commit: fd1d97e00b077c5d4956efbf2951a0261b0ac674 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jul 31 20:13:45 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jul 31 20:13:45 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd1d97e0
sci-biology/vcftools: version bump Package-Manager: portage-2.3.0 .../files/vcftools-0.1.13-buildsystem.patch | 53 ++++++++++++++++++++++ sci-biology/vcftools/metadata.xml | 11 +++++ sci-biology/vcftools/vcftools-0.1.13.ebuild | 45 ++++++++++++++++++ 3 files changed, 109 insertions(+) diff --git a/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch new file mode 100644 index 0000000..8519766 --- /dev/null +++ b/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch @@ -0,0 +1,53 @@ +diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile +--- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200 ++++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200 +@@ -3,8 +3,8 @@ + # ($Revision: 1.1 $) + + # Compiler +-CC = gcc +-CPP = g++ ++CC ?= gcc ++CPP ?= g++ + # Output executable + EXECUTABLE = vcftools + # Flag used to turn on compilation of PCA routines +@@ -12,9 +12,9 @@ + VCFTOOLS_PCA = 0 + endif + # Compiler flags +-CFLAGS = -O2 -m64 ++CFLAGS ?= -O2 -m64 + #CFLAGS = -Wall -O2 -pg -m64 +-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 ++CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 + #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64 + # Included libraries (zlib) + LIB = -lz +@@ -29,13 +29,13 @@ + # Define flag for PCA routine compilation + CPPFLAGS += -DVCFTOOLS_PCA + # Add LAPACK library +- LIB += -llapack ++ LIB += `$(PKG_CONFIG) --libs lapack` + # Add PCA source code + OBJS+= dgeev.o + endif + + vcftools: $(OBJS) +- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB) + ifdef BINDIR + cp $(CURDIR)/$@ $(BINDIR)/$@ + endif +@@ -47,8 +47,8 @@ + -include $(OBJS:.o=.d) + + %.o: %.cpp +- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o +- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d ++ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o ++ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d + + # remove compilation products + clean: diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml new file mode 100644 index 0000000..77f6f92 --- /dev/null +++ b/sci-biology/vcftools/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">vcftools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/vcftools/vcftools-0.1.13.ebuild b/sci-biology/vcftools/vcftools-0.1.13.ebuild new file mode 100644 index 0000000..ae83847 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.13.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module 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="LGPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="lapack? ( virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-buildsystem.patch + tc-export CXX PKG_CONFIG +} + +src_compile() { + local myconf + use lapack && myconf="VCFTOOLS_PCA=1" + emake -C cpp ${myconf} +} + +src_install(){ + perl_set_version + dobin cpp/${PN} + insinto ${VENDOR_LIB} + doins perl/*.pm + dobin perl/{fill,vcf}-* + dodoc README.txt +}
