Moving to sci-biology/sim4

diff --git a/app-sci/sim4/ChangeLog b/app-sci/sim4/ChangeLog
deleted file mode 100644 (file)
index 9ece425..0000000
--- a/app-sci/sim4/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for app-sci/sim4
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/sim4/ChangeLog,v 1.4 2004/11/01 02:56:24 ribosome Exp $
-
-  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> sim4-20030921.ebuild:
-  Added to x86.
-
-  23 Jun 2004; David Holm <dholm@gentoo.org> sim4-20030921.ebuild:
-  Added to ~ppc.
-
-*sim4-20030921 (22 Jun 2004)
-
-  22 Jun 2004; Olivier Fisette <ribosome@gentoo.org>
-  sim4-20030921.ebuild, metadata.xml :
-  Initial import.  Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>.
-  Reference: Gentoo Bugzilla, bug #54041
-

diff --git a/app-sci/sim4/Manifest b/app-sci/sim4/Manifest
deleted file mode 100644 (file)
index 75123ee..0000000
--- a/app-sci/sim4/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-MD5 224d14e93bd4831898bb3bd516a5ae06 sim4-20030921.ebuild 583
-MD5 e226ff793221817d83664fe1cae4cd38 ChangeLog 618
-MD5 50eefd281ea304818febea2f397775ed metadata.xml 1221
-MD5 743d4ddb73b01bef0fb3408b4b7b129f files/digest-sim4-20030921 55

diff --git a/app-sci/sim4/files/digest-sim4-20030921 b/app-sci/sim4/files/digest-sim4-20030921
deleted file mode 100644 (file)
index d0f3b94..0000000
--- a/app-sci/sim4/files/digest-sim4-20030921
+++ /dev/null
@@ -1 +0,0 @@
-MD5 7062ed6e5b5c9a327213c0f9cae7a90a sim4.tar.gz 60814

diff --git a/app-sci/sim4/metadata.xml b/app-sci/sim4/metadata.xml
deleted file mode 100644 (file)
index 88d86e8..0000000
--- a/app-sci/sim4/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?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>
-               sim4 is a similarity-based tool for aligning an expressed DNA sequence
-               (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
-               end matches when the two input sequences overlap at one end (i.e., the
-               start of one sequence overlaps the end of the other).sim4 employs a
-               blast-based technique to first determine the basic matching blocks
-               representing the "exon cores". In this first stage, it detects all
-               possible exact matches of W-mers (i.e., DNA words of size W) between
-               the two sequences and extends them to maximal scoring gap-free
-               segments. In the second stage, the exon cores are extended into the
-               adjacent as-yet-unmatched fragments using greedy alignment algorithms,
-               and heuristics are used to favor configurations that conform to the
-               splice-site recognition signals (GT-AG, CT-AC). If necessary, the
-               process is repeated with less stringent parameters on the unmatched
-               fragments.
-       </longdescription>
-</pkgmetadata>

diff --git a/app-sci/sim4/sim4-20030921.ebuild b/app-sci/sim4/sim4-20030921.ebuild
deleted file mode 100644 (file)
index c2454a4..0000000
--- a/app-sci/sim4/sim4-20030921.ebuild
+++ /dev/null
@@ -1,23 +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/sim4/sim4-20030921.ebuild,v 1.4 2004/11/01 02:56:24 ribosome Exp $
-
-DESCRIPTION="A program to align cDNA and genomic DNA"
-HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
-SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz"
-LICENSE="GPL-2"
-
-SLOT="0"
-KEYWORDS="x86 ~ppc"
-IUSE=""
-
-S=${WORKDIR}/${PN}.2003-09-21
-
-src_compile() {
-       emake || die
-}
-
-src_install() {
-       dobin sim4
-       dodoc README.psublast README.sim4 VERSION
-}