[gentoo-commits] proj/sci:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/

[Martin Mokrejs]

commit:     120da1074b01f60b3b7b98776c8cae7d38ac451e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 26 16:20:38 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 26 16:20:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=120da107

sci-biology/vcftool: version bump; adjust to new build system

Package-Manager: portage-2.3.0

 .../files/vcftools-0.1.13-buildsystem.patch        | 53 ---------------------
 sci-biology/vcftools/vcftools-0.1.13.ebuild        | 45 ------------------
 sci-biology/vcftools/vcftools-0.1.14.ebuild        | 55 ++++++++++++++++++++++
 3 files changed, 55 insertions(+), 98 deletions(-)

diff --git a/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch
deleted file mode 100644
index 8519766..0000000
--- a/sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-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/vcftools-0.1.13.ebuild b/sci-biology/vcftools/vcftools-0.1.13.ebuild
deleted file mode 100644
index ae83847..0000000
--- a/sci-biology/vcftools/vcftools-0.1.13.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# 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
-}

diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild
new file mode 100644
index 0000000..0e792f8
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild
@@ -0,0 +1,55 @@
+# 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 autotools
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="https://vcftools.github.io
+	http://vcftools.sourceforge.net"
+SRC_URI="https://github.com/vcftools/vcftools/archive/vcftools-vcftools-v0.1.14-14-g2543f81.tar.gz"
+#SRC_URI="https://codeload.github.com/vcftools/vcftools/legacy.tar.gz/master -> ${P}.tar.gz"
+#SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/vcftools-vcftools-2543f81
+#S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	# epatch "${FILESDIR}"/${P}-buildsystem.patch
+	tc-export CXX PKG_CONFIG
+	eautoreconf
+}
+
+src_configure(){
+	econf --enable-pca # --with-pmdir=DIR   install Perl modules in DIR
+}
+
+#src_compile() {
+#	local myconf
+#	use lapack && myconf="VCFTOOLS_PCA=1"
+#	emake -C cpp ${myconf}
+#}
+
+src_install(){
+	perl_set_version
+	dobin src/cpp/"${PN}"
+	doman src/cpp/"${PN}".1
+	insinto "${VENDOR_LIB}"
+	doins src/perl/*.pm
+	dobin src/perl/{fill,vcf}-*
+	dodoc README.md
+}