sci-biology/bowtie: Version Bump, Fix compilation with gcc-4.7, #421919

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

3 files changed, 97 insertions, 2 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 3dd84e690308..519ba8efed2f 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bowtie
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.13 2011/03/06 17:18:05 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.14 2012/06/19 11:34:11 jlec Exp $
+
+*bowtie-0.12.8 (19 Jun 2012)
+
+  19 Jun 2012; Justin Lecher <jlec@gentoo.org> +bowtie-0.12.8.ebuild,
+  +files/bowtie-0.12.8-gcc-47.patch:
+  Version Bump, Fix compilation with gcc-4.7, #421919
 
 *bowtie-0.12.7 (06 Mar 2011)
 
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000000000000..eb6670183490
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.8.ebuild,v 1.1 2012/06/19 11:34:11 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS=""
+}
+
+src_install() {
+	dobin bowtie bowtie-*
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL
+}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
new file mode 100644
index 000000000000..3c8a1e1d9ca4
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
@@ -0,0 +1,45 @@
+ alphabet.h |   24 ++++++++++++------------
+ 1 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/alphabet.h b/alphabet.h
+index b464ddf..08d0281 100644
+--- a/alphabet.h
++++ b/alphabet.h
+@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
+ 	return s_rc;
+ }
+ 
++/// Reverse a string in-place
++template <typename TStr>
++static inline void reverseInPlace(TStr& s) {
++	typedef typename Value<TStr>::Type TVal;
++	size_t len = length(s);
++	for(size_t i = 0; i < (len>>1); i++) {
++		TVal tmp = s[i];
++		s[i] = s[len-i-1];
++		s[len-i-1] = tmp;
++	}
++}
++
+ /**
+  * Reverse-complement s in-place.  Ns go to Ns.
+  */
+@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ 	}
+ }
+ 
+-/// Reverse a string in-place
+-template <typename TStr>
+-static inline void reverseInPlace(TStr& s) {
+-	typedef typename Value<TStr>::Type TVal;
+-	size_t len = length(s);
+-	for(size_t i = 0; i < (len>>1); i++) {
+-		TVal tmp = s[i];
+-		s[i] = s[len-i-1];
+-		s[len-i-1] = tmp;
+-	}
+-}
+-
+ /**
+  * Return the reverse-complement of s.
+  */