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commit: 88a8a7c98513e17af66a583de1bc0b5ad414771c |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Mar 30 19:20:56 2015 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Mar 30 19:20:56 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=88a8a7c9 |
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|
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sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 format output support |
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|
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sci-biology/exonerate-gff3/ChangeLog | 12 +++++ |
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.../exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild | 53 ++++++++++++++++++++++ |
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.../files/exonerate-gff3-2.2.0-asneeded.patch | 15 ++++++ |
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sci-biology/exonerate-gff3/metadata.xml | 9 ++++ |
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4 files changed, 89 insertions(+) |
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|
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diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog |
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new file mode 100644 |
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index 0000000..fc492c8 |
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--- /dev/null |
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+++ b/sci-biology/exonerate-gff3/ChangeLog |
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@@ -0,0 +1,12 @@ |
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+# ChangeLog for sci-biology/exonerate-gff3 |
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+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+*exonerate-gff3-2.2.0-r1 (30 Mar 2015) |
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+ |
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+ 30 Mar 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch, |
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+ +metadata.xml: |
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+ sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 |
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+ format output support |
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+ |
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|
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diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild |
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new file mode 100644 |
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index 0000000..fd24728 |
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--- /dev/null |
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+++ b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild |
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@@ -0,0 +1,53 @@ |
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+# Copyright 1999-2015 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild,v 1.5 2013/01/25 16:24:50 jlec Exp $ |
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+ |
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+EAPI=4 |
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+ |
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+AUTOTOOLS_AUTORECONF=true |
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+ |
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+inherit autotools-utils toolchain-funcs git-r3 |
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+ |
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+DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output" |
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+HOMEPAGE="https://github.com/hotdogee/exonerate-gff3" |
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+EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+KEYWORDS="~amd64" |
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+IUSE="utils test threads" |
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+ |
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+REQUIRED_USE="test? ( utils )" |
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+ |
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+# block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate |
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+DEPEND=" |
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+ !sci-biology/exonerate |
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+ dev-libs/glib:2" |
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+RDEPEND="${DEPEND}" |
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+ |
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+AUTOTOOLS_IN_SOURCE_BUILD=1 |
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+ |
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+PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) |
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+ |
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+src_prepare() { |
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+ tc-export CC |
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+ sed \ |
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+ -e 's: -O3 -finline-functions::g' \ |
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+ -i configure.in || die |
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+ autotools-utils_src_prepare |
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+} |
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+ |
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+src_configure() { |
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+ local myeconfargs=( |
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+ $(use_enable utils utilities) |
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+ $(use_enable threads pthreads) |
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+ --enable-largefile |
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+ --enable-glib2 |
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+ ) |
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+ autotools-utils_src_configure |
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+} |
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+ |
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+src_install() { |
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+ autotools-utils_src_install |
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+ doman doc/man/man1/*.1 |
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+} |
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|
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diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch |
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new file mode 100644 |
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index 0000000..3268055 |
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--- /dev/null |
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+++ b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch |
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@@ -0,0 +1,15 @@ |
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+Fix build with --as-needed |
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+ |
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+https://bugs.gentoo.org/268094 |
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+ |
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+--- configure.in |
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++++ configure.in |
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+@@ -289,7 +289,7 @@ |
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+ if test "$enable_pthreads" = yes; then |
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+ echo "Using PTHREADS" |
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+ CFLAGS="$CFLAGS -DUSE_PTHREADS" |
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+- LDFLAGS="$LDFLAGS -lpthread" |
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++ LIBS="$LIBS -lpthread" |
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+ elif test "$enable_pthreads" = no; then |
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+ echo "Not using pthreads" |
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+ else |
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|
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diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml |
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new file mode 100644 |
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index 0000000..2bc8930 |
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--- /dev/null |
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+++ b/sci-biology/exonerate-gff3/metadata.xml |
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@@ -0,0 +1,9 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <herd>sci-biology</herd> |
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+ <maintainer> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+</pkgmetadata> |