Bump to EAPI=5 and fix file collision, bug #422643; thanks Martin Mokrejs contacting upstream regarding this issue

(Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key E9402A79B03529A2!)

2 files changed, 22 insertions, 17 deletions

diff --git a/sci-biology/phrap/ChangeLog b/sci-biology/phrap/ChangeLog
index ab217fde3a9f..a9bc4e43e1ce 100644
--- a/sci-biology/phrap/ChangeLog
+++ b/sci-biology/phrap/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/phrap
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/ChangeLog,v 1.3 2013/03/11 16:36:19 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/ChangeLog,v 1.4 2015/06/16 08:34:28 jlec Exp $
+
+*phrap-1.080812-r1 (16 Jun 2015)
+
+  16 Jun 2015; Justin Lecher <jlec@gentoo.org> +phrap-1.080812-r1.ebuild,
+  -phrap-1.080812.ebuild:
+  Bump to EAPI=5 and fix file collision, bug #422643; thanks Martin Mokrejs
+  contacting upstream regarding this issue
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -15,4 +22,3 @@
   +phrap-1.080812.ebuild:
   Import from Science overlay, bug 114094. Thanks to Brady Catherman and Martin
   Mokrejs.
-
diff --git a/sci-biology/phrap/phrap-1.080812.ebuild b/sci-biology/phrap/phrap-1.080812-r1.ebuild
index 666e423e2541..b4f9ba8c34fa 100644
--- a/sci-biology/phrap/phrap-1.080812.ebuild
+++ b/sci-biology/phrap/phrap-1.080812-r1.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/phrap-1.080812.ebuild,v 1.4 2013/02/17 10:28:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/phrap-1.080812-r1.ebuild,v 1.1 2015/06/16 08:34:28 jlec Exp $
 
-DESCRIPTION="Phrap, swat, cross_match: Shotgun assembly and alignment utilities"
+EAPI=5
+
+DESCRIPTION="Shotgun assembly and alignment utilities"
 HOMEPAGE="http://www.phrap.org/"
 SRC_URI="phrap-${PV}-distrib.tar.gz"
 
@@ -12,8 +14,9 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="dev-lang/perl
-		dev-perl/perl-tk"
+RDEPEND="
+	dev-lang/perl
+	dev-perl/perl-tk"
 
 S="${WORKDIR}"
 
@@ -25,18 +28,14 @@ pkg_nofetch() {
 	einfo "and put it in ${DISTDIR}"
 }
 
-src_compile() {
-	sed -i 's/CFLAGS=/#CFLAGS=/' makefile
-	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview
-	emake || die "emake failed"
-	# TODO: we need to extract staden sources because for compilation some of those
-	# files are needed: http://www.phrap.org/phredphrap/phrap.html
-	# (look for gcphrap and other gc* programs)
-	# emake gcphrap || die
+src_prepare() {
+	sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die
+	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die
 }
 
 src_install() {
-	dobin cluster cross_match loco phrap phrapview swat
+	dobin cross_match loco phrap phrapview swat
+	newbin cluster cluster_phrap
 	for i in {general,phrap,swat}.doc ; do
 		newdoc ${i} ${i}.txt
 	done