diff options
author | Justin Lecher <jlec@gentoo.org> | 2012-07-19 11:31:13 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2012-07-19 11:31:13 +0000 |
commit | 39c3a22d8c1537ddc7888546fcfa72e6bb312ead (patch) | |
tree | 75a3a66b8aaef1363b1d3582b1b44ef9e48d6079 /sci-biology/vcftools | |
parent | Remove older unstable and buggy versions (diff) | |
download | gentoo-2-39c3a22d8c1537ddc7888546fcfa72e6bb312ead.tar.gz gentoo-2-39c3a22d8c1537ddc7888546fcfa72e6bb312ead.tar.bz2 gentoo-2-39c3a22d8c1537ddc7888546fcfa72e6bb312ead.zip |
sci-biology/vcftools: Version BUmp, fix build system
(Portage version: 2.2.0_alpha120/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/vcftools')
-rw-r--r-- | sci-biology/vcftools/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch | 50 | ||||
-rw-r--r-- | sci-biology/vcftools/vcftools-0.1.8.ebuild | 47 |
3 files changed, 104 insertions, 1 deletions
diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog index aa0c44d7c6cb..27ec7612ae59 100644 --- a/sci-biology/vcftools/ChangeLog +++ b/sci-biology/vcftools/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/vcftools # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.3 2012/01/02 21:51:52 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.4 2012/07/19 11:31:13 jlec Exp $ + +*vcftools-0.1.8 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> +vcftools-0.1.8.ebuild, + +files/vcftools-0.1.8-buildsystem.patch: + Version BUmp, fix build system *vcftools-0.1.7 (02 Jan 2012) diff --git a/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch new file mode 100644 index 000000000000..37caee9c28dd --- /dev/null +++ b/sci-biology/vcftools/files/vcftools-0.1.8-buildsystem.patch @@ -0,0 +1,50 @@ + cpp/Makefile | 16 +++++++++++----- + 1 files changed, 11 insertions(+), 5 deletions(-) + +diff --git a/cpp/Makefile b/cpp/Makefile +index 42d03e4..2f4d4f6 100644 +--- a/cpp/Makefile ++++ b/cpp/Makefile +@@ -3,7 +3,7 @@ + # ($Revision: 1.1 $) + + # Compiler +-CPP = g++ ++CPP ?= g++ + # Output executable + EXECUTABLE = vcftools + # Flag used to turn on compilation of PCA routines +@@ -11,7 +11,7 @@ ifndef VCFTOOLS_PCA + VCFTOOLS_PCA = 0 + endif + # Compiler flags +-CPPFLAGS = -O2 -Wall -Wextra ++CPPFLAGS = -Wall -Wextra + #CPPFLAGS = -g + # Included libraries (zlib) + LIB = -lz +@@ -28,15 +28,21 @@ ifeq ($(VCFTOOLS_PCA), 1) + # Define flag for PCA routine compilation + CPPFLAGS += -DVCFTOOLS_PCA + # Add LAPACK library +- LIB += -llapack ++ LIB += `pkg-config --libs lapack` + # Add PCA source code + SOURCES += dgeev.cpp + endif + ++objects := $(patsubst %.cpp,%.o,$(SOURCES)) ++ + all: vcftools + +-vcftools: $(SOURCES) +- $(CPP) $(CPPFLAGS) $(SOURCES) -o $@ $(LIB) ++vcftools: $(objects) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(objects) -o $@ $(LIB) ++ ++.cpp.o: $(SOURCES) ++ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $< ++ + ifdef BINDIR + cp $(CURDIR)/$@ $(BINDIR)/$@ + endif diff --git a/sci-biology/vcftools/vcftools-0.1.8.ebuild b/sci-biology/vcftools/vcftools-0.1.8.ebuild new file mode 100644 index 000000000000..b378d7823283 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.8.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.8.ebuild,v 1.1 2012/07/19 11:31:13 jlec Exp $ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}_${PV}" + +DESCRIPTION="Tools for working with VCF (Variant Call Format) files" +HOMEPAGE="http://vcftools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-buildsystem.patch + tc-export CXX +} + +src_compile() { + local myconf + use lapack && myconf="VCFTOOLS_PCA=1" + emake -C cpp ${myconf} +} + +src_install(){ + dobin cpp/${PN} + insinto /usr/share/${PN}/perl + doins perl/*.pm + exeinto /usr/share/${PN}/perl + doexe perl/{fill,vcf}-* + echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}" + echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}" + doenvd "${S}/99${PN}" + dodoc README.txt +} |