reinit the tree, so we can have metadata

6 files changed, 174 insertions, 0 deletions

diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
new file mode 100644
index 000000000000..c3e170942280
--- /dev/null
+++ b/sci-biology/probcons/Manifest
@@ -0,0 +1,8 @@
+AUX gcc-4.3.patch 1300 SHA256 e9669d83770557834b54268f0b4e404981b91084587d69f6492c7160c1659d6b SHA512 a1839f844cd9ce0cd7a9542c0e4abaa859ed8f4f42de1dfae01af72ceb0326019379ba17ae56d4756bbb7d649da0b5deeb624cbcd5176de8a5ab34123fb689bd WHIRLPOOL 87c1ab62d7ead97f5dfe5ad01826eca1bd80887ff86efba50935419095156fff338350923ff21ec9673924a430760144e0ef364178daeb7e13340087a07eac40
+AUX probcons-1.12-cxxflags.patch 1957 SHA256 5342d2f86fc2d440db1649e0e1f4cf094d8e5a5861c145fb410d014bc9cd8a27 SHA512 033e92e414d3e2d1db867aec980d82759a662cf46692e3cc908bb7b3428d5eca105fb81cbdd8764c54dd3d759d29e713ef085fc48aac183426d26fe68a48a38e WHIRLPOOL 42c13cf76077bcaccf7eeea31f8defbbc82108b4314ba2cf494a8220d57dbf89a2cdb943fec36a21c46fcda7ad7c4abfc4eecfe8280ea2679d5b740c56150431
+AUX probcons-1.12-gcc-4.6.patch 306 SHA256 75bff1b697a732e183f1d4e20153b7b37afb4d3242f43305651c044809a02761 SHA512 f8a393cce2a860ea54aa18add7ba236aa43e21893925e4484b272190e29aa2dc27bf20b11edc5694446f027c6d8d6ff3c3f92383f0b0c8958b1b1d5b7564f828 WHIRLPOOL 5bc8ae7d4d35e6989fe2606b86ea236e3baaf72ecba15bd4ec15d10bad09eef47c3a7cb508329a38607c403d75906183f8381f0cda11b4b835067434694146b4
+DIST probcons_v1_12.tar.gz 43200 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383 SHA512 ce061ea5cca4204d6e66beb893c1ba508f094b7ea3ee08196dc75a5443ebd0afca14dc8d7cd6c8da4ce1578b8750ea1981e5815408c0b122e8f97ec27b3bf008 WHIRLPOOL 82810ebf7ee18bb16268fcd526a2e5318812f4eef009ef13430f71457687d7d6f6a1bda3ee4f9ce8ab1251387315d7e105494ecfd3ba30da6fad7c4ac6304715
+EBUILD probcons-1.12-r1.ebuild 1184 SHA256 92b6899bc4b4c622babc99b487a98870b14ad8cddfa9aadf0a7f1d52f4777676 SHA512 da6c987d200faa0aa9a8a243eb8ac9a6ebe7381e9b1488477dbc659106df88aaeca8bb6005c25bbfad0757c5178e15b346a2872562705f76a921cccd68f8a466 WHIRLPOOL bd5637413ef1b319c4059c46561c4c0ed6f76b5ccda6b264b41afd9f36f524e6fd0c1e37aaad062dd293923d82a16bea82503b7cee8142861d559a25bf36deb1
+MISC ChangeLog 2534 SHA256 0a1a0f7c6dec4c3915219e2a959a14c05056a3efa24e73fdb3512570f34e0e1b SHA512 614bf838fc10d45811306fdd8f9ab65eb25066eb33482ed086d875c2550c99b42449c48840edd6d5e5e406b83781e27e63107c48592b557f748f8d5c7b5bba54 WHIRLPOOL 4329796d453f9304df3b76ff4ce1f1d56fb2d14a3a37f16e5fb507879ef2f972f4005fea35a500ead13fec8f78cd83dea859b2c71feda8ce1a3e0a7b1b2574f0
+MISC ChangeLog-2015 2437 SHA256 7d9d0fb934a1fc4e86dd6341350c939b45f9836b2ecb6a275d3712626c3ca4b1 SHA512 8d48e29d79fcf12a7ddb5396f1706f782e80471e50d07950c5f61fc5b3e2f0314676fc84424df5b64dda0dab15a55b97205ebb728afbfdf4aca53404665983ea WHIRLPOOL 6d99fce52c6fa9115cbd8dc50a95a1e6f564e1514b88dd72fc0e9ed027aac8e5dc84e1c6dd46e382770a4eca387f96fc376bafde4743d5ab261f180c91900479
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/probcons/files/gcc-4.3.patch b/sci-biology/probcons/files/gcc-4.3.patch
new file mode 100644
index 000000000000..37c45c03a98f
--- /dev/null
+++ b/sci-biology/probcons/files/gcc-4.3.patch
@@ -0,0 +1,44 @@
+diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc
+--- probcons.orig/CompareToRef.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/CompareToRef.cc	2008-04-08 16:39:41.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/FixRef.cc probcons/FixRef.cc
+--- probcons.orig/FixRef.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/FixRef.cc	2008-04-08 16:39:33.000000000 -0700
+@@ -17,6 +17,7 @@
+ #include <algorithm>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/Main.cc probcons/Main.cc
+--- probcons.orig/Main.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/Main.cc	2008-04-08 16:39:14.000000000 -0700
+@@ -21,6 +21,7 @@
+ #include <climits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc
+--- probcons.orig/ProjectPairwise.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/ProjectPairwise.cc	2008-04-08 16:39:25.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
new file mode 100644
index 000000000000..e07ebe1a613f
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
@@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index 75fc47a..4a19140 100644
+--- a/Makefile
++++ b/Makefile
+@@ -15,6 +15,8 @@ CXX = g++
+ #    c) RELEASE mode
+ ################################################################################
+ 
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+ 
+ # debug mode    
+@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+ 
+ # 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
+@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot
+ all : $(TARGETS)
+ 
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+-	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm
+ 
+ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+-	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc
+ 
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+-	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc
+ 
+ project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+-	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc
+ 
+ makegnuplot : MakeGnuPlot.cc
+-	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+ 
+ .PHONY : clean
+ clean:
diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
new file mode 100644
index 000000000000..1596f3b31916
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
@@ -0,0 +1,15 @@
+ SafeVector.h |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/SafeVector.h b/SafeVector.h
+index abf4b64..9c3292e 100644
+--- a/SafeVector.h
++++ b/SafeVector.h
+@@ -8,6 +8,7 @@
+ #ifndef SAFEVECTOR_H
+ #define SAFEVECTOR_H
+ 
++#include <cstddef>
+ #include <cassert>
+ #include <vector>
+ 
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/probcons/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild
new file mode 100644
index 000000000000..01973b88cab9
--- /dev/null
+++ b/sci-biology/probcons/probcons-1.12-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}_v${PV/./_}"
+
+DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
+HOMEPAGE="http://probcons.stanford.edu/"
+SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+# Gnuplot is explicitly runtime-only, it's run using system()
+RDEPEND="
+	!sci-geosciences/gmt
+	sci-visualization/gnuplot"
+DEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-cxxflags.patch \
+		"${FILESDIR}"/gcc-4.3.patch \
+		"${FILESDIR}"/${P}-gcc-4.6.patch
+}
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin probcons project makegnuplot
+	# Overlap with imagemagick
+	newbin compare compare-probcons
+	dodoc README
+}
+
+pkg_postinst() {
+	ewarn "The 'compare' binary is installed as 'compare-probcons'"
+	ewarn "to avoid overlap with other packages."
+	einfo "You may also want to download the user manual"
+	einfo "from http://probcons.stanford.edu/manual.pdf"
+}