initial import of cbcanalyzer

(Portage version: 2.0.51.20-r4)

5 files changed, 77 insertions, 0 deletions

diff --git a/sci-biology/cbcanalyzer/ChangeLog b/sci-biology/cbcanalyzer/ChangeLog
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+++ b/sci-biology/cbcanalyzer/ChangeLog
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+# ChangeLog for sci-biology/treeviewx
+# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cbcanalyzer/ChangeLog,v 1.1 2005/04/25 19:46:25 apokorny Exp $
+
+*cbcanalyzer-1.0.0 (25 Apr 2005)
+
+  25 Apr 2005; Andreas Pokorny <apokorny@gentoo.org>
+  cbcanalyzer-1.0.0.ebuild, ChangeLog, metadata.xml:
+  Initial import 
+
diff --git a/sci-biology/cbcanalyzer/Manifest b/sci-biology/cbcanalyzer/Manifest
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index 000000000000..d3d6abe499ba
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+++ b/sci-biology/cbcanalyzer/Manifest
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+MD5 b3bb233ba682021e39caf5bdb21d1ad5 cbcanalyzer-1.0.0.ebuild 861
+MD5 098b7b16e103a67726d7c71c07685b5e metadata.xml 1617
+MD5 e589d5c182691a0f5ce68cd1b7279163 ChangeLog 378
+MD5 f69a329aa4d9ac75cae676a247c6fa52 files/digest-cbcanalyzer-1.0.0 70
diff --git a/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild b/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild
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index 000000000000..d08ba9486d13
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+++ b/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild
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+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild,v 1.1 2005/04/25 19:46:25 apokorny Exp $
+
+DESCRIPTION="Creates phylogenetic trees measuring compensatory base changes"
+HOMEPAGE="http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de/"
+SRC_URI="http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de/${P}.tar.gz"
+LICENSE="GPL-2"
+
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+IUSE=""
+
+DEPEND=">=x11-libs/wxGTK-2.4.2
+	>=dev-libs/boost-1.32-r1"
+
+
+# cbcanalyzer works with wxGTK-2.4/wxGTK-2.5 gtk1 gtk2
+# but only the non unicode versions
+
+src_install() {
+	make install DESTDIR=${D} || die
+}
+
+pkg_postinst() {
+	einfo
+	einfo "To visualize trees you might want to install sci-biology/njplot"
+	einfo "and sci-biology/treeviewx."
+	einfo
+}
+
diff --git a/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0 b/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0
new file mode 100644
index 000000000000..c1fd3fa395ba
--- /dev/null
+++ b/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0
@@ -0,0 +1 @@
+MD5 8ad9c083dd80bab335a2a4cf6b7397a9 cbcanalyzer-1.0.0.tar.gz 1729756
diff --git a/sci-biology/cbcanalyzer/metadata.xml b/sci-biology/cbcanalyzer/metadata.xml
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index 000000000000..fa6b3d622192
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+++ b/sci-biology/cbcanalyzer/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>apokorny@gentoo.org</email>
+		<name>Andreas Pokorny</name>
+	</maintainer>
+	<herd>sci</herd>
+	<longdescription lang="en" >
+		CBCAnalyzer reads several CT-file formats (ct, RNAviz ct or Mac ct),
+		and generates a so called ``bracket-dot-bracket'' format that typically 
+		is used as input for other tools such as RNAforester, RNAmovie or 
+		MARNA. The latter one creates a multiple alignment based on primary
+		sequences and secondary structures that now can be used as input for
+		CBCDetect. CBCAnalyzer counts compensatory base changes in all against all 
+		of the aligned sequences. 
+		    The count (distance) matrix obtained by CBCDetect is used as input 
+		for CBCTree that reconstructs a phylogram by using the algorithm of BIONJ.
+	</longdescription>
+	<longdescription lang="de" >
+		CBCAnalyzer liest unterschiedliche CT-Format (ct, RNAviz ct oder Mac ct),
+		und generiert daraus ein sogenanntes ``Klammer-Punkt-Klammer'' Format, dass 
+		normalerweise als Eingabe für Programme wie RNAforester, RNAmovie oder
+		MARNA dient. Letzteres erzeugt ein multiples Aligment primaer basierend auf der 
+		Sequenz und sekundär basierend auf der Struktur, dies als Eingabe für
+		CBCDetect verwendet werden. CBCAnalyzer zählt dann kompensierende
+		Basiswechsel in allen Sequenzen. 
+		   Diese Zähl oder Distanzmatrix aus CBCDetect wird als Eingabe für CBCTree
+	    verwendet, um ein Phylogram mit Hilfe des BIONJ-Algorithmus zu erzeugen.
+	</longdescription>
+</pkgmetadata>