Ebuild clean-up. Readded version 2.1.23c.

Package-Manager: portage-2.1.1-r1

diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
index 80f1b256584c83bf0ce468a4b0dce3d2a748fbec..6399439d1d289a0c2a43604476e1aeaf7beb090a 100644 (file)
--- a/sci-biology/wise/ChangeLog
+++ b/sci-biology/wise/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/wise
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.10 2006/11/03 03:08:09 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.11 2006/11/10 23:06:26 ribosome Exp $
+
+  10 Nov 2006; Olivier Fisette <ribosome@gentoo.org> +wise-2.1.23c.ebuild,
+  wise-2.2.0.ebuild:
+  Ebuild clean-up. Readded version 2.1.23c. (I forgot we need it for threads
+  support.)
 
   03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -wise-2.1.23c.ebuild:
   Pruned old version.

diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index 9912dd22fb50d494adbf4f769e8d49e512e8db76..bd21df90f8c26e211b2c928189d7bd99f4837b80 100644 (file)
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -6,19 +6,27 @@ AUX wise-env 40 RMD160 2ac8408df8a36f789c28d8d55cf892dba78359c5 SHA1 76bce2a14ae
 MD5 7321fc88d375cef4db1411e6e6c867ab files/wise-env 40
 RMD160 2ac8408df8a36f789c28d8d55cf892dba78359c5 files/wise-env 40
 SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36 files/wise-env 40
-DIST wise2.2.0.tar.gz 2108151
-EBUILD wise-2.2.0.ebuild 1695 RMD160 cdd1e21384c8b7b7263e30acfca364528a1c76a8 SHA1 3d5c7e48db7bd1cdd59d29ae0ca3a4ee2e5766ec SHA256 066133d42e6558c5f938bfb74ee89d3efb4a6b7b43e7ba8360068b8d191899dd
-MD5 a65fe2f917c76f2a8764a4bd19951ec4 wise-2.2.0.ebuild 1695
-RMD160 cdd1e21384c8b7b7263e30acfca364528a1c76a8 wise-2.2.0.ebuild 1695
-SHA256 066133d42e6558c5f938bfb74ee89d3efb4a6b7b43e7ba8360068b8d191899dd wise-2.2.0.ebuild 1695
-MISC ChangeLog 1387 RMD160 e8d2c61d1631e6ad6f2e53ebc350d96f08785669 SHA1 ca35c606ab7ac133b6fa737b3e5d588a49386a22 SHA256 b5056a84a39ea2edbc2e82b5a4dd037ef370ad4b2d2d536da8a757f289223e26
-MD5 9c5a382966c1be8aa666ce08f9bc6acf ChangeLog 1387
-RMD160 e8d2c61d1631e6ad6f2e53ebc350d96f08785669 ChangeLog 1387
-SHA256 b5056a84a39ea2edbc2e82b5a4dd037ef370ad4b2d2d536da8a757f289223e26 ChangeLog 1387
+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 1815 RMD160 22954de912b45b8d5a8789302fb892e4b3a98dc1 SHA1 adbfdb0329cec45fee7256d298adacaeeaeeac40 SHA256 212f4f96ecd88fb9a6f9afcd467c6d95ba3d8377d901d16537b5c24d51f49770
+MD5 444878551a5c48a4a0466e436551f16d wise-2.1.23c.ebuild 1815
+RMD160 22954de912b45b8d5a8789302fb892e4b3a98dc1 wise-2.1.23c.ebuild 1815
+SHA256 212f4f96ecd88fb9a6f9afcd467c6d95ba3d8377d901d16537b5c24d51f49770 wise-2.1.23c.ebuild 1815
+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 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 dfe3a28949733a00d7126ed491e8b3f2 files/digest-wise-2.2.0 62
-RMD160 3689c7d27604f3731dbffaf41917b12c6c8e36ae files/digest-wise-2.2.0 62
-SHA256 6805978226c3839281c6681bb0f41566a665482fdc7de7367bc392a7f2bf3f9d files/digest-wise-2.2.0 62
+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

diff --git a/sci-biology/wise/files/digest-wise-2.1.23c b/sci-biology/wise/files/digest-wise-2.1.23c
new file mode 100644 (file)
index 0000000..59d95fc
--- /dev/null
+++ b/sci-biology/wise/files/digest-wise-2.1.23c
@@ -0,0 +1,3 @@
+MD5 c058f9c3f4d5621caf581bb736f7b1f1 wise2.1.23c.tar.gz 2099297
+RMD160 3677760c3cb6dc7000caf2b24937669725b54cb0 wise2.1.23c.tar.gz 2099297
+SHA256 4200caa7edc81805c17f9032becc0c9d53a20be6693ba1e6dfdfa7a88e6a016a wise2.1.23c.tar.gz 2099297

diff --git a/sci-biology/wise/files/digest-wise-2.2.0 b/sci-biology/wise/files/digest-wise-2.2.0
index ad9dcdce97a35310190f5690d1689611973a9c86..7a34670f3cfbe1e0952bd86cf7dcbabd564dd80f 100644 (file)
--- a/sci-biology/wise/files/digest-wise-2.2.0
+++ b/sci-biology/wise/files/digest-wise-2.2.0
@@ -1 +1,3 @@
 MD5 0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz 2108151
+RMD160 a4292fbfb405d19b628fe5c829d746297e740862 wise2.2.0.tar.gz 2108151
+SHA256 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780 wise2.2.0.tar.gz 2108151

diff --git a/sci-biology/wise/wise-2.1.23c.ebuild b/sci-biology/wise/wise-2.1.23c.ebuild
new file mode 100644 (file)
index 0000000..9f0aa79
--- /dev/null
+++ b/sci-biology/wise/wise-2.1.23c.ebuild
@@ -0,0 +1,65 @@
+# 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
+}

diff --git a/sci-biology/wise/wise-2.2.0.ebuild b/sci-biology/wise/wise-2.2.0.ebuild
index ae8855c2ca10c0fb15c11f00f115b138f95834e2..ad04919484a5d0a8361e184e5ab6c0cd63cbd962 100644 (file)
--- a/sci-biology/wise/wise-2.2.0.ebuild
+++ b/sci-biology/wise/wise-2.2.0.ebuild
@@ -1,6 +1,6 @@
 # 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-2.2.0.ebuild,v 1.7 2006/04/06 22:00:07 tcort Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.8 2006/11/10 23:06:26 ribosome Exp $
 
 inherit eutils toolchain-funcs
 
@@ -50,16 +50,16 @@ src_compile() {
 }
 
 src_install() {
-       dobin "${S}"/src/bin/*
-       dolib "${S}"/src/base/libwisebase.a
-       dolib "${S}"/src/dynlibsrc/libdyna.a
-       dobin "${S}"/src/dynlibsrc/testgendb
-       dolib "${S}"/src/models/libmodel.a
+       dobin "${S}"/src/bin/* || die "Failed to install program"
+       dolib "${S}"/src/base/libwisebase.a || die "Failed to install libwisebase"
+       dolib "${S}"/src/dynlibsrc/libdyna.a || die "Failed to install libdyna"
+       dobin "${S}"/src/dynlibsrc/testgendb || die "Failed to install testgendb"
+       dolib "${S}"/src/models/libmodel.a || die "Failed to install libmodel"
        insinto /usr/share/${PN}
-       doins -r "${S}"/wisecfg
+       doins -r "${S}"/wisecfg || die "Failed to install wisecfg"
        insinto /usr/share/doc/${PF}
-       doins "${S}"/docs/*.ps
-       newenvd "${FILESDIR}"/${PN}-env 24wise
+       doins "${S}"/docs/*.ps || die "Failed to install documentation"
+       newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
 }
 
 src_test() {