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
+}
