From a68dc6cefca98dda97b74819cdff1159d51487d6 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 16:04:48 +0000 Subject: [PATCH] Moving to sci-biology/sim4 --- app-sci/sim4/ChangeLog | 17 ----------------- app-sci/sim4/Manifest | 4 ---- app-sci/sim4/files/digest-sim4-20030921 | 1 - app-sci/sim4/metadata.xml | 25 ------------------------- app-sci/sim4/sim4-20030921.ebuild | 23 ----------------------- 5 files changed, 70 deletions(-) delete mode 100644 app-sci/sim4/ChangeLog delete mode 100644 app-sci/sim4/Manifest delete mode 100644 app-sci/sim4/files/digest-sim4-20030921 delete mode 100644 app-sci/sim4/metadata.xml delete mode 100644 app-sci/sim4/sim4-20030921.ebuild diff --git a/app-sci/sim4/ChangeLog b/app-sci/sim4/ChangeLog deleted file mode 100644 index 9ece425515de..000000000000 --- 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 sim4-20030921.ebuild: - Added to x86. - - 23 Jun 2004; David Holm sim4-20030921.ebuild: - Added to ~ppc. - -*sim4-20030921 (22 Jun 2004) - - 22 Jun 2004; Olivier Fisette - sim4-20030921.ebuild, metadata.xml : - Initial import. Ebuild submitted by Olivier Fisette . - Reference: Gentoo Bugzilla, bug #54041 - diff --git a/app-sci/sim4/Manifest b/app-sci/sim4/Manifest deleted file mode 100644 index 75123ee484ac..000000000000 --- 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 index d0f3b94a5800..000000000000 --- 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 index 88d86e89fbdb..000000000000 --- a/app-sci/sim4/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - ribosome@gentoo.org - Olivier Fisette - - sci - - 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. - - diff --git a/app-sci/sim4/sim4-20030921.ebuild b/app-sci/sim4/sim4-20030921.ebuild deleted file mode 100644 index c2454a42c881..000000000000 --- 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 -} -- 2.26.2