sci-biology/psipred: Version Bump

(Portage version: 2.2.0_alpha116/cvs/Linux x86_64)

4 files changed, 72 insertions, 9 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
index a71403d952fa..9136f15b10a5 100644
--- a/sci-biology/psipred/ChangeLog
+++ b/sci-biology/psipred/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/psipred
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.5 2011/05/24 12:18:04 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.6 2012/07/10 20:30:58 jlec Exp $
+
+*psipred-3.3 (10 Jul 2012)
+
+  10 Jul 2012; Justin Lecher <jlec@gentoo.org> psipred-3.2.1.ebuild,
+  +psipred-3.3.ebuild, metadata.xml:
+  Version Bump
 
 *psipred-3.2.1 (24 May 2011)
 
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
index c6856dc7f2cf..210ad0db014c 100644
--- a/sci-biology/psipred/metadata.xml
+++ b/sci-biology/psipred/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
+	<herd>sci</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
 </pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild
index 53e1af6f902e..308e810d5d7e 100644
--- a/sci-biology/psipred/psipred-3.2.1.ebuild
+++ b/sci-biology/psipred/psipred-3.2.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.2.1.ebuild,v 1.1 2011/05/24 12:18:04 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.2.1.ebuild,v 1.2 2012/07/10 20:30:58 jlec Exp $
 
 EAPI=4
 
@@ -10,7 +10,9 @@ MY_P="${PN}$(delete_all_version_separators)"
 
 DESCRIPTION="Protein Secondary Structure Prediction"
 HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
+SRC_URI="
+	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
 
 LICENSE="psipred"
 SLOT="0"
diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild
new file mode 100644
index 000000000000..44637dcde3d7
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.3.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.3.ebuild,v 1.1 2012/07/10 20:30:58 jlec Exp $
+
+EAPI=4
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	sci-biology/ncbi-tools++"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}