remove sci-biology/dotur, deprecated by upstream, use sci-biology/mothur instead

5 files changed, 3 insertions, 83 deletions

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index d1893d551696..dc95fd0f631e 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,18 +1,11 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST bowtie-0.10.0-src.zip 10255341 RMD160 33218e30da716cf358ca0df68e5dfedb16948e91 SHA1 2d9f0e2a9b2ff8db0798a35564e11fbf69479bcd SHA256 48eb4f5ed98f344ebd2739cbdef77b9747abb2b5bf290781ddb853471c0b72cf
 DIST bowtie-0.10.1-src.zip 10258866 RMD160 99628de52fda58ee358f1ac629634210be24cf3e SHA1 f509f442d824a7b2b0650f29d2b3625aea1a1466 SHA256 71a64c08eee4147f670d52a8e9f61d28d9c67fa595ece93d55d9524e15fed809
+DIST bowtie-0.11.3-src.zip 10284698 RMD160 48d64a0be0d7f937d627540f499697e7672d2a08 SHA1 72f285fee3027b940f4c6b058b977d6fb0b33532 SHA256 4d3fb0e8ed8dbfe89449a84e6bcca9057a2ddc6565e90e8dfc0a09fdd93be85b
 DIST bowtie-0.9.9.2-src.zip 10234128 RMD160 ad728d8f23742ece2d9d2bfe708b76cdcabf32b0 SHA1 f1d2afd5391d08f7481fe0eb5f38e9d3878e9598 SHA256 c002647a0412ed736cfbd879b3a3194286d2973c6e3e32b2f7d749bebbd96228
 EBUILD bowtie-0.10.0.ebuild 861 RMD160 cd67e587879e0f019d5b3a74b15c365aebc4eaed SHA1 bf86360991819d2bebbe89d0bbefc01b3e13a30d SHA256 1ccb7b06831dd21d88325ca4d527d5e0848e6453130db4cbdeced5db00c3bfe9
 EBUILD bowtie-0.10.1.ebuild 859 RMD160 08afd397a1e50da00b9209180a8cf94ae7896c33 SHA1 e7e5add9032a345ce2688f4b17417c9693039f13 SHA256 474c8f2ee5303e04d39e8642187daa3531c91327c921f99a3a16b986e4f57842
+EBUILD bowtie-0.11.3.ebuild 910 RMD160 e4d55e9f7006d7f63db8a872c1091b584f6e3eb0 SHA1 9d91f1c677a3d6496b397f6ffd34cb22a962e12d SHA256 de86e171dc83139cac5e0e714f7ee6ee78b43864cc387c5cf4daf27988a40a9f
 EBUILD bowtie-0.9.9.2.ebuild 803 RMD160 02b3cc8d5fc424b1ab859ca3b5556f59c09cbfa4 SHA1 5a910d97e8112e54ed8bb52346f3834498c22b7d SHA256 837f262ce03aeda12bf4a63d833fde9ce2e43eb633c9fd58ab3835c38467690b
 MISC ChangeLog 1158 RMD160 b12a398746cb4d84286743aae050cf99aa9fe356 SHA1 d3fb4e4b0660a65154505622fd25b7ae4310d00d SHA256 985c6692ef350e72e232a512f37b1683193a3ed751f198eaed59d3f249ec2f0f
+MISC FIXME 20 RMD160 132d20fa79ddf75230b665998fb0ced9d4bdcf7f SHA1 2384754a781629ba13c7699e7c4951dc50284fcf SHA256 7fcb5ee422506111207f718c3d9aefc1abef4d716543eb449a8cecf512578beb
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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-=RAhM
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diff --git a/sci-biology/dotur/ChangeLog b/sci-biology/dotur/ChangeLog
deleted file mode 100644
index 544c4c0acbd2..000000000000
--- a/sci-biology/dotur/ChangeLog
+++ /dev/null
@@ -1,19 +0,0 @@
-# ChangeLog for sci-biology/dotur
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dotur/ChangeLog,v 1.3 2009/08/05 21:10:14 maekke Exp $
-
-  05 Aug 2009; Markus Meier <maekke@gentoo.org> dotur-1.53.ebuild:
-  x86 stable, bug #279347
-
-  02 Aug 2009; <chainsaw@gentoo.org> dotur-1.53.ebuild:
-  Marked stable on AMD64 as requested by Andrey "weaver" Kislyuk
-  <weaver@gentoo.org> in bug #279347. Arch-tested by Chad A. Simmons who
-  reports he has no test-suite; reporter confirmed and agreed compile-test
-  was sufficient.
-
-  12 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> +ChangeLog, +Manifest:
-  Import from Science overlay
-
-  04 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
-  New package, ebuild written by me
-
diff --git a/sci-biology/dotur/Manifest b/sci-biology/dotur/Manifest
deleted file mode 100644
index d604a4d1c175..000000000000
--- a/sci-biology/dotur/Manifest
+++ /dev/null
@@ -1,14 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST dotur-1.53.tgz 68803 RMD160 bea01d059b160e0493dd3d57efd3d0927b6ebd43 SHA1 5301de0af907e1245cf486bf4227e3a70015e90f SHA256 f3f1a33e0332fd4fe810a2ff96a4f804e6ca62fa5571a997928524876d661c1f
-EBUILD dotur-1.53.ebuild 760 RMD160 dbb7658eace6797369d66f82d338c600851c9dd4 SHA1 42f2177edf74f5316ac48b4666e645b72e9b796e SHA256 ab1cfc2dda79764a753070e4059db324d49711810e1721923cf0c70ef15490a1
-MISC ChangeLog 791 RMD160 5289c1375731299f355932fcd39d0ead78dd5c92 SHA1 5a603c3ba9012af2cc52b91012da9e63d735697a SHA256 cc113977ec87f75ec0fe92e73466769f0adf3a2df2473ee283c611788794d045
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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-RFEAnRvyzxXyiYGY+wZjAwCWfBMuIrCj
-=jfUa
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diff --git a/sci-biology/dotur/dotur-1.53.ebuild b/sci-biology/dotur/dotur-1.53.ebuild
deleted file mode 100644
index 5352362369b7..000000000000
--- a/sci-biology/dotur/dotur-1.53.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dotur/dotur-1.53.ebuild,v 1.3 2009/08/05 21:10:14 maekke Exp $
-
-EAPI=2
-
-inherit toolchain-funcs
-
-DESCRIPTION="Distance Based OTU and Richness Determination for DNA sequences"
-HOMEPAGE="http://schloss.micro.umass.edu/software/dotur.html"
-SRC_URI="http://schloss.micro.umass.edu/software/${PN}/${P}.tgz"
-
-LICENSE="as-is"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/DOTUR-${PV}"
-
-src_compile() {
-	sed -i '1 i #include <string.h>\n#include <algorithm>' dotur.C
-	$(tc-getCXX) ${CXXFLAGS} -O3 dotur.C -o dotur || die
-}
-
-src_install() {
-	dobin dotur || die
-	dodoc README
-}
diff --git a/sci-biology/dotur/metadata.xml b/sci-biology/dotur/metadata.xml
deleted file mode 100644
index 3302123e5718..000000000000
--- a/sci-biology/dotur/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>