Initial import for package sim4-20030921

5 files changed, 60 insertions, 0 deletions

diff --git a/app-sci/sim4/ChangeLog b/app-sci/sim4/ChangeLog
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+# ChangeLog for app-sci/sim4
+# Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/sim4/ChangeLog,v 1.1 2004/06/22 16:36:47 ribosome Exp $
+
+*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
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index 000000000000..82dc6bc394f6
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+++ b/app-sci/sim4/Manifest
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+MD5 76e50343d7ef1ac2e18e48967aeb8a9a sim4-20030921.ebuild 490
+MD5 5c8c249ac6d18770f8f4bb68a4a69947 ChangeLog 363
+MD5 f86947a3b9bc4a06b4338fd6df45071a metadata.xml 1124
+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
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index 000000000000..d0f3b94a5800
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+++ b/app-sci/sim4/files/digest-sim4-20030921
@@ -0,0 +1 @@
+MD5 7062ed6e5b5c9a327213c0f9cae7a90a sim4.tar.gz 60814
diff --git a/app-sci/sim4/metadata.xml b/app-sci/sim4/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<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
new file mode 100644
index 000000000000..a346a9c33a1a
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+++ b/app-sci/sim4/sim4-20030921.ebuild
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+# Copyright 1999-2004 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/sim4/sim4-20030921.ebuild,v 1.1 2004/06/22 16:36:47 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"
+IUSE=""
+
+S=${WORKDIR}/${PN}.2003-09-21
+
+src_compile() {
+	emake || die
+}
+
+src_install() {
+	dobin sim4
+	dodoc README.psublast README.sim4 VERSION
+}