sci-biology/profphd: Fix for newer perl, version Bump

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 67 insertions, 4 deletions

diff --git a/sci-biology/profphd/ChangeLog b/sci-biology/profphd/ChangeLog
index 5f1300e41b35..5b29b3af77b8 100644
--- a/sci-biology/profphd/ChangeLog
+++ b/sci-biology/profphd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/profphd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/ChangeLog,v 1.3 2013/04/24 14:28:05 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/ChangeLog,v 1.4 2014/04/24 11:38:57 jlec Exp $
+
+*profphd-1.0.40 (24 Apr 2014)
+
+  24 Apr 2014; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild,
+  +profphd-1.0.40.ebuild, +files/profphd-1.0.39-perl.patch:
+  Fix for newer perl, version Bump
 
   24 Apr 2013; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild:
   Updated deps
diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
new file mode 100644
index 000000000000..10682271601c
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
@@ -0,0 +1,16 @@
+ src/prof/prof | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/prof/prof b/src/prof/prof
+index 4f26024..356442d 100755
+--- a/src/prof/prof
++++ b/src/prof/prof
+@@ -238,7 +238,7 @@ See each keyword for more help.  Most of these are likely to be broken.
+ 
+ alternative connectivity patterns (default=3)
+ 
+-=item 3
++=item C<3>
+ 
+ predict sec + acc + htm
+ 
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
index 77e853cd685c..72bf2e8fff12 100644
--- a/sci-biology/profphd/profphd-1.0.39.ebuild
+++ b/sci-biology/profphd/profphd-1.0.39.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.39.ebuild,v 1.3 2013/04/24 14:28:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.39.ebuild,v 1.4 2014/04/24 11:38:57 jlec Exp $
 
 EAPI=5
 
+inherit eutils
+
 DESCRIPTION="Secondary structure and solvent accessibility predictor"
 HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
 SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
@@ -24,6 +26,7 @@ src_prepare() {
 	sed \
 		-e '/ln -s/s:prof$:profphd:g' \
 		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${P}-perl.patch
 }
 
 src_compile() {
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
new file mode 100644
index 000000000000..0995a72af1a7
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.40.ebuild,v 1.1 2014/04/24 11:38:57 jlec Exp $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+	dev-perl/librg-utils-perl
+	sci-libs/profnet
+	sci-libs/profphd-utils
+"
+
+src_prepare() {
+	sed \
+		-e '/ln -s/s:prof$:profphd:g' \
+		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
+}
+
+src_compile() {
+	emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}