Moved from app-sci/cutg to sci-biology/cutg.

7 files changed, 147 insertions, 0 deletions

diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog
new file mode 100644
index 000000000000..99f12437ffbd
--- /dev/null
+++ b/sci-biology/cutg/ChangeLog
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+# ChangeLog for app-sci/cutg
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.1 2004/12/23 21:19:57 ribosome Exp $
+
+*cutg-143 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +cutg-143.ebuild, +cutg-144.ebuild:
+  Moved from app-sci/cutg to sci-biology/cutg.
+
+*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/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
new file mode 100644
index 000000000000..d81a49b14c73
--- /dev/null
+++ b/sci-biology/cutg/Manifest
@@ -0,0 +1,6 @@
+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/sci-biology/cutg/cutg-143.ebuild b/sci-biology/cutg/cutg-143.ebuild
new file mode 100644
index 000000000000..8dbbe5af181a
--- /dev/null
+++ b/sci-biology/cutg/cutg-143.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-143.ebuild,v 1.1 2004/12/23 21:19:57 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/sci-biology/cutg/cutg-144.ebuild b/sci-biology/cutg/cutg-144.ebuild
new file mode 100644
index 000000000000..46b0aaceef27
--- /dev/null
+++ b/sci-biology/cutg/cutg-144.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-144.ebuild,v 1.1 2004/12/23 21:19:57 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/sci-biology/cutg/files/digest-cutg-143 b/sci-biology/cutg/files/digest-cutg-143
new file mode 100644
index 000000000000..55572f7df18e
--- /dev/null
+++ b/sci-biology/cutg/files/digest-cutg-143
@@ -0,0 +1 @@
+MD5 8f3ccb3c31e1383ac987d8e46c9f5610 CUTG.143.tar.gz 117357602
diff --git a/sci-biology/cutg/files/digest-cutg-144 b/sci-biology/cutg/files/digest-cutg-144
new file mode 100644
index 000000000000..f79c6a6dc995
--- /dev/null
+++ b/sci-biology/cutg/files/digest-cutg-144
@@ -0,0 +1 @@
+MD5 2bea63f0124ef7cb360bddeb0465e548 CUTG.144.tar.gz 124856915
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
new file mode 100644
index 000000000000..b89e0f65dac4
--- /dev/null
+++ b/sci-biology/cutg/metadata.xml
@@ -0,0 +1,16 @@
+<?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>