Version Bump, respect *FLAGS, #337426 & #354927

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

3 files changed, 41 insertions, 11 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index a7a31f8e8221..3dd84e690308 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bowtie
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.12 2010/09/30 07:24:16 grobian Exp $
+# 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 $
+
+*bowtie-0.12.7 (06 Mar 2011)
+
+  06 Mar 2011; Justin Lecher <jlec@gentoo.org> -bowtie-0.10.1.ebuild,
+  +bowtie-0.12.7.ebuild:
+  Version Bump, respect *FLAGS, #337426 & #354927
 
   30 Sep 2010; Fabian Groffen <grobian@gentoo.org> bowtie-0.12.5.ebuild:
   Marked ~x64-macos, bug #339187
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 4dae9e7fa8ea..1363b8e38cb5 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,8 +1,18 @@
-DIST bowtie-0.10.1-src.zip 10258866 RMD160 99628de52fda58ee358f1ac629634210be24cf3e SHA1 f509f442d824a7b2b0650f29d2b3625aea1a1466 SHA256 71a64c08eee4147f670d52a8e9f61d28d9c67fa595ece93d55d9524e15fed809
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST bowtie-0.12.3-src.zip 10314474 RMD160 a5e9fc5de69c8c4e64e30bcfaf8303b3021e5b8f SHA1 7bf3ca4071638d36ff5139f8ccd976315e98c4b3 SHA256 aac6e02cc95058e19092f6f56e87ed2eac3df11ecce889050c6feea2b2344b84
 DIST bowtie-0.12.5-src.zip 10319902 RMD160 41e02aec08e77ce7944eb5440fdd78efb99d5a97 SHA1 90448c971d30797a63dcbc72246874a163174215 SHA256 244aa3ccbc15c88970196b0fb958c8455504902b5414987bf224c9dd92984cce
-EBUILD bowtie-0.10.1.ebuild 859 RMD160 08afd397a1e50da00b9209180a8cf94ae7896c33 SHA1 e7e5add9032a345ce2688f4b17417c9693039f13 SHA256 474c8f2ee5303e04d39e8642187daa3531c91327c921f99a3a16b986e4f57842
+DIST bowtie-0.12.7-src.zip 7697786 RMD160 7b2210d4526c4818936b729b0e68f4c13a101fc6 SHA1 0eb752db072a2da6fc6dac55d2ab825422e994ce SHA256 609a6a0ad0b1a5d97908ca17da7bbf5d6dc407c7b9c49713cdc9c40f056a586a
 EBUILD bowtie-0.12.3.ebuild 919 RMD160 b372dda86b94c59ba0dc9c71107c95efc31bde20 SHA1 ae85bfd3054996ec82274aaf9da78ae8e02b4eb1 SHA256 a48446e9cb918d99b3488e9b9ef3125ad2d8df2f2c8cd0fc0a1524a22663d301
 EBUILD bowtie-0.12.5.ebuild 931 RMD160 3bef3c346e7e5b1f5a8d11b2dd7f7d1ae5b57ea4 SHA1 dffb1225ae29c88e099355ceb525e4bb9c7d977e SHA256 cb12a3f471f9dd8e0b0eee6fff065929177895ce1d1f5995071380d944628d1f
-MISC ChangeLog 1786 RMD160 52a52c41ec0505248fb3e59e39b5e34ba38dede1 SHA1 b8de6eb0cdf5448501d767ce953ef5be46fa5188 SHA256 d6d345c32bc6ad70c9e69d2b627fdf3c8595367a5cb221f85a299ef1871d7067
+EBUILD bowtie-0.12.7.ebuild 1113 RMD160 ab7fd92e2198de8abeb753ecb802c4034100c6d2 SHA1 9b53b20d6e3f41c0a21f91939a7ec648365d5ff6 SHA256 ffc3c1ccaef5fb1b19f53946d19b4f1528076c7dc5b23d5d1ba1924612a820ec
+MISC ChangeLog 1959 RMD160 f33dedc34a7402580c50a5c6541abc0fcdf0bb05 SHA1 c3c3caa25113487cb8b9e58482b563f9af56765b SHA256 38288cf679c0fccde58767977cc176dfe8a7e03fecd25e4e58cf1057552ec327
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk1zwdwACgkQgAnW8HDreRagtQCeJYpemnMh1eacS1FntwC5Qrhw
+aOUAniMizzUznurd90WElVaUTJackIfr
+=olU0
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/bowtie/bowtie-0.10.1.ebuild b/sci-biology/bowtie/bowtie-0.12.7.ebuild
index 9d05b852c3ea..f4dd3c11bde5 100644
--- a/sci-biology/bowtie/bowtie-0.10.1.ebuild
+++ b/sci-biology/bowtie/bowtie-0.12.7.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.10.1.ebuild,v 1.3 2009/09/22 11:43:28 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.7.ebuild,v 1.1 2011/03/06 17:18:05 jlec Exp $
 
-EAPI="2"
+EAPI="4"
+
+inherit toolchain-funcs
 
 DESCRIPTION="An ultrafast memory-efficient short read aligner"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/"
@@ -11,7 +13,7 @@ SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
 LICENSE="Artistic"
 SLOT="0"
 IUSE=""
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 DEPEND="app-arch/unzip"
 RDEPEND=""
@@ -19,12 +21,24 @@ 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() {
-	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile" || die
+#src_prepare() {
+#	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile" || die
+#}
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS=""
 }
 
 src_install() {
 	dobin bowtie bowtie-* || die
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/* || die
 	newman MANUAL bowtie.1
 	dodoc AUTHORS NEWS TUTORIAL
 }