Version bump

Package-Manager: portage-2.2.0_alpha134/cvs/Linux x86_64

3 files changed, 53 insertions, 21 deletions

diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog
index fe95fdbb5394..a227c899b47d 100644
--- a/sci-biology/bwa/ChangeLog
+++ b/sci-biology/bwa/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/bwa
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.11 2011/11/30 08:44:21 weaver Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.12 2013/01/21 06:15:22 weaver Exp $
+
+*bwa-0.6.2 (21 Jan 2013)
+
+  21 Jan 2013; Andrey Kislyuk <weaver@gentoo.org> +bwa-0.6.2.ebuild:
+  Version bump
 
 *bwa-0.6.1 (30 Nov 2011)
 
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index e040ac6ec458..a65c0a25037f 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,19 +1,11 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST bwa-0.5.0.tar.bz2 103638 RMD160 73803a59de42ca0763dedd56e47b09b23f115a87 SHA1 8a82efc5d8ebca7431c335d154cf203ff2aaf4b3 SHA256 02749e290d07ee7c96a9d219be7290f4b0f21fa6fc8e1405d8a6a657cd0dbc77
-DIST bwa-0.5.9.tar.bz2 113890 RMD160 9dda52d0019b0dfeb0794c2d4d4509f8add63551 SHA1 dc5d7ddd54b4f972c4e3667ce10449e1d428b419 SHA256 e1e4c522f75d7829bb1f0eb3920d31b8240f9343ebf977f9cd3540cabb9bdaf2
-DIST bwa-0.6.1.tar.bz2 129994 RMD160 78e531439551ee9ae50f251b317c2e2c1e4c5386 SHA1 89b0bebb5d8b1839bb2b146e9bdd520733a98d38 SHA256 15cc04a0085f3a0114835730e8e46ed72d36f0b34ced67594d4e04779f397be9
-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-0.5.9.ebuild 868 RMD160 fe01a1a2f9b667f71ff33ede267b9ea4ca76be5a SHA1 48f8aa65dee41b30a9463dbdcee4a612b8701764 SHA256 83ebad8206f365b9f747a86e9014a9ff6cd21670eb024fe790aee36a64b833bf
-EBUILD bwa-0.6.1.ebuild 870 RMD160 9cf99df547d902fdcd3fce4848f5195a149c48db SHA1 e521064f522cc4074e3b2755718fadc11799a0ee SHA256 d9f895635056831740589d9c6d09068bf30d84f46b72d7866bf6ced83324435b
-MISC ChangeLog 1754 RMD160 ee66ecf01ef67a9c4c967becc3b2a35e24802a59 SHA1 18d4acfa089bc53fff0e0fe5f6e5e073273fee33 SHA256 33e96b6638e724257f64f3c6f5fb85d4d3c4b4f37fda976d649da873a9fe8fb7
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.11 (GNU/Linux)
-
-iEYEARECAAYFAk7V7OoACgkQ8xSwyhbn2OYhGACcCWGPsT2SE21v4lT4nJnySJ+A
-uxAAoJDNUcFdCQMyb+x9EsfZD+3neuOb
-=YO6Q
------END PGP SIGNATURE-----
+DIST bwa-0.5.0.tar.bz2 103638 SHA256 02749e290d07ee7c96a9d219be7290f4b0f21fa6fc8e1405d8a6a657cd0dbc77 SHA512 5378072bfc54a3143de71ea34f821e745707564183b790366310a83395c07f37bb836cff3dc1743a5db97065595baa2bd5243f74abf07ad09878344ab85bce08 WHIRLPOOL 9a3ab47d7e7532a21e2d3a3a9d6e29aab551392ca87bb13360e768f06169380ebc32dfba88ffc3e822ea057752b61a56c76042ca3a63257473f51d8fb996349f
+DIST bwa-0.5.9.tar.bz2 113890 SHA256 e1e4c522f75d7829bb1f0eb3920d31b8240f9343ebf977f9cd3540cabb9bdaf2
+DIST bwa-0.6.1.tar.bz2 129994 SHA256 15cc04a0085f3a0114835730e8e46ed72d36f0b34ced67594d4e04779f397be9 SHA512 21e6374184ffd3978e92b62d9f761ea3a1e95ba65984aa6ecb8c7cf821d4ed8364377631025d46ccc96e9ab3ec136b5cd6310c7cb33ea9f83f55a6c1d8f991cf WHIRLPOOL 757572b9fb647635923c0c0a1ad2ec23d97d0f2a61181fdd66fb15724e72fcd9c32fbb5ebde0f9c9164b5c63559a4fb586a3f13936bddf2907dad9cd8e0e94b2
+DIST bwa-0.6.2.tar.bz2 128409 SHA256 8783e5640d8e4ae028e048c56db1d6b4adff6234d1047bd4f98247ffc3be69e6 SHA512 c0fa98c488839062e681f2879f7edc882bfaa99e978c4c075eaa967fcfc2d3eb626c66fd8a998794d4c5e72559594d3dde9b5cccc5baf5e1fbff167c73a5a63b WHIRLPOOL 448be4cb092d45c6649069b5ac36feb29c7671e9bc6d8c9cc51394a0c97f89a21a9ef8564774d9de1e6c7a66b900d93cd4cac55ba890b6889fb2d59c0a51033e
+EBUILD bwa-0.5.0-r1.ebuild 831 SHA256 2b0219d864e7e802096e5399acbd12445addf3ec9c01e2df0775ad79201014b2 SHA512 5252e984615c3af8b19b591653a68245ac464e86b32478513ad8ca540723ad0c9e6352145c29bd0c07fd8575c576e0828757a014f9ca25062cf8bb26c794ecd3 WHIRLPOOL f4719db02887417230bfaa47182289ca640e0be11b22ebe9f0ab59b4fee190348ffc05e4f8ab68112d84b17e86c84dceceaf4bb2ca0b1861c53a3f81cf1a2944
+EBUILD bwa-0.5.0.ebuild 665 SHA256 fe6a5dd9d7439ef97a1cbe94d0facb29dbc513e5c6fdc7944151850307205f3f SHA512 48c07646e27a787c9acb248866fae68def77cd2c9cde363d27013593cfedb4b5d5418497e3ce771daf999d0d3d548ecc5d66cc7d36996a2540b37027e67dc4c8 WHIRLPOOL 2c283bf4d8e40dacfac95c1470cad311cc5ede18963004ba3897f0cef0a9ca7750d4f08480f3dfe3d563dfae1ad869b3f98a525597d916bf43f36585c37add97
+EBUILD bwa-0.5.9.ebuild 868 SHA256 83ebad8206f365b9f747a86e9014a9ff6cd21670eb024fe790aee36a64b833bf SHA512 4850248d1c22e8d510eb4fc80a093ff0655c514fb52083d7e473c7c93f1690005ca3b91fe5db7bea34aa4be0c7270407b52e3df17cc6a4f7e1ab42e8360911c5 WHIRLPOOL f73b884476027671ca36364c3a4394bab09b032394d486b005f6a6e573fa7e104c0160e152171340f762e4d56ea9ffbd591da5637cb6eb14301690560d352338
+EBUILD bwa-0.6.1.ebuild 870 SHA256 d9f895635056831740589d9c6d09068bf30d84f46b72d7866bf6ced83324435b SHA512 ddc9a8ce246d5de0a0cc76baa3147bf4fa091179dcaac00ced810f27c1c861baee3610b1a5d83a7c0e4ba7172635578eea164cead588a857978b963c24f4bb27 WHIRLPOOL d9354eb700666ed583af66e919e190c172d1df14ffd5383d7f09d32be3c4337205a8003059824bc198c689ccd078ad5689d4a3d46df522d5685c5311ae928541
+EBUILD bwa-0.6.2.ebuild 870 SHA256 16b8d1bc0542261324e189f0331ac7ece261bc66c988affe177d6c49cba27280 SHA512 6b6f1b39fd795745e48cf72dfb67a6860002d117f9cc3615bd8cea261d95b850120322913028e914dc35b90698828d81cdc214c77e1a67b5634bfc8c674add77 WHIRLPOOL bd960bf958ab3a40c6c648f7cdbef849028f0624cc766cf110334fedcf8e243e16f32ee341cad02f995258b6b9f7216af368d3d7b823cf2ecb84de7f940c984e
+MISC ChangeLog 1865 SHA256 4495de0e8ab1217519c7304ebdb14d03c6d8283b3bd79f336421b6f93eccd399 SHA512 93e6fe89dac9f49cd2fa318fa08ce0815c33553b20cbff299419969f7c5d8be59aeb87e95fd7a2f50cb6558d7e214c5b0275f89c691a4bbac92249516be4f9fd WHIRLPOOL 0a73ea5a1222d8d04f21bc0da84bf7fa48df4a11c6fa9afb7bebef2f4cf672c7c37ccb691e53a19fd6c269461bedbaedbc2ff32eb109698f2bd3626277cd39c9
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
diff --git a/sci-biology/bwa/bwa-0.6.2.ebuild b/sci-biology/bwa/bwa-0.6.2.ebuild
new file mode 100644
index 000000000000..9430a23b2e0d
--- /dev/null
+++ b/sci-biology/bwa/bwa-0.6.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.6.2.ebuild,v 1.1 2013/01/21 06:15:22 weaver 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
+}