sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf

Package-Manager: portage-2.2.0_alpha180

4 files changed, 38 insertions, 29 deletions

diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog
new file mode 100644
index 000000000..8e35f8604
--- /dev/null
+++ b/sci-biology/gap2caf/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/gap2caf
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and fix license; make it build with eautoreconf
+
diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest
index 3dbd5c548..7d17476c0 100644
--- a/sci-biology/gap2caf/Manifest
+++ b/sci-biology/gap2caf/Manifest
@@ -1,2 +1,2 @@
-DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a
-DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d
+DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a SHA512 2a843d861b7be6d656793f4876953596b91a93c3da7d23ee8edc10c4620e33fc96a16beaeaaf4f66c1f5c5084eb8a9a255d4fa8e1ca6e87e96372f2459167c90 WHIRLPOOL f5a3360de7c6b8741e5e85a9bc25198de4dbcbebdee73ba48a7e1460eb4d778648a5c93f0bb44c10e15a4fa46dd0c741fc10c8e33ae8c50e2c7cd9914a56aa81
+DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d SHA512 ddd273d281557595c90b93304cd03205adbe1367845ef43763a8c75d06c2729d99ca8622439ff5c31217595481a9ac4ccedf87c5948821aeaeb73c96133dc411 WHIRLPOOL f086f7f81884091a34c9933a2bb901146eefcd2dc4cb4b940228de3a51daee4c1f9d5613ca34ec345bcce48fc53bed6c4a408f5b5d6e87ac5c4deda222daee24
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 861bbc8f0..ca12aedf2 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
 inherit autotools eutils
 
 DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
-		http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
+SRC_URI="
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
+	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
 
-LICENSE="as-is staden"
+LICENSE="GRL staden"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-DEPEND="sci-biology/staden
-		>=dev-lang/tcl-8.5"
+DEPEND="
+	sci-biology/staden
+	>=dev-lang/tcl-8.5"
 RDEPEND="${DEPEND}"
 
 #src_prepare(){
@@ -29,13 +28,14 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -i 's:/include/tcl8.4:/include:' configure.ac || die
-	sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die
-	sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die
-	eaclocal
-	eautomake
-	eautoconf
-	sed -i 's:/include/tcl8.4:/include:' configure
-	sed -i 's:libtcl8.4:libtcl8.5:' configure
+	sed -i 's:libtcl8.4:libtcl:' configure.ac || die
+	sed \
+		-e 's:tcl8.4:tcl:' \
+		-e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \
+		-i src/Makefile.am || die
+	eautoreconf
+	sed -i 's:/include/tcl8.4:/include:' configure || die
+	sed -i 's:libtcl8.4:libtcl:' configure || die
 }
 
 src_configure(){
@@ -45,12 +45,13 @@ src_configure(){
 	#LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
 	# STADENROOT=/usr/share/staden \
 	# STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
-	econf --with-stadenroot=/usr \
-	--with-tcl=/usr \
-	--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src || die
+	econf \
+		--with-stadenroot=/usr \
+		--with-tcl=/usr \
+		--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src
 	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
 	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
-	sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die
+	sed -i 's:tcl8.4:tcl:' src/Makefile || die
 
 	# The below tricks in overall do not help, only for -ltk_utils somehow
 	sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
@@ -68,7 +69,7 @@ src_install(){
 	#
 	# Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
 	dobin src/gap2caf
-	dodoc README || die
+	dodoc README
 }
 
 # BUG #259848
diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/gap2caf/metadata.xml
+++ b/sci-biology/gap2caf/metadata.xml
@@ -1,9 +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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>