diff options
| -rw-r--r-- | sci-biology/sim4/ChangeLog | 23 | ||||
| -rw-r--r-- | sci-biology/sim4/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/sim4/files/digest-sim4-20030921 | 1 | ||||
| -rw-r--r-- | sci-biology/sim4/metadata.xml | 25 | ||||
| -rw-r--r-- | sci-biology/sim4/sim4-20030921.ebuild | 23 |
5 files changed, 76 insertions, 0 deletions
diff --git a/sci-biology/sim4/ChangeLog b/sci-biology/sim4/ChangeLog new file mode 100644 index 000000000000..7d35659dd32e --- /dev/null +++ b/sci-biology/sim4/ChangeLog @@ -0,0 +1,23 @@ +# 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 new file mode 100644 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 new file mode 100644 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 @@ -0,0 +1,23 @@ +# 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 +} |