+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
AUX mb_readline_312.patch 1108 RMD160 5901513567ef2198b4c9c1baeb1ecc295af3eee8 SHA1 c5526cf58fe15cb22c401de19de7056a66c37414 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22
MD5 57580efc7486284feeda8665c1c45d4e files/mb_readline_312.patch 1108
RMD160 5901513567ef2198b4c9c1baeb1ecc295af3eee8 files/mb_readline_312.patch 1108
SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 files/mb_readline_312.patch 1108
-DIST mrbayes-3.1.1_src.tar.gz 429222
DIST mrbayes-3.1.2.tar.gz 545968 RMD160 b90b9406f34806bcd18bc49dc998b7ed444e93c3 SHA1 db73f53361688e1451ec155ccbdd130c3f889817 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
-EBUILD mrbayes-3.1.1.ebuild 799 RMD160 4a32b028b47c391a8b7d9c664889a733401376b5 SHA1 2395e8dd21afa9f5f8bf4d9950daabf821edcc84 SHA256 364e4b1c5c2099711b9d8dd343a35655bcd33cfb263dc79c55f6999f4976100f
-MD5 d32107e408cf25891856c3a19f433c21 mrbayes-3.1.1.ebuild 799
-RMD160 4a32b028b47c391a8b7d9c664889a733401376b5 mrbayes-3.1.1.ebuild 799
-SHA256 364e4b1c5c2099711b9d8dd343a35655bcd33cfb263dc79c55f6999f4976100f mrbayes-3.1.1.ebuild 799
EBUILD mrbayes-3.1.2.ebuild 1216 RMD160 cb84d89448d39339aed4e747d0a3f14966c45bd7 SHA1 599f30c7e2e336cea08929cb97c6e31b2a852147 SHA256 f1d58766fa325ca688041f1f8adc991bbd3226145fa01de3e446f16721ab8406
MD5 3c2a03c5d06e8aab8286660198daf9f6 mrbayes-3.1.2.ebuild 1216
RMD160 cb84d89448d39339aed4e747d0a3f14966c45bd7 mrbayes-3.1.2.ebuild 1216
SHA256 f1d58766fa325ca688041f1f8adc991bbd3226145fa01de3e446f16721ab8406 mrbayes-3.1.2.ebuild 1216
-MISC ChangeLog 2201 RMD160 fd6afbdd317e2e0ed447ab0e183e5ebff51f360e SHA1 2acc9682845329ac3b528d3c4a7d41b6083c3360 SHA256 671044ca7ea29294b7db5d2954ff0a37945d4a7b89c0116481f65a7ebff80633
-MD5 05529aa0174224143c394b452d68e383 ChangeLog 2201
-RMD160 fd6afbdd317e2e0ed447ab0e183e5ebff51f360e ChangeLog 2201
-SHA256 671044ca7ea29294b7db5d2954ff0a37945d4a7b89c0116481f65a7ebff80633 ChangeLog 2201
+MISC ChangeLog 2310 RMD160 bff9043c5fd2d86811dcda2b59c9bc624f905a79 SHA1 4d1f4974b31d2033bbe57dbbd893a99254d77d82 SHA256 5ec28af07616be2d42b7188caa8022ecc06e5c904423b20b6ea0a2c9a7800aca
+MD5 69aba7cb730235f461e00d30062efbb5 ChangeLog 2310
+RMD160 bff9043c5fd2d86811dcda2b59c9bc624f905a79 ChangeLog 2310
+SHA256 5ec28af07616be2d42b7188caa8022ecc06e5c904423b20b6ea0a2c9a7800aca ChangeLog 2310
MISC metadata.xml 730 RMD160 46eda6e69c53a0e301343cfc645c343c5aa9fdd6 SHA1 06e33f8fa877635c7e771e74e3edeb8cba146fb3 SHA256 fe9b9273c53a7c502d6688d63557fe603f63a47c8ff17355b9db7cdc0b78f446
MD5 fe3ba34f23a65b9df157e14ae85b1310 metadata.xml 730
RMD160 46eda6e69c53a0e301343cfc645c343c5aa9fdd6 metadata.xml 730
SHA256 fe9b9273c53a7c502d6688d63557fe603f63a47c8ff17355b9db7cdc0b78f446 metadata.xml 730
-MD5 633f96bc05400c5b178fdc58853587b5 files/digest-mrbayes-3.1.1 69
-RMD160 e096b2877d2203b9394425eb43c47fe774da7156 files/digest-mrbayes-3.1.1 69
-SHA256 9fe82b4f13d533a317ec9e2a2536598b7867e9369bafa0fece4944d3fd11f554 files/digest-mrbayes-3.1.1 69
MD5 7a779abc67948fa9bd32f81f9cd3ece5 files/digest-mrbayes-3.1.2 241
RMD160 f2a15583dc160c5445d30604e38da5f451be0886 files/digest-mrbayes-3.1.2 241
SHA256 8b97ef1f24e6277b4ea0784252a6422e453a482e4f6d2b1d4e375ef46a9f35a3 files/digest-mrbayes-3.1.2 241
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoAsC5mJXAu5GbtIRAtriAJwMHXZp9l8AV+n4NSzNNaVOareH+wCeIuBw
+r9ciixdIjsne6NlA+g0fxEA=
+=m2Hb
+-----END PGP SIGNATURE-----
+++ /dev/null
-MD5 bb4992eab3402c8c6c28d0db6c25a6ae mrbayes-3.1.1_src.tar.gz 429222
+++ /dev/null
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.1.ebuild,v 1.6 2006/11/03 14:22:28 grobian Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Bayesian Inference of Phylogeny"
-HOMEPAGE="http://mrbayes.csit.fsu.edu/"
-SRC_URI="mirror://sourceforge/${PN}/${P}_src.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="mpi"
-
-DEPEND="mpi? ( virtual/mpi )"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- sed -e "s:OPTFLAGS ?= -O3:OPTFLAGS = ${CFLAGS}:" \
- -e "s:CC = gcc:CC = $(tc-getCC):" \
- -i Makefile || die
- if use mpi; then
- sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die
- fi
-}
-
-src_compile() {
- emake || die "emake failed"
-}
-
-src_install() {
- dobin mb
- dodoc readme.txt
-}
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
DIST primer3_1.0.0.tar.gz 936696 RMD160 c08329cafcb8bf702a1654b4348a418b20e55c88 SHA1 0227f1f26c8b45dff9033543bee4387ade173c73 SHA256 fcbcf2e540e0062f3fa0d723b443b04a1c31e3e03e3aa5d97e3b2f910499f34b
-DIST primer3_1.0b.tar.gz 937824 RMD160 a0ab773aa7af3f8c158f46bf32c658776ba8ba2b SHA1 ea7ca4968437b02033f274c5033f7274b2f42d01 SHA256 54d3f1f7c20850b89f7f393c152afa9f9f93e0c29a58a45710973e13be07c9c7
EBUILD primer3-1.0.0.ebuild 854 RMD160 33c4fd85db4f6f0cb59e8a3df76115b1dd5acd1f SHA1 9f5083f05e34f4ddcd4bfddbce9ffe9273d1360e SHA256 57c0f9b5fcecc6c501e75a4bcd88d0e5b6ecaf2e562b369cbf551ce8eeb4071e
MD5 28730bf8d276dea79cfa528cf3d9d55d primer3-1.0.0.ebuild 854
RMD160 33c4fd85db4f6f0cb59e8a3df76115b1dd5acd1f primer3-1.0.0.ebuild 854
SHA256 57c0f9b5fcecc6c501e75a4bcd88d0e5b6ecaf2e562b369cbf551ce8eeb4071e primer3-1.0.0.ebuild 854
-EBUILD primer3-1.0b.ebuild 828 RMD160 d429cbc693fc0f79433c8b54f12bed43eec70612 SHA1 b4132756ed0c0e9b4008d55a8096a2211848eb9c SHA256 c04840d74a541e4fb0e21c5b9e046a7d6bb64611c16a2efd3091403ba7416e56
-MD5 4d55ba4aedb4c55ae5269c94f4030806 primer3-1.0b.ebuild 828
-RMD160 d429cbc693fc0f79433c8b54f12bed43eec70612 primer3-1.0b.ebuild 828
-SHA256 c04840d74a541e4fb0e21c5b9e046a7d6bb64611c16a2efd3091403ba7416e56 primer3-1.0b.ebuild 828
-MISC ChangeLog 2230 RMD160 b9c57cc75cb107b1fac6daec02bea2a6d7d80420 SHA1 c2fe0fe25a04701148c00e4a181ec49c98aa1fa1 SHA256 10d1f4ca26c352a9464c407080117eb1d0bdc3793e34febf814f99fe6a30da21
-MD5 71898559a64b4beee98f72ab2041f7f2 ChangeLog 2230
-RMD160 b9c57cc75cb107b1fac6daec02bea2a6d7d80420 ChangeLog 2230
-SHA256 10d1f4ca26c352a9464c407080117eb1d0bdc3793e34febf814f99fe6a30da21 ChangeLog 2230
+MISC ChangeLog 2337 RMD160 50241e7c316d7bfd16dcb3ac22b2691e9a389652 SHA1 fc607b344e8f78f57483fe29cbc8aab7af523870 SHA256 6e554e8ae64bb6f01f7f509a953ffc453754af61eb95447be30ed1eea204c4c1
+MD5 9e7020b0d50c98655ba1a026a4fd1ba0 ChangeLog 2337
+RMD160 50241e7c316d7bfd16dcb3ac22b2691e9a389652 ChangeLog 2337
+SHA256 6e554e8ae64bb6f01f7f509a953ffc453754af61eb95447be30ed1eea204c4c1 ChangeLog 2337
MISC metadata.xml 721 RMD160 52ec41dfbf0405bbf4d209a6c940ed519ef90f09 SHA1 7c1c44b75d2cf8549959e2947509e58cd6c433ed SHA256 0add5594c686e3cf605ad8bba0ab855d92bbf75e019ef8b79c3ca802164244ca
MD5 8cdd554f8d2dc15deccdb6c23a375bab metadata.xml 721
RMD160 52ec41dfbf0405bbf4d209a6c940ed519ef90f09 metadata.xml 721
MD5 91d7203581da4a746de7b12d26b929a6 files/digest-primer3-1.0.0 241
RMD160 7ddf10bb30198b32859ce793e99b9bde3d585aa0 files/digest-primer3-1.0.0 241
SHA256 e960b016d3d9583d0c812d4758b446570867e0a023366c91f83a0a0c8711ca9e files/digest-primer3-1.0.0 241
-MD5 1edcee8ca67f5d93725b5425d228b69b files/digest-primer3-1.0b 238
-RMD160 9360bf5faa05ab4b934ba1618f1c4d56b52e21db files/digest-primer3-1.0b 238
-SHA256 626655e18ba8d058d30c42dfd9eed65f04fc8287d613c56e2702d268c0450c4f files/digest-primer3-1.0b 238
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoAwP5mJXAu5GbtIRAtXiAJ4ikAzP5/4KvaQjx6XQvqIW+9brpwCcCCU+
++wVtzvVzSb0qeXP9wuMvFME=
+=bT9g
+-----END PGP SIGNATURE-----
+++ /dev/null
-MD5 6237b2c3ead5f361fe32bbd4d5cb9dfb primer3_1.0b.tar.gz 937824
-RMD160 a0ab773aa7af3f8c158f46bf32c658776ba8ba2b primer3_1.0b.tar.gz 937824
-SHA256 54d3f1f7c20850b89f7f393c152afa9f9f93e0c29a58a45710973e13be07c9c7 primer3_1.0b.tar.gz 937824
+++ /dev/null
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.0b.ebuild,v 1.1 2006/11/03 01:52:10 ribosome Exp $
-
-DESCRIPTION="Design primers for PCR reactions."
-HOMEPAGE="http://frodo.wi.mit.edu/primer3/primer3_code.html"
-SRC_URI="http://frodo.wi.mit.edu/${PN}/${PN}_${PV}.tar.gz"
-LICENSE="whitehead"
-
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-
-RDEPEND=""
-
-S="${WORKDIR}/${PN}_${PV}/src"
-
-src_compile() {
- emake -e || die
-}
-
-src_test () {
- cd ../test
- perl primer_test.pl primer3_core || die
-}
-
-src_install () {
- dobin primer3_core || die "Could not install program."
- dodoc ../{how-to-cite.txt,README.${PN}_${PV}.txt,example} || \
- die "Could not install documentation."
-}
MD5 7321fc88d375cef4db1411e6e6c867ab files/wise-env 40
RMD160 2ac8408df8a36f789c28d8d55cf892dba78359c5 files/wise-env 40
SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36 files/wise-env 40
-DIST wise2.1.23c.tar.gz 2099297 RMD160 3677760c3cb6dc7000caf2b24937669725b54cb0 SHA1 e518aea38e0b137581865f14c5c0dd00c474b526 SHA256 4200caa7edc81805c17f9032becc0c9d53a20be6693ba1e6dfdfa7a88e6a016a
DIST wise2.2.0.tar.gz 2108151 RMD160 a4292fbfb405d19b628fe5c829d746297e740862 SHA1 77cc08e9cda9416641370c9b45191192fc7cacd3 SHA256 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
-EBUILD wise-2.1.23c.ebuild 1809 RMD160 283a07c1907e221e82009322fc69d99d9e68a0d1 SHA1 144e99324c5968c2d513b1b14f74382d1da84567 SHA256 cceaeb48c474cdfa311debf6fac3dd43506a9d23d5a38002f51052d4183ad3c1
-MD5 1af8c0502168ef76a276d372594a634f wise-2.1.23c.ebuild 1809
-RMD160 283a07c1907e221e82009322fc69d99d9e68a0d1 wise-2.1.23c.ebuild 1809
-SHA256 cceaeb48c474cdfa311debf6fac3dd43506a9d23d5a38002f51052d4183ad3c1 wise-2.1.23c.ebuild 1809
EBUILD wise-2.2.0.ebuild 1992 RMD160 08f042a0d66114274fb53e09825e72542a9d8017 SHA1 4b67d463939053e4bffc6888886065af6e222653 SHA256 870d611892d5d9ea940ad1e5ca566dd2edace22850621b353b852451e6edd23c
MD5 cb75d7d3eb6924151331adcb1dc85af7 wise-2.2.0.ebuild 1992
RMD160 08f042a0d66114274fb53e09825e72542a9d8017 wise-2.2.0.ebuild 1992
SHA256 870d611892d5d9ea940ad1e5ca566dd2edace22850621b353b852451e6edd23c wise-2.2.0.ebuild 1992
-MISC ChangeLog 1573 RMD160 a097ff83638dd7da11d3e062cc04bc2eb4fd438b SHA1 37ea73ecbc829aa3791e7967e596395a726a5651 SHA256 ab0f800ba11ea47dcf774d6e6b75db14d45f2703caab96d7de2b4e897989a86b
-MD5 34fb11b76551a2427af72adc2cd38107 ChangeLog 1573
-RMD160 a097ff83638dd7da11d3e062cc04bc2eb4fd438b ChangeLog 1573
-SHA256 ab0f800ba11ea47dcf774d6e6b75db14d45f2703caab96d7de2b4e897989a86b ChangeLog 1573
+MISC ChangeLog 1680 RMD160 fdc4c9a2dbd2678fa753f26df8a66c0f801e1ef6 SHA1 66a305a8f9cd2f5b1838d081f16da6a7808c28f5 SHA256 3ff7cb7e89abf064cb9b94518c3667b4d803436ccbb75677e2c661bb5788b7fb
+MD5 f4f876adcbd393b9893ccdea8d1b1985 ChangeLog 1680
+RMD160 fdc4c9a2dbd2678fa753f26df8a66c0f801e1ef6 ChangeLog 1680
+SHA256 3ff7cb7e89abf064cb9b94518c3667b4d803436ccbb75677e2c661bb5788b7fb ChangeLog 1680
MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
MD5 aec0225cc3c4bc9490275e897849b449 metadata.xml 165
RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 metadata.xml 165
SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 metadata.xml 165
-MD5 5ea26e49016cda3ac95a41eb97ecd550 files/digest-wise-2.1.23c 238
-RMD160 78984bd7354ee5628140a9a20294293f464e1949 files/digest-wise-2.1.23c 238
-SHA256 7304d1f57a4c7c008925b4a91b77fa64ec1d02d0575a3e7779f421b5391c0926 files/digest-wise-2.1.23c 238
MD5 4c93bc0d8fb6e6f60096991d470c317d files/digest-wise-2.2.0 232
RMD160 ff75c61b2fe24031ee9777872e6254140e888d2f files/digest-wise-2.2.0 232
SHA256 9809ad3161c35ce94a73c205ea93cb0d8e58b652784dd1fb84602e087aa28f4e files/digest-wise-2.2.0 232
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.4.5 (GNU/Linux)
+Version: GnuPG v1.4.4 (GNU/Linux)
-iD8DBQFFW3ycI1lqEGTUzyQRAq96AKCSEjmA4UbdasHDK2TP9C/XBzFLogCfSYtN
-/E2H1lYJVo4KOQpRKGJRBEM=
-=vs56
+iD8DBQFFoAwO5mJXAu5GbtIRAgySAJoCwegS8txwdThIWfMOT+MShDq/qwCfaBye
+zD/bQi72p2Srcdbfou/QdmI=
+=hYFG
-----END PGP SIGNATURE-----
+++ /dev/null
-MD5 c058f9c3f4d5621caf581bb736f7b1f1 wise2.1.23c.tar.gz 2099297
-RMD160 3677760c3cb6dc7000caf2b24937669725b54cb0 wise2.1.23c.tar.gz 2099297
-SHA256 4200caa7edc81805c17f9032becc0c9d53a20be6693ba1e6dfdfa7a88e6a016a wise2.1.23c.tar.gz 2099297
+++ /dev/null
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.1.23c.ebuild,v 1.3 2006/11/10 23:06:26 ribosome Exp $
-
-inherit eutils toolchain-funcs flag-o-matic
-
-DESCRIPTION="Intelligent algorithms for DNA searches"
-LICENSE="BSD"
-HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}2/${PN}${PV}.tar.gz"
-
-SLOT="0"
-IUSE="threads"
-KEYWORDS="~alpha ~sparc ia64 x86"
-
-RDEPEND="=sci-biology/hmmer-2.3.2-r1"
-
-DEPEND="${RDEPEND}
- app-shells/tcsh
- dev-lang/perl
- virtual/tetex"
-
-S="${WORKDIR}/${PN}${PV}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- if use threads; then
- append-flags "-DPTHREAD"
- sed -e "s/#EXTRALIBS = -lpthread/EXTRALIBS = -lpthread/" -i makefile || die
- fi
- sed -e "s/CC = cc/CC = $(tc-getCC)/" \
- -e "s/CFLAGS = -c -O/CFLAGS = -c ${CFLAGS}/" \
- -i makefile || die
- cd "${S}"/docs
-}
-
-src_compile() {
- cd src
- make all || die
- cd "${S}"/docs
- for i in appendix dynamite wise2 wise3arch; do
- latex ${i} || die
- latex ${i} || die
- dvips ${i}.dvi -o || die
- done
-}
-
-src_install() {
- dobin "${S}"/bin/* || die "Installing program failed"
- dolib "${S}"/base/libwisebase.a || die "Failed to install libwisebase"
- dolib "${S}"/dynlibsrc/libdyna.a || die "Failed to install libdyna"
- dobin "${S}"/dynlibsrc/testgendb || die "Failed to install testgendb"
- dolib "${S}"/models/libmodel.a || die "Failed to install libmodel"
- insinto /usr/share/${PN}
- doins -r "${S}"/wisecfg || die "Failed to install wisecfg"
- insinto /usr/share/doc/${PF}
- doins "${S}"/docs/*.ps || die "Failed to install documentation"
- newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
-}
-
-src_test() {
- cd "${S}"/src
- WISECONFIGDIR="${S}/wisecfg" make test || die
-}