Moving to sci-biology/gibbs

diff --git a/app-sci/gibbs/ChangeLog b/app-sci/gibbs/ChangeLog
deleted file mode 100644 (file)
index 980d546..0000000
--- a/app-sci/gibbs/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for app-sci/gibbs
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/gibbs/ChangeLog,v 1.5 2004/11/01 01:50:38 ribosome Exp $
-
-  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> gibbs-1995.9.ebuild:
-  Added to x86.
-
-  01 Jul 2004; Jeremy Huddleston <eradicator@gentoo.org> gibbs-1995.9.ebuild:
-  virtual/glibc -> virtual/libc
-
-*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
deleted file mode 100644 (file)
index e4ef490..0000000
--- a/app-sci/gibbs/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-MD5 17a84693174a8644121605e0d8ea1b12 gibbs-1995.9.ebuild 1223
-MD5 25a6b1c34b2fe30ed4afcd478880dcab ChangeLog 655
-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
deleted file mode 100644 (file)
index cd65b2c..0000000
--- a/app-sci/gibbs/files/digest-gibbs-1995.9
+++ /dev/null
@@ -1 +0,0 @@
-MD5 42ec045ea1da932814e645c256c48f38 gibbs9_95.tar 598016

diff --git a/app-sci/gibbs/files/gibbs-demo b/app-sci/gibbs/files/gibbs-demo
deleted file mode 100644 (file)
index c58ae3b..0000000
--- a/app-sci/gibbs/files/gibbs-demo
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/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
deleted file mode 100644 (file)
index 40c32db..0000000
--- a/app-sci/gibbs/gibbs-1995.9.ebuild
+++ /dev/null
@@ -1,45 +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/gibbs/gibbs-1995.9.ebuild,v 1.4 2004/11/01 01:50:38 ribosome 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/${SRC_NAME}.tar"
-
-LICENSE="public-domain"
-
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-
-DEPEND="virtual/libc"
-
-S=${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
deleted file mode 100644 (file)
index 1a57aad..0000000
--- a/app-sci/gibbs/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?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>