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

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

4 files changed, 117 insertions, 10 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/Manifest b/sci-biology/vcftools/Manifest
index e69164e6f34f..4ffa860871a9 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1,14 +1,18 @@
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-EBUILD vcftools-0.1.7.ebuild 904 RMD160 4b283a92fe9c12bbf688babc135f48cf2d7b341f SHA1 c2c55854166e9e0f7ef04d3def35a919c4c3896d SHA256 8387dc4756bce66f6a59888e7d340340dd4b48a5af02f9a2bbbf0778892f7d52
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+AUX vcftools-0.1.8-buildsystem.patch 1161 SHA256 d414e300b18857cb4440d1a4587a9335ba1238d9a6ab1b232098586160ad145d SHA512 faaa57e20b29bf7ef5818f104d2be25a54b9b1cfd9f20df0325cf500f73fd693728f6f59fd2f6b6bec30f9c7c0b4301fe4fad364f833776feea47df018b27a4a WHIRLPOOL 45649955d5fbc3b761e7b2c3a83a4c27588b42a54fe23662eacb6f9c7e419ee25c50a05c2a5cb9d4cb0e1f82dffbe5d2aacf70cd8f53de6401cd10da9519b0d7
+DIST vcftools_0.1.7.tar.gz 489145 SHA256 e40685f082aef92511a80af723cb813b87773537eb4fed630716682e8c80a4c0 SHA512 130304d7c4c0058d4547d04f4e52e75c5562ef7c636b7c788654a00f300da15d12eb5d66e94c2e764049275d242b7ce05bfa7f3beb99c857c5d84d26009ea329 WHIRLPOOL 9bf171456b6d2902b4ed5dfc47cb84b2c6615a647c7c04e215a1592bcaa29edb87bbc5fede57df4a68549bc03284eb8800e821c6336e56e11f4d61e98f98827c
+DIST vcftools_0.1.8.tar.gz 568268 SHA256 bf360b315181b2f06c85a19c1ce1c539ecce81f187f4da9ae7f8616300573a61 SHA512 5dc35d8adaea16716e5383427c9458fcf965cee1feb980f8ade166ae67403c7f1ae4d74d1218f23c4032187588834f801ea602d86fe94033dc922fe3f58f0c04 WHIRLPOOL ca9a9448bafee8a0c27752e7a6c18c8050b55f9402c072ee313bcb9bd85c2369e2f76f339429c317b37e5a889472667a4e3fc7b3ba9fb221932022e7c997da37
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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
+}