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