reinit the tree, so we can have metadata

5 files changed, 150 insertions, 0 deletions

diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
new file mode 100644
index 000000000000..a849ef2db919
--- /dev/null
+++ b/sci-biology/amap/Manifest
@@ -0,0 +1,7 @@
+AUX amap-2.2-includes.patch 1088 SHA256 3b22dd095d3dcf674528eb4641f325f7f3e30dc2f8d1173eefa8e1474d1fc5e2 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044 WHIRLPOOL fe51978a3a6538e9c57731bfa3b511b342ee95dc93b0fce75f0afef25f6b5d398cf323206e75dac10d0f1bdba538f6a1dfa056d6e0dfa5d68e961579ea6ee863
+AUX amap-2.2-makefile.patch 1201 SHA256 e5ab2e395a610632080c8736bd7e5e91ca36e87ee2165c8b2780772fb85f0cdc SHA512 8cd43b70299e12f32dd6b46a73e6ef10c7e85b5ec6d152aef69f54954a1083c92570c40bf35ea363084a3626161c3e28d214bb2c5fb76bb396d9be2edaa869a3 WHIRLPOOL dbf74ca0a9f32c9bba5e1ccc7346b4de6ffb5b6ff5d4002ee5ed3358b18f2073d917399eb797cb588f78aa97e2c20f94566ca92332e04986c4b72ba46f02e044
+DIST amap.2.2.tar.gz 102861 SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f WHIRLPOOL 2d4b8ff711888bce570aa823e323525b104aef16c57090dc18c3fdcec39a98012b2597b7015bbe9a3626b15d438e488deffcaef96f426fc73a47f10f117c237e
+EBUILD amap-2.2-r3.ebuild 1135 SHA256 76f1e79ba6494cab86c84d6549a1b7a653708d40ad87f33523ed26ccb9fa040c SHA512 d5bbb29ad83fd210b3ba7f84884f4bb517d132fbdaa58b658c679cccd96f1219f9fe3d6f8f58a029a10c782e916f441a9e8de969390c168c0202fb230fdb21a1 WHIRLPOOL a7cc931377e49f60abd1daa81dcfbb026e9faa1afcc989e31f328d14282bd4af172ececf659d1e8bade4b0c9b0647f7ea3f5880130099637c27b68e67b54e940
+MISC ChangeLog 2489 SHA256 326205792fcd67fe106972194e905ba9ae25bb794fba715b7fce5199ca999402 SHA512 e21b9c2380fe0cf29d67e329413ee2183fb4af8c4917220ac2d32899be795c7619614d9f9dc57714ebc34512f766f05986a9a8750de16e52a8b12b72f1805d30 WHIRLPOOL 6df50410fe7d249640317502a9b7a4805b2b5df76d5080bb1df9a49ae5c0c9ed40f860f46a15c421c73036d9e2e519d217cbd93bf13eff7982cb19ac6a731d23
+MISC ChangeLog-2015 1909 SHA256 483d897d4db46baf9efcd1e7208f33d86c8fc33c4adbf438751f082034b380a4 SHA512 6307597849b1d2ca56d5f9a4a8f1d59f6ee6bcad9776f0c322844d244c35aa3fa0e52d80ee039dc2e29785194748a2d5e643efade58d27861b105043df70d2c6 WHIRLPOOL e4118bc4e5f0d46a34816927483e6c1de832197c9cbffb739e58062e446ca2ecd1d0313c12a1e1f0af6a1c111d9a0dc8d58c574e290d281460483bcfab6c125b
+MISC metadata.xml 257 SHA256 4fb4f49e90ca33b7ed48e29dad0b163cb069e546927f1935e1ef75df1faf0087 SHA512 5be44a06c71b100dfe66effc1d12a9801f6daf2e252f74b6499528644db9b3dd00d51827a984817b78755e8d544f9c674c27c6a370c4c4414ce26a09b478b69b WHIRLPOOL 1ba3dd46c533b22c9b1ac469d0f110149fe5b2081961928d96913b72698c527c317cb17f9ce74451100d7769646b7fd0e3d7c534149474f1d04520704e4e7b1e
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..7776e25bc56e
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r3.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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
+}
diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch
new file mode 100644
index 000000000000..77c4261db5cf
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-includes.patch
@@ -0,0 +1,44 @@
+Fixes build with gcc 4.3 and 4.6
+
+http://bugs.gentoo.org/217921
+http://bugs.gentoo.org/360517
+
+--- amap-align/align/Amap.cc
++++ amap-align/align/Amap.cc
+@@ -12,6 +12,8 @@
+ #include "ProbabilisticModel.h"
+ #include "EvolutionaryTree.h"
+ #include "SparseMatrix.h"
++#include <limits>
++#include <climits>
+ #include <string>
+ #include <sstream>
+ #include <iomanip>
+@@ -23,6 +25,7 @@
+ #include <cstdlib>
+ #include <cerrno>
+ #include <iomanip>
++#include <cstring>
+ 
+ string parametersInputFilename = "";
+ string parametersOutputFilename = "no training";
+--- amap-align/align/MultiSequenceDag.h
++++ amap-align/align/MultiSequenceDag.h
+@@ -13,6 +13,7 @@
+ #include <map>
+ #include <queue>
+ #include <iostream>
++#include <limits>
+ #include "MultiSequence.h"
+ #include "SparseMatrix.h"
+ 
+--- amap-align/align/SafeVector.h.org	2011-03-26 11:50:11.935069583 +0100
++++ amap-align/align/SafeVector.h	2011-03-26 11:50:21.112553151 +0100
+@@ -9,6 +9,7 @@
+ #define SAFEVECTOR_H
+ 
+ #include <cassert>
++#include <cstddef>
+ #include <vector>
+ 
+ /////////////////////////////////////////////////////////////////
diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch
new file mode 100644
index 000000000000..5a9841c98255
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-makefile.patch
@@ -0,0 +1,35 @@
+Respect {CXX,LD}FLAGS
+
+http://bugs.gentoo.org/332009
+
+--- amap-align/align/Makefile
++++ amap-align/align/Makefile
+@@ -15,6 +15,8 @@
+ #    c) RELEASE mode
+ ################################################################################
+ 
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"'
+ 
+ # debug mode    
+@@ -26,8 +28,7 @@
+ 
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+-
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+ ################################################################################
+ # 3) Dependencies
+ ################################################################################
+ 
+@@ -38,7 +37,7 @@
+ all : $(TARGETS)
+ 
+ amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc
+-	$(CXX) $(CXXFLAGS) -lm -o amap Amap.cc 
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm
+ 
+ .PHONY : clean
+ clean:
diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml
new file mode 100644
index 000000000000..e051c9b41035
--- /dev/null
+++ b/sci-biology/amap/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>sci-biology@gentoo.org</email>
+	<name>Gentoo Biology Project</name>
+</maintainer>
+</pkgmetadata>