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