From e5ce74fb32afe018ef0d58ff9bfb8192abb62019 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sat, 25 Feb 2017 16:46:24 +0100
Subject: [PATCH] sci-biology/exonerate: Modernise to EAPI 6

Package-Manager: Portage-2.3.3, Repoman-2.3.1
---
 ....0-r1.ebuild => exonerate-2.2.0-r2.ebuild} | 38 +++++++++----------
 .../files/exonerate-2.2.0-asneeded.patch      |  4 +-
 2 files changed, 20 insertions(+), 22 deletions(-)
 rename sci-biology/exonerate/{exonerate-2.2.0-r1.ebuild => exonerate-2.2.0-r2.ebuild} (53%)

diff --git a/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
similarity index 53%
rename from sci-biology/exonerate/exonerate-2.2.0-r1.ebuild
rename to sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
index 966f7c2f8e01..567b906ca21d 100644
--- a/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild
+++ b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
@@ -1,50 +1,48 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=6
 
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils toolchain-funcs
+inherit autotools toolchain-funcs
 
 DESCRIPTION="Generic tool for pairwise sequence comparison"
-HOMEPAGE="http://www.ebi.ac.uk/~guy/exonerate/"
-SRC_URI="http://www.ebi.ac.uk/~guy/exonerate/${P}.tar.gz"
+HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
+SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos"
-IUSE="utils test threads"
-
+IUSE="test threads utils"
 REQUIRED_USE="test? ( utils )"
 
 DEPEND="dev-libs/glib:2"
 RDEPEND="${DEPEND}"
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
 PATCHES=( "${FILESDIR}"/${P}-asneeded.patch )
 
 src_prepare() {
-	tc-export CC
+	default
 	sed \
 		-e 's: -O3 -finline-functions::g' \
 		-i configure.in || die
-	autotools-utils_src_prepare
+	mv configure.{in,ac} || die
+
+	eautoreconf
 }
 
 src_configure() {
-	local myeconfargs=(
-		$(use_enable utils utilities)
+	tc-export CC
+
+	econf \
+		--enable-glib2 \
+		--enable-largefile \
+		$(use_enable utils utilities) \
 		$(use_enable threads pthreads)
-		--enable-largefile
-		--enable-glib2
-	)
-	autotools-utils_src_configure
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
+
 	doman doc/man/man1/*.1
 }
diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
index 3268055cd544..5c428979a1af 100644
--- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
+++ b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch
@@ -2,8 +2,8 @@ Fix build with --as-needed
 
 https://bugs.gentoo.org/268094
 
---- configure.in
-+++ configure.in
+--- a/configure.in
++++ b/configure.in
 @@ -289,7 +289,7 @@
  if test "$enable_pthreads" = yes; then
      echo "Using PTHREADS"
-- 
2.26.2