sci-biology/vcftools: Version BUmp, fix build system

(Portage version: 2.2.0_alpha120/cvs/Linux x86_64)

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
+}