Moving to sci-biology/cutg

diff --git a/app-sci/cutg/ChangeLog b/app-sci/cutg/ChangeLog
deleted file mode 100644 (file)
index e1b2938..0000000
--- a/app-sci/cutg/ChangeLog
+++ /dev/null
@@ -1,37 +0,0 @@
-# ChangeLog for app-sci/cutg
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/cutg/ChangeLog,v 1.7 2004/11/23 20:23:18 ribosome Exp $
-
-*cutg-144 (23 Nov 2004)
-
-  23 Nov 2004; Olivier Fisette <ribosome@gentoo.org> +cutg-144.ebuild:
-  New version.
-
-  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -cutg-142.ebuild,
-  cutg-143.ebuild:
-  Removed old version. Added 143 to x86.
-
-*cutg-143 (29 Sep 2004)
-
-  29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -cutg-141.0.ebuild,
-  cutg-142.ebuild, +cutg-143.ebuild:
-  Added 142 to x86. Added new version 142. Removed old version.
-
-*cutg-142 (10 Aug 2004)
-
-  10 Aug 2004; Olivier Fisette <ribosome@gentoo.org>
-  cutg-141.0.ebuild:
-  Added to x86.
-  cutg-142.ebuild:
-  Updated package.
-
-  26 Jun 2004; David Holm <dholm@gentoo.org> cutg-141.0.ebuild:
-  Added to ~ppc.
-
-*cutg-141.0 (24 Jun 2004)
-
-  24 Jun 2004; Olivier Fisette <ribosome@gentoo.org>
-  cutg-141.0.ebuild, metadata.xml :
-  Initial import.  Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>.
-  Reference: Gentoo Bugzilla, bug #54322
-

diff --git a/app-sci/cutg/Manifest b/app-sci/cutg/Manifest
deleted file mode 100644 (file)
index d81a49b..0000000
--- a/app-sci/cutg/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-MD5 e4a9cb7a750c45b5f064e0791a6db623 cutg-143.ebuild 1178
-MD5 2bb31e68b962982d6890f9636a4bac63 ChangeLog 1115
-MD5 d14f29edef39d8d89b39a5787c3d141c metadata.xml 594
-MD5 3e219869a7440d22d1a3e3b6605429f4 cutg-144.ebuild 1179
-MD5 94ad06877dbe9065273a7ee15904c7ec files/digest-cutg-143 63
-MD5 e35ab30eae79e0600feabc028e0db162 files/digest-cutg-144 63

diff --git a/app-sci/cutg/cutg-143.ebuild b/app-sci/cutg/cutg-143.ebuild
deleted file mode 100644 (file)
index c0704b3..0000000
--- a/app-sci/cutg/cutg-143.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/cutg/cutg-143.ebuild,v 1.3 2004/11/01 01:48:18 ribosome Exp $
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz"
-LICENSE="public-domain"
-
-SLOT="0"
-KEYWORDS="x86 ~ppc"
-IUSE="no-emboss no-rawdb"
-
-S=${WORKDIR}
-
-src_compile() {
-       # Index the database for use with emboss if emboss is installed and
-       # the user did not explicitly request not to index the database.
-       if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then
-               mkdir CODONS
-               einfo "Indexing CUTG for usage with EMBOSS."
-               EMBOSS_DATA=. cutgextract -auto -directory ${S} || die \
-                       "Indexing CUTG failed."
-       fi
-}
-
-src_install() {
-       if ! use no-rawdb; then
-               mkdir -p ${D}/usr/share/${PN}
-               mv *.codon *.spsum ${D}/usr/share/${PN}
-       fi
-       dodoc README
-       if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then
-               mkdir -p ${D}/usr/share/EMBOSS/data/CODONS
-               cd CODONS
-               for file in *; do
-                       mv ${file} ${D}/usr/share/EMBOSS/data/CODONS
-               done
-       fi
-}

diff --git a/app-sci/cutg/cutg-144.ebuild b/app-sci/cutg/cutg-144.ebuild
deleted file mode 100644 (file)
index e198ba2..0000000
--- a/app-sci/cutg/cutg-144.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/cutg/cutg-144.ebuild,v 1.1 2004/11/23 20:23:18 ribosome Exp $
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz"
-LICENSE="public-domain"
-
-SLOT="0"
-KEYWORDS="~x86 ~ppc"
-IUSE="no-emboss no-rawdb"
-
-S=${WORKDIR}
-
-src_compile() {
-       # Index the database for use with emboss if emboss is installed and
-       # the user did not explicitly request not to index the database.
-       if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then
-               mkdir CODONS
-               einfo "Indexing CUTG for usage with EMBOSS."
-               EMBOSS_DATA=. cutgextract -auto -directory ${S} || die \
-                       "Indexing CUTG failed."
-       fi
-}
-
-src_install() {
-       if ! use no-rawdb; then
-               mkdir -p ${D}/usr/share/${PN}
-               mv *.codon *.spsum ${D}/usr/share/${PN}
-       fi
-       dodoc README
-       if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then
-               mkdir -p ${D}/usr/share/EMBOSS/data/CODONS
-               cd CODONS
-               for file in *; do
-                       mv ${file} ${D}/usr/share/EMBOSS/data/CODONS
-               done
-       fi
-}

diff --git a/app-sci/cutg/files/digest-cutg-143 b/app-sci/cutg/files/digest-cutg-143
deleted file mode 100644 (file)
index 55572f7..0000000
--- a/app-sci/cutg/files/digest-cutg-143
+++ /dev/null
@@ -1 +0,0 @@
-MD5 8f3ccb3c31e1383ac987d8e46c9f5610 CUTG.143.tar.gz 117357602

diff --git a/app-sci/cutg/files/digest-cutg-144 b/app-sci/cutg/files/digest-cutg-144
deleted file mode 100644 (file)
index f79c6a6..0000000
--- a/app-sci/cutg/files/digest-cutg-144
+++ /dev/null
@@ -1 +0,0 @@
-MD5 2bea63f0124ef7cb360bddeb0465e548 CUTG.144.tar.gz 124856915

diff --git a/app-sci/cutg/metadata.xml b/app-sci/cutg/metadata.xml
deleted file mode 100644 (file)
index b89e0f6..0000000
--- a/app-sci/cutg/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-       <maintainer>
-               <email>ribosome@gentoo.org</email>
-               <name>Olivier Fisette</name>
-       </maintainer>
-       <herd>sci</herd>
-       <longdescription>
-               Codon usage tables maintained at the Kazusa DNA Research Institute.
-               Codon usage in individual genes has been calculated using the
-               nucleotide sequence data obtained from the GenBank Genetic Sequence
-               Database. The compilation of codon usage is synchronized with each
-               major release of GenBank.
-       </longdescription>
-</pkgmetadata>