diff options
| -rw-r--r-- | sci-biology/vcftools/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/vcftools/files/vcftools-0.1.13-buildsystem.patch | 53 | ||||
| -rw-r--r-- | sci-biology/vcftools/vcftools-0.1.13.ebuild | 45 | ||||
| -rw-r--r-- | sci-biology/vcftools/vcftools-0.1.14.ebuild | 55 |
4 files changed, 56 insertions, 99 deletions
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index 315e34181..0fa99d3bb 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1 +1 @@ -DIST vcftools_0.1.13.tar.gz 609408 SHA256 083367ef33576e14ad1f61e366c30bc13a37cb850950a9f58f20eddf0a36d4c4 SHA512 a6456c8d13a75079931a8f19076cf1c56037453203847d1424c369a1868cb67200fae7e5724fcc8af531dfbb2d6791421862e1e9697ab2e968195059ab544fd2 WHIRLPOOL bba2820f85fd689d1d042bc24df9d845c5970f8571d6519cf0d10ce39231b459d789cfa2d55cd99c350c0caf080d8f86319918f1a23478f15cb7fb0612fac2ab +DIST vcftools-vcftools-v0.1.14-14-g2543f81.tar.gz 241876 SHA256 9d9eece6e766ec75162d1edc0e95df1710896f4230531cbc92826f53505ec6e5 SHA512 29735d6ab7c1f91c155bc86fdab462cd590fbf296d1f3ad99a99e2a4882a0f30c50cb222d875fbc2d7cf480244385c29184096f083d34cd0ef9b6f93737ef6a9 WHIRLPOOL f3a7ccc443830466157a2168e12fdc5b061456c316b2f0891ab8c9ed4edc96654d39389a5268ecc051092154e20f83efa3de357fa6aaa823fc8b69819d2676da 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 85197664a..000000000 --- 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 ae8384797..000000000 --- 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 000000000..0e792f8b2 --- /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 +} |