sci-biology/bowtie: Version Bump

Package-Manager: portage-2.2.0_alpha188/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 67 insertions, 8 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index b6687cb2229d..fc0badbf1e6c 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/bowtie
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.15 2013/03/11 14:53:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.16 2013/07/17 07:09:36 jlec Exp $
+
+*bowtie-1.0.0 (17 Jul 2013)
+
+  17 Jul 2013; Justin Lecher <jlec@gentoo.org> +bowtie-1.0.0.ebuild:
+  Version Bump
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 4f7e583a0c77..7625370a182b 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,21 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX bowtie-0.12.8-gcc-47.patch 1077 SHA256 1516e8c3ca57cba14e28a864042a0637998fb2633f8fe3b4d7529e0f5c2a275f SHA512 60f4ab651c183efdcd34c26ebe9f88ae3b2ee1a9ed730b6f127ac126720849dc6c0dca719b24e089c76ca5e77b1c0d5d0f4628927553fb9a4fa95e9c5ee236b0 WHIRLPOOL 79b603d84e544eafe08a6b214f104c799df68bdd58a404f0a0dbe1b08e130610936769dd43da63a0c6031f5ed5302dc85d798126a37bdc2b61b8ffeabc8e9dcc
 DIST bowtie-0.12.3-src.zip 10314474 SHA256 aac6e02cc95058e19092f6f56e87ed2eac3df11ecce889050c6feea2b2344b84
 DIST bowtie-0.12.5-src.zip 10319902 SHA256 244aa3ccbc15c88970196b0fb958c8455504902b5414987bf224c9dd92984cce
 DIST bowtie-0.12.7-src.zip 7697786 SHA256 609a6a0ad0b1a5d97908ca17da7bbf5d6dc407c7b9c49713cdc9c40f056a586a
-DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d
+DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
+DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1
 EBUILD bowtie-0.12.3.ebuild 919 SHA256 a48446e9cb918d99b3488e9b9ef3125ad2d8df2f2c8cd0fc0a1524a22663d301 SHA512 d899ac3e1a1de456acb84f1c33384d2a880dcf30780657bc711bf26fd483036f0c22c7aec3e8bdb960d6f640b38aab8340952bfb11d7d1fff7a751e052099761 WHIRLPOOL 4518d7c25c7a4198701cf55eabeb1dc258f9cc5312acfe73376ec3fc92cb0c2e67e5f7957f9252b46edc5a9d55be078bab9771d0168a6ee83e36c8cf2581ae7e
 EBUILD bowtie-0.12.5.ebuild 931 SHA256 cb12a3f471f9dd8e0b0eee6fff065929177895ce1d1f5995071380d944628d1f SHA512 dbce82ee8952f30f59f0fc5a714797025ad323eb277d877e600b949e3366ecb3504b26f36afa345101d216f0ca4be301d8099589a37eae755e5816c459e3c734 WHIRLPOOL 10a4e18f7e3c55ad0f8f96ae93b9ce57ba4e959ef407c265d874c558b2239e482b9fd927e813de28eb5d2e9a606909613196e9d6b81f9206c3d4f0630a6b1885
 EBUILD bowtie-0.12.7.ebuild 1113 SHA256 ffc3c1ccaef5fb1b19f53946d19b4f1528076c7dc5b23d5d1ba1924612a820ec SHA512 0b59ca1226f16e80305e9cc16db23d1e3ee29598a277fa0266a3b3fbfa10fa05a66c7125333532eab95f97da6ce36d74c0cd02c4477a3eb0b2551fbafe497c60 WHIRLPOOL 2e55d37e494b8bf11d8bb364a214fa818066adda618d2b32f6564ca8dae6e70e28223e30788696faea30122521f50dde7e0ac1608f7f1dc8e056d7c3b1645314
 EBUILD bowtie-0.12.8.ebuild 1045 SHA256 a3ff2f39d8f5f1e59dcbf121769d1c866d22d42181c9104f3d3a4d59e6d4492f SHA512 e0fd7218fece5434eb33acb45cfcf652427d43adc8612d1bb6fb2b05e2ecb097b1cd593ac8b74e97a8156366e988d48761e1a6d0f98930bdb553db2db6f4f038 WHIRLPOOL d4a64f336f939a3681a624ae47cff9e54743b0d25651a13053768314c14a5514a53ed38e1afff564f332b4d9ab9436119bca6a953e06a00d35ae57a7368286f3
-MISC ChangeLog 2291 SHA256 76615f63b1750871940b12d3f9727d7433209d8dee91b6d088713aa8138b5c62 SHA512 8edb321974c11cc42d802f0022e0552df14fadf84aa0eee5aff379825422b57dd45ed1bbd8af536cdd56afcdf7052c4063212ce8af71d11313e62a1399f2ed23 WHIRLPOOL b40da51beb03f585aec5906c28c2edad493b7361b21db0df51d8c12aed63fdffb13d37e308e1d56e4b767cc756614044582a46f698228ac1ca56ba1939f843bc
+EBUILD bowtie-1.0.0.ebuild 939 SHA256 18c8d2cdfe87339784f91ac9b3c1e79789be674b500d6f58865d274f816744a6 SHA512 522b5a85b1dc4c6790d432ac8ae44276cc71ad8ff1c99d851f1678ae2940d35bfdab49eb5b41fede73e54f50d8f7dc2cbb6dcb3b1ac1c280a147557009b93360 WHIRLPOOL 93ab55f1fa59d32828d0a199c666a8d60785fe0963fe7bb740c526ee847f95618f76fb91fe7f5f104e42929ae7a11dc32eb36afc4cfb4c6d1c2623ebdd0e3eba
+MISC ChangeLog 2405 SHA256 11237cb7f932af6344b6f8d8019bc2908af8f6c7e658fce3b76aca56ffe32de7 SHA512 7e70545b63567aae9b452fe704dc7d53e2f3baa673b1559b19baedbd20b8adb91903a9be178fdda233d8657fdef4798c68a43729e8f5a957962a4e2c4a29e61a WHIRLPOOL aee2e84b7ce1740a0edda5921aac836a3268bef448b344a0c6a8e056d83f5dba1b8069ad48463a884d0216a2d45e5b89995e20a3b10af1e8a7d97f989de5fe7f
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild
new file mode 100644
index 000000000000..d43ba58ccb85
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.0.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-1.0.0.ebuild,v 1.1 2013/07/17 07:09:36 jlec Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin bowtie bowtie-*
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+
+	insinto /usr/share/${PN}
+	doins -r genomes indexes
+
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL doc/README
+	dohtml manual.html style.css
+}