Initial import, see bug ##28808

6 files changed, 79 insertions, 0 deletions

diff --git a/app-sci/gibbs/ChangeLog b/app-sci/gibbs/ChangeLog
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@@ -0,0 +1,11 @@
+# ChangeLog for app-sci/gibbs
+# Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/gibbs/ChangeLog,v 1.1 2004/05/27 12:25:58 phosphan Exp $
+
+*gibbs-1995.9 (27 May 2004)
+
+  27 May 2004; Patrick Kursawe <phosphan@gentoo.org> gibbs-1995.9.ebuild,
+  metadata.xml, files/gibbs-demo:
+  Initial import, ebuild by Frank Vernaillen <fr_ve@hotmail.com> and
+  olivier.fisette@sympatico.ca in bug #28808
+
diff --git a/app-sci/gibbs/Manifest b/app-sci/gibbs/Manifest
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index 000000000000..ef90f7ea915c
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+++ b/app-sci/gibbs/Manifest
@@ -0,0 +1,5 @@
+MD5 14e8ddb2aaec2984c80b9ae4da5fbc66 gibbs-1995.9.ebuild 1234
+MD5 847f9cb5a5a77425c64a76cb9f3b8b8f ChangeLog 462
+MD5 3c9575b8f66a5705761203f6ff59812e metadata.xml 379
+MD5 66fc93b605c52540a93a218f931abc01 files/digest-gibbs-1995.9 58
+MD5 5d1c8a0323c1506ec063c702ff2013ba files/gibbs-demo 313
diff --git a/app-sci/gibbs/files/digest-gibbs-1995.9 b/app-sci/gibbs/files/digest-gibbs-1995.9
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index 000000000000..cd65b2c83449
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+++ b/app-sci/gibbs/files/digest-gibbs-1995.9
@@ -0,0 +1 @@
+MD5 42ec045ea1da932814e645c256c48f38 gibbs9_95.tar 598016
diff --git a/app-sci/gibbs/files/gibbs-demo b/app-sci/gibbs/files/gibbs-demo
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index 000000000000..c58ae3b88e04
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+++ b/app-sci/gibbs/files/gibbs-demo
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+gibbs /usr/share/gibbs/examples/porins.b185 11 100 -R2000 -s230
+gibbs /usr/share/gibbs/examples/iomps.b58 11 125 -s1
+gibbs /usr/share/gibbs/examples/Igfold.b60x 12,12,12 90,90,90 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 12 150 -s1
+gibbs /usr/share/gibbs/examples/hth90seqs 18,18,18 20,20,20 -s1
diff --git a/app-sci/gibbs/gibbs-1995.9.ebuild b/app-sci/gibbs/gibbs-1995.9.ebuild
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index 000000000000..c0beca2e03c9
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+++ b/app-sci/gibbs/gibbs-1995.9.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2004 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/gibbs/gibbs-1995.9.ebuild,v 1.1 2004/05/27 12:25:58 phosphan Exp $
+
+DESCRIPTION="A Gibbs sampling algorithm for local alignment of subtle sequence signals in multiple protein sequences."
+
+HOMEPAGE="http://www.people.fas.harvard.edu/~junliu/index1.html"
+
+SRC_NAME="gibbs9_95"    # 9_95 refers to the september 1995 version
+SRC_URI="http://www.fas.harvard.edu/~junliu/Software/${SRC_NAME}.tar"
+
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND="virtual/glibc"
+
+S=${WORKDIR}/${SRC_NAME}/code
+
+src_compile() {
+	LIBS="-lm" make -e || die
+}
+
+src_install() {
+	cd ${WORKDIR}/${SRC_NAME}
+	dobin gibbs purge scan
+	dobin ${FILESDIR}/gibbs-demo
+
+	dodoc README
+
+	insinto /usr/share/${PN}
+	doins demo.out
+	insinto /usr/share/${PN}/examples
+	doins examples/*
+}
+
+pkg_postinst() {
+	einfo 'Testcase: To ensure the gibbs sampler works correctly,'
+	einfo 'run "gibbs-demo > mydemo.out" and compare "mydemo.out"'
+	einfo 'with "/usr/share/gibbs/demo.out" using diff. The files'
+	einfo 'should differ only by their timing statistics and the'
+	einfo 'paths of the example files.'
+}
diff --git a/app-sci/gibbs/metadata.xml b/app-sci/gibbs/metadata.xml
new file mode 100644
index 000000000000..1a57aad8a742
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+++ b/app-sci/gibbs/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<longdescription>
+		The Gibbs motif sampler stochastically examines candidate alignments
+		in an effort to find the best alignment as measured by the maximum
+		a posteriori (MAP) log-likelihood ratio.
+	</longdescription>
+</pkgmetadata>