From 68fb542a3f5c3892a386e1ed39668df9537adae1 Mon Sep 17 00:00:00 2001
From: Olivier Fisette <ribosome@gentoo.org>
Date: Fri, 25 Jun 2004 03:31:35 +0000
Subject: Initial import for app-sci/cutg

---
 app-sci/cutg/ChangeLog               | 11 ++++++++++
 app-sci/cutg/cutg-141.0.ebuild       | 39 ++++++++++++++++++++++++++++++++++++
 app-sci/cutg/files/digest-cutg-141.0 |  1 +
 app-sci/cutg/metadata.xml            | 16 +++++++++++++++
 app-sci/prints/Manifest              |  4 ++++
 5 files changed, 71 insertions(+)
 create mode 100644 app-sci/cutg/ChangeLog
 create mode 100644 app-sci/cutg/cutg-141.0.ebuild
 create mode 100644 app-sci/cutg/files/digest-cutg-141.0
 create mode 100644 app-sci/cutg/metadata.xml
 create mode 100644 app-sci/prints/Manifest

(limited to 'app-sci')

diff --git a/app-sci/cutg/ChangeLog b/app-sci/cutg/ChangeLog
new file mode 100644
index 000000000000..f90bfff55bb9
--- /dev/null
+++ b/app-sci/cutg/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for app-sci/cutg
+# Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/cutg/ChangeLog,v 1.1 2004/06/25 03:31:35 ribosome Exp $
+
+*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/cutg-141.0.ebuild b/app-sci/cutg/cutg-141.0.ebuild
new file mode 100644
index 000000000000..407f65037b46
--- /dev/null
+++ b/app-sci/cutg/cutg-141.0.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2004 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/cutg/cutg-141.0.ebuild,v 1.1 2004/06/25 03:31:35 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.141.tar.gz"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~x86"
+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 ${S} || die \
+			"Indexing CUTG failed."
+	fi
+}
+
+src_install() {
+	if ! use no-rawdb; then
+		insinto /usr/share/${PN}
+		doins *.codon *.spsum
+	fi
+	dodoc README
+	if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then
+		insinto /usr/share/EMBOSS/data/CODONS
+		cd CODONS
+		for file in *; do
+			doins ${file}
+		done
+	fi
+}
diff --git a/app-sci/cutg/files/digest-cutg-141.0 b/app-sci/cutg/files/digest-cutg-141.0
new file mode 100644
index 000000000000..8bcb59f3592a
--- /dev/null
+++ b/app-sci/cutg/files/digest-cutg-141.0
@@ -0,0 +1 @@
+MD5 e8081fc857459b7ad02573eee8c47c8a CUTG.141.tar.gz 105858375
diff --git a/app-sci/cutg/metadata.xml b/app-sci/cutg/metadata.xml
new file mode 100644
index 000000000000..b89e0f65dac4
--- /dev/null
+++ b/app-sci/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>
diff --git a/app-sci/prints/Manifest b/app-sci/prints/Manifest
new file mode 100644
index 000000000000..73944c826df4
--- /dev/null
+++ b/app-sci/prints/Manifest
@@ -0,0 +1,4 @@
+MD5 4584bb68e344b7974c45cdf0f5e85162 prints-37.0.ebuild 1410
+MD5 b94b32b4d99a5af47af5debcd9d57efd ChangeLog 449
+MD5 1ac1b9a7f4647c51e178fee97f2e8fa8 metadata.xml 876
+MD5 480ec57dbfe7db281e30726e6e1160bd files/digest-prints-37.0 365
-- 
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