sci-biology/bowtie: Drop old

Package-Manager: portage-2.2.0_alpha196/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 19 insertions, 129 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 77ad1374cccd..efbaedea431d 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.18 2013/07/27 22:19:25 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.19 2013/08/11 13:32:35 jlec Exp $
+
+  11 Aug 2013; Justin Lecher <jlec@gentoo.org> -bowtie-0.12.3.ebuild,
+  -bowtie-0.12.5.ebuild, -bowtie-0.12.7.ebuild:
+  Drop old
 
   27 Jul 2013; Agostino Sarubbo <ago@gentoo.org> bowtie-0.12.8.ebuild:
   Stable for x86, wrt bug #477134
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 18b8cc8dd69c..018c0e04ee12 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -2,32 +2,26 @@
 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 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 1042 SHA256 6a046f6367ef3f1a13e64328691c683209114ada08734069b402f0f51f236829 SHA512 11c72bb3165862499d97dc1ff6bfee68efc19bcb01e807d4470e156b2dc802dccb9b88e0011fedfe8aa1df28512cefec7ea8ba18c33a21c2df19021883df66d5 WHIRLPOOL 992c246fa35ffbe2ae8fdf3aefa458fa756d6b4e36513a5d1254c6003ea2b1854d5a334ff251c20bd87b28b354b760d1629d24f410bb93089b6c0774e2b32c39
 EBUILD bowtie-1.0.0.ebuild 939 SHA256 18c8d2cdfe87339784f91ac9b3c1e79789be674b500d6f58865d274f816744a6 SHA512 522b5a85b1dc4c6790d432ac8ae44276cc71ad8ff1c99d851f1678ae2940d35bfdab49eb5b41fede73e54f50d8f7dc2cbb6dcb3b1ac1c280a147557009b93360 WHIRLPOOL 93ab55f1fa59d32828d0a199c666a8d60785fe0963fe7bb740c526ee847f95618f76fb91fe7f5f104e42929ae7a11dc32eb36afc4cfb4c6d1c2623ebdd0e3eba
-MISC ChangeLog 2617 SHA256 449bacdb14bc7c40ba9418ace4e4d80c9daadf8795700a8bbc46761842df1d1a SHA512 4bac2383100c8e82c56848b307400996a4cefb0f9dd441c9e6c865b12c135d69a4dc37eb66b4ee916ca810ad0036c0bb2aa7ace93832cf950944b50ca27778d7 WHIRLPOOL 09098284363197a7c974591e19f1ad6ea5b884fdd49159ca00ac4a7b63506d2802bb7622d031e76dbe0df9b9972511ff695cf42b89cac04ac3442c4d55757eb2
+MISC ChangeLog 2748 SHA256 bb44b4b2d25e16a841b4928e763c5b04eca87de163cbcae9d11a90c0f2950e4f SHA512 ed9212cb8a75bdd57c759529376e9e9b5ea48239b026e74007be7ce4f6d723af982a0817c59c6de854afa9243f395f1bf48efd2d0431d819df0188bc386373b5 WHIRLPOOL df9b814021585c0163bea0e50c0df50621034f29a3f780ecdd26735bbcbc916ee6d793ff74fc1cf8ae2146b2c4b34332f87fdcb06a21acc37d8145a9a74ce77e
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/bowtie/bowtie-0.12.3.ebuild b/sci-biology/bowtie/bowtie-0.12.3.ebuild
deleted file mode 100644
index 1bc1efeff004..000000000000
--- a/sci-biology/bowtie/bowtie-0.12.3.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.3.ebuild,v 1.3 2010/07/16 17:22:29 hwoarang Exp $
-
-EAPI="2"
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
-
-src_prepare() {
-	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile" || die
-}
-
-src_install() {
-	dobin bowtie bowtie-* || die
-	exeinto /usr/share/${PN}/scripts
-	doexe scripts/* || die
-	newman MANUAL bowtie.1
-	dodoc AUTHORS NEWS TUTORIAL
-}
diff --git a/sci-biology/bowtie/bowtie-0.12.5.ebuild b/sci-biology/bowtie/bowtie-0.12.5.ebuild
deleted file mode 100644
index 28540c3e52de..000000000000
--- a/sci-biology/bowtie/bowtie-0.12.5.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.5.ebuild,v 1.2 2010/09/30 07:24:16 grobian Exp $
-
-EAPI="2"
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
-
-src_prepare() {
-	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile" || die
-}
-
-src_install() {
-	dobin bowtie bowtie-* || die
-	exeinto /usr/share/${PN}/scripts
-	doexe scripts/* || die
-	newman MANUAL bowtie.1
-	dodoc AUTHORS NEWS TUTORIAL
-}
diff --git a/sci-biology/bowtie/bowtie-0.12.7.ebuild b/sci-biology/bowtie/bowtie-0.12.7.ebuild
deleted file mode 100644
index f4dd3c11bde5..000000000000
--- a/sci-biology/bowtie/bowtie-0.12.7.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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-0.12.7.ebuild,v 1.1 2011/03/06 17:18:05 jlec Exp $
-
-EAPI="4"
-
-inherit toolchain-funcs
-
-DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
-# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
-
-#src_prepare() {
-#	sed -i 's/$(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
-}