a7d689c4b246c700f7d37b8b3666f4904bd625d6
 DIST amap.2.2.tar.gz 102861 BLAKE2B 7f9b1cb747946232db0b5b469896cc4f83ef78d190e929e28f37df790dfac342e6e7f913797bc9ff00191253318db2d42f79577dc72128d62a21d0e241bfb0e1 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f
 EBUILD amap-2.2-r5.ebuild 1104 BLAKE2B 120ae0dd66942b77dc7acc28d05b6f76c9dc1152dea85b419f2a84cab1a7ef2be373575bdd0f0edabfba1765c3a4db83b699c25ae0855c7e162d19d13f6b404f SHA512 60ad29cc9bb1698ff04eec6fa719f66a9fe0ebc57698f6986abc7b401a4781248140a73d36828d9592dae3176148fc0ee27e6baf0d302e461387b13b98ff9530
+EBUILD amap-2.2-r6.ebuild 1081 BLAKE2B abfa680a1d4f14cbb4fcffb646a781d59ad65022f0f75257e372cd0ca49e4de33da02447dbc7312f6c62a2ae561dfdc4ad406e546c84ecfe5ed790eceb440cf8 SHA512 df5007ef8960c066b9b6b49a2d2272b959d81a70835173afc1c456154d4b6394720e974db756f0e67fa78f661f2c8c403cf0dc1a74ce11fc995da661ff13cc37
 MISC metadata.xml 258 BLAKE2B 51009df26b3682090e316b4cf4a3afad84001705063be6c74a28fb11bacde48b758dc280bf9d4d049c69e728d9660e737072674ad5ff8068da4f6a49f1f4e203 SHA512 05153e39b77e8b1437a0ba80b66b6bb1b4837d719765cb157b23d5425a625ddb4056422dcbf28d182e039583a0b3863e8429efe80da85a035c96f4c4788ced6d
diff --git a/sci-biology/amap/amap-2.2-r6.ebuild b/sci-biology/amap/amap-2.2-r6.ebuild
new file mode 100644
index 000000000000..487616726fc4
--- /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
+}