Moved from app-sci/sim4 to sci-biology/sim4.

5 files changed, 76 insertions, 0 deletions

diff --git a/sci-biology/sim4/ChangeLog b/sci-biology/sim4/ChangeLog
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index 000000000000..7d35659dd32e
--- /dev/null
+++ b/sci-biology/sim4/ChangeLog
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+# ChangeLog for app-sci/sim4
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/sim4/ChangeLog,v 1.1 2004/12/23 16:05:37 ribosome Exp $
+
+*sim4-20030921 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <olivier@gentoo.org> +metadata.xml,
+  +sim4-20030921.ebuild:
+  Moved from app-sci/sim4 to sci-biology/sim4.
+
+  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/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
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index 000000000000..75123ee484ac
--- /dev/null
+++ b/sci-biology/sim4/Manifest
@@ -0,0 +1,4 @@
+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/sci-biology/sim4/files/digest-sim4-20030921 b/sci-biology/sim4/files/digest-sim4-20030921
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index 000000000000..d0f3b94a5800
--- /dev/null
+++ b/sci-biology/sim4/files/digest-sim4-20030921
@@ -0,0 +1 @@
+MD5 7062ed6e5b5c9a327213c0f9cae7a90a sim4.tar.gz 60814
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
new file mode 100644
index 000000000000..88d86e89fbdb
--- /dev/null
+++ b/sci-biology/sim4/metadata.xml
@@ -0,0 +1,25 @@
+<?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/sci-biology/sim4/sim4-20030921.ebuild b/sci-biology/sim4/sim4-20030921.ebuild
new file mode 100644
index 000000000000..ba96b4c63f9c
--- /dev/null
+++ b/sci-biology/sim4/sim4-20030921.ebuild
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+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/sim4/sim4-20030921.ebuild,v 1.1 2004/12/23 16:05:37 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
+}