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commit: bdf7251db30941f3912dd646d37fb125fbabf018 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Sep 25 09:24:17 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Sep 25 09:39:01 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bdf7251d |
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|
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sci-biology/vcftools: Version bump to 0.1.14 |
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|
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Gentoo-bug: 594924 |
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* EAPI=6 |
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* Properly RDEPEND on dev-lang/perl |
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|
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Package-Manager: portage-2.3.1 |
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Closes: https://github.com/gentoo/gentoo/pull/2407 |
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|
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/vcftools/Manifest | 1 + |
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.../files/vcftools-0.1.14-buildsystem.patch | 50 ++++++++++++++++++++++ |
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sci-biology/vcftools/vcftools-0.1.14.ebuild | 39 +++++++++++++++++ |
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3 files changed, 90 insertions(+) |
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|
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diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest |
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index acbb214..9a014b1 100644 |
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--- a/sci-biology/vcftools/Manifest |
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+++ b/sci-biology/vcftools/Manifest |
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@@ -1 +1,2 @@ |
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+DIST vcftools-0.1.14.tar.gz 342369 SHA256 76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 WHIRLPOOL 6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8 |
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DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863 |
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|
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diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch |
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new file mode 100644 |
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index 00000000..126a709 |
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--- /dev/null |
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+++ b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch |
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@@ -0,0 +1,50 @@ |
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+* Add prefix in Makefiles, not the configure script |
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+* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, |
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+ as it is more flexible and helps us with LAPACK |
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+* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS |
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+ |
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+--- a/configure.ac |
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++++ b/configure.ac |
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+@@ -34,7 +34,7 @@ |
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+ [--with-pmdir=DIR], |
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+ [install Perl modules in DIR]), |
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+ [PMDIR=${withval}], |
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+- [PMDIR='${prefix}'/"$pmdir_relative_path"]) |
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++ [PMDIR="$pmdir_relative_path"]) |
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+ |
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+ AC_SUBST([PMDIR]) |
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+ |
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+@@ -73,9 +73,9 @@ |
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+ [pca=${enableval}], |
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+ [pca=no]) |
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+ |
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+-if test "x${pca}" = "xyes" ; then |
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+- AC_CHECK_LIB(lapack, dgeev_) |
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+-fi |
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++AS_IF([test "x${pca}" = "xyes"],[ |
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++ AC_SEARCH_LIBS([dgeev_], [lapack]) |
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++]) |
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+ |
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+ # Generate output. |
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+ AC_CONFIG_FILES([Makefile |
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+--- a/src/cpp/Makefile.am |
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++++ b/src/cpp/Makefile.am |
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+@@ -1,6 +1,6 @@ |
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+ bin_PROGRAMS = vcftools |
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+ |
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+-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) |
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++vcftools_CPPFLAGS = $(ZLIB_CFLAGS) |
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+ vcftools_LDADD = $(ZLIB_LIBS) |
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+ |
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+ vcftools_SOURCES = \ |
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+--- a/src/perl/Makefile.am |
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++++ b/src/perl/Makefile.am |
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+@@ -24,7 +24,7 @@ |
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+ vcf-tstv \ |
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+ vcf-validator |
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+ |
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+-pmdir = $(PMDIR) |
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++pmdir = $(exec_prefix)/$(PMDIR) |
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+ |
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+ dist_pm_DATA = \ |
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+ FaSlice.pm \ |
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|
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diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild |
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new file mode 100644 |
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index 00000000..9281435 |
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--- /dev/null |
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+++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild |
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@@ -0,0 +1,39 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=6 |
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+ |
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+inherit autotools flag-o-matic perl-functions toolchain-funcs |
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+ |
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+DESCRIPTION="Tools for working with VCF (Variant Call Format) files" |
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+HOMEPAGE="http://vcftools.sourceforge.net/" |
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+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz" |
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+ |
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+LICENSE="LGPL-3" |
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+SLOT="0" |
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+KEYWORDS="~x86 ~amd64" |
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+IUSE="lapack" |
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+ |
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+RDEPEND="dev-lang/perl:= |
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+ lapack? ( virtual/lapack )" |
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+DEPEND="${RDEPEND} |
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+ virtual/pkgconfig" |
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+ |
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+PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) |
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+ |
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+src_prepare() { |
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+ default |
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+ eautoreconf |
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+} |
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+ |
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+src_configure() { |
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+ perl_set_version |
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+ |
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+ append-flags $($(tc-getPKG_CONFIG) --cflags lapack) |
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+ append-libs $($(tc-getPKG_CONFIG) --libs lapack) |
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+ |
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+ econf \ |
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+ $(use_enable lapack pca) \ |
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+ --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}" |
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+} |