sci-biology/caftools: Drop old; Bump to EAPI=5 and fix license

Package-Manager: portage-2.2.0_alpha180

5 files changed, 38 insertions, 64 deletions

diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog
new file mode 100644
index 000000000..af2ad47b4
--- /dev/null
+++ b/sci-biology/caftools/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/caftools
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild,
+  caftools-2.0.2.ebuild, metadata.xml:
+  Drop old; Bump to EAPI=5 and fix license
+
diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
index 61d49e197..dbbbb7f44 100644
--- a/sci-biology/caftools/Manifest
+++ b/sci-biology/caftools/Manifest
@@ -1,2 +1,2 @@
-DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2
-DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9
+DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d WHIRLPOOL 84313e00f6f4c018bc65b6e173827a6e1ef8fd2dc5e5e63e186fb56bc9e5b66b2f25037a1536a8cb57af71603b31ed74ff505dbc43d4deb7d2eeae57ea729bfe
+DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 WHIRLPOOL 13c2e24ce803c09f1d596a4c05f146b869e5ebdeff9f648a0468853feb7d142927d3d78339ac2414482335e5f7ca8352ea9b196f8542f4b3ff5e36fef762398e
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
index c1932e1f4..3f8ece67d 100644
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ b/sci-biology/caftools/caftools-2.0.2.ebuild
@@ -1,45 +1,45 @@
-# 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 eutils
 
 DESCRIPTION="CAF is a text format for describing sequence assemblies"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.2.tar.gz
-		ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz"
-# another source with only the old version is at
-# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz
-# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/
+SRC_URI="
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
+	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
 
-LICENSE="as-is"
+LICENSE="GRL"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND="sci-libs/io_lib
-		>=dev-lang/perl-5.002"
+DEPEND="
+	sci-libs/io_lib
+	dev-lang/perl"
 RDEPEND="${DEPEND}"
 
 src_prepare(){
-	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
-	mv "${WORKDIR}"/caftools-2.0/man/*.1 "${WORKDIR}"/caftools-2.0/man/*.5 "${S}"/man || die
+	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch
+	mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
 }
 
 src_configure(){
-	econf || die
-	sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
-	sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
+	default
+	sed \
+		-e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
+		-i Makefile src/Makefile || die
 }
 
 # TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
 # The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
 # not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
 src_install(){
-	emake install DESTDIR="${D}" || die
+	default
 	doman man/*.[1-5] || die
-	einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-	einfo "for some reason caf_find_misassemblies is gone from 2.0.2 version"
+	elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
+	elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
 }
diff --git a/sci-biology/caftools/caftools-2.0.ebuild b/sci-biology/caftools/caftools-2.0.ebuild
deleted file mode 100644
index 482bddf92..000000000
--- a/sci-biology/caftools/caftools-2.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils
-
-DESCRIPTION="CAF is a text format for describing sequence assemblies"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz"
-# another source with only the old version is at
-# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz
-# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/
-
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-libs/io_lib
-		>=dev-lang/perl-5.002"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/Makefile.in.patch || die
-}
-
-src_configure(){
-	econf || die
-	sed -i 's#prefix = /usr#prefix = $(DESTDIR)/usr#' Makefile || die
-	sed -i 's#prefix = /usr#\#prefix = $(DESTDIR)/usr#' src/Makefile || die
-}
-
-src_install(){
-	emake install DESTDIR="${D}" || die
-	einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-}
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
index 4f255d9b2..e57f444c5 100644
--- a/sci-biology/caftools/metadata.xml
+++ b/sci-biology/caftools/metadata.xml
@@ -1,10 +1,14 @@
 <?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>
-	<longdescription>CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.</longdescription>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <longdescription>
+  CAF is a text format for describing sequence assemblies. It is acedb-compliant
+  and is an extension of the ace-file format used earlier, but with support for 
+  base quality measures and a more extensive description of the Sequence data.
+  </longdescription>
 </pkgmetadata>