From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/probcons/Manifest | 8 ++++ sci-biology/probcons/files/gcc-4.3.patch | 44 ++++++++++++++++++ .../probcons/files/probcons-1.12-cxxflags.patch | 47 +++++++++++++++++++ .../probcons/files/probcons-1.12-gcc-4.6.patch | 15 +++++++ sci-biology/probcons/metadata.xml | 8 ++++ sci-biology/probcons/probcons-1.12-r1.ebuild | 52 ++++++++++++++++++++++ 6 files changed, 174 insertions(+) create mode 100644 sci-biology/probcons/Manifest create mode 100644 sci-biology/probcons/files/gcc-4.3.patch create mode 100644 sci-biology/probcons/files/probcons-1.12-cxxflags.patch create mode 100644 sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch create mode 100644 sci-biology/probcons/metadata.xml create mode 100644 sci-biology/probcons/probcons-1.12-r1.ebuild (limited to 'sci-biology/probcons') 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 + #include + #include ++#include + #include + #include + +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 + #include + #include ++#include + #include + #include + +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 + #include + #include ++#include + #include + #include + +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 + #include + #include ++#include + #include + #include + 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) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc + + .PHONY : clean + clean: diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch new file mode 100644 index 000000000000..1596f3b31916 --- /dev/null +++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch @@ -0,0 +1,15 @@ + SafeVector.h | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/SafeVector.h b/SafeVector.h +index abf4b64..9c3292e 100644 +--- a/SafeVector.h ++++ b/SafeVector.h +@@ -8,6 +8,7 @@ + #ifndef SAFEVECTOR_H + #define SAFEVECTOR_H + ++#include + #include + #include + diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/probcons/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild new file mode 100644 index 000000000000..01973b88cab9 --- /dev/null +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${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" +} -- cgit v1.2.3