Version BUmp, #354925

Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64

3 files changed, 55 insertions, 3 deletions

diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog
index cb7facb66cd8..f0d534e625f9 100644
--- a/sci-biology/bwa/ChangeLog
+++ b/sci-biology/bwa/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/bwa
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.9 2010/10/09 20:15:55 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.10 2011/05/01 09:19:52 jlec Exp $
+
+*bwa-0.5.9 (01 May 2011)
+
+  01 May 2011; Justin Lecher <jlec@gentoo.org> +bwa-0.5.9.ebuild:
+  Version BUmp, #354925
 
 *bwa-0.5.8a (09 Oct 2010)
 
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index da507ad9c980..5f96ac7e106e 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,7 +1,19 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST bwa-0.5.0.tar.bz2 103638 RMD160 73803a59de42ca0763dedd56e47b09b23f115a87 SHA1 8a82efc5d8ebca7431c335d154cf203ff2aaf4b3 SHA256 02749e290d07ee7c96a9d219be7290f4b0f21fa6fc8e1405d8a6a657cd0dbc77
 DIST bwa-0.5.8a.tar.bz2 113239 RMD160 0c927c0583739a58334bc489d565cc5266e8076c SHA1 181a86b855a8c1597c1f7b1880bea664ae651e22 SHA256 71eb89d8a63da3f13e4e4bb012747c40db452efa6dc11b92cce70f4393004429
+DIST bwa-0.5.9.tar.bz2 113890 RMD160 9dda52d0019b0dfeb0794c2d4d4509f8add63551 SHA1 dc5d7ddd54b4f972c4e3667ce10449e1d428b419 SHA256 e1e4c522f75d7829bb1f0eb3920d31b8240f9343ebf977f9cd3540cabb9bdaf2
 EBUILD bwa-0.5.0-r1.ebuild 831 RMD160 aa22abb0bb7049b2abe2016e1ad4b5e695f87967 SHA1 e4e2183a50a7a4b47027a357ba88b722feead9d7 SHA256 2b0219d864e7e802096e5399acbd12445addf3ec9c01e2df0775ad79201014b2
 EBUILD bwa-0.5.0.ebuild 665 RMD160 465763b0779d89b9fd4860772b90b84fb271c5db SHA1 cd9ba9f0ad934eca1423b47284bd967a67492afd SHA256 fe6a5dd9d7439ef97a1cbe94d0facb29dbc513e5c6fdc7944151850307205f3f
 EBUILD bwa-0.5.8a.ebuild 871 RMD160 46c516b179afac8193a5059f02b9be578aaf2d92 SHA1 30e52dd78eec6b060fce091956812049af249c10 SHA256 e92d6032fc3c467e2f9938bd760aec9d57766456b885aa9ff74de595cb39aee5
-MISC ChangeLog 1503 RMD160 fc0d4cfd875f205411f80dbbd45fd03edeff5c2f SHA1 aff8dcf97a61d37cfa4ae63a4e7674f21049db95 SHA256 a1a74f6c0c480c7c58baa6f8217361a4dd10d99342d78cc9205477809621bb6e
+EBUILD bwa-0.5.9.ebuild 868 RMD160 fe01a1a2f9b667f71ff33ede267b9ea4ca76be5a SHA1 48f8aa65dee41b30a9463dbdcee4a612b8701764 SHA256 83ebad8206f365b9f747a86e9014a9ff6cd21670eb024fe790aee36a64b833bf
+MISC ChangeLog 1619 RMD160 453de9d884abbe41b02f653c79b4763571e59cfa SHA1 5710c51324208df17b08b63c24c5f8e4e39c091b SHA256 d92aeda30f46fec5db7eeecd91cfe29258ad0eb1b25015bf6089602d5b532a91
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk29Jb0ACgkQgAnW8HDreRbDIwCfTuro2Cn55kh5/Ang+GSoh2xJ
+MkIAn0lfJQcx42ThUlJnvQhCEbtIcyoG
+=ww7F
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/bwa/bwa-0.5.9.ebuild b/sci-biology/bwa/bwa-0.5.9.ebuild
new file mode 100644
index 000000000000..97e541ed1774
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.5.9.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.5.9.ebuild,v 1.1 2011/05/01 09:19:52 jlec Exp $
+
+EAPI=2
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
+HOMEPAGE="http://bio-bwa.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+src_prepare() {
+	sed -e "s/\$(CC) \$(CFLAGS)/\$(CC) \$(LDFLAGS) \$(CFLAGS)/" \
+		-i "${S}"/Makefile || die #336348
+	append-flags -pthread
+}
+
+src_compile() {
+	emake -e CC="$(tc-getCC)" || die
+}
+
+src_install() {
+	dobin bwa || die
+	doman bwa.1 || die
+	exeinto /usr/share/${PN}
+	doexe solid2fastq.pl || die
+	doexe qualfa2fq.pl || die
+	dodoc ChangeLog NEWS || die
+}