diff options
Diffstat (limited to 'sci-biology/sim4')
| -rw-r--r-- | sci-biology/sim4/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/sim4/metadata.xml | 21 | ||||
| -rw-r--r-- | sci-biology/sim4/sim4-20030921-r1.ebuild | 26 | ||||
| -rw-r--r-- | sci-biology/sim4/sim4-20030921.ebuild | 19 |
4 files changed, 67 insertions, 0 deletions
diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest new file mode 100644 index 000000000000..f2a25200b895 --- /dev/null +++ b/sci-biology/sim4/Manifest @@ -0,0 +1 @@ +DIST sim4.tar.gz 60814 RMD160 5acad71daa94893025a21b73b416dd3903078be5 SHA1 11a9170ea03990268d409056084415d725c6290b SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml new file mode 100644 index 000000000000..ea9731279003 --- /dev/null +++ b/sci-biology/sim4/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</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-r1.ebuild b/sci-biology/sim4/sim4-20030921-r1.ebuild new file mode 100644 index 000000000000..178bf92ab5da --- /dev/null +++ b/sci-biology/sim4/sim4-20030921-r1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +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="~amd64 ~ppc ~x86" +IUSE="" + +S=${WORKDIR}/${PN}.2003-09-21 + +src_compile() { + echo "$(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm" + $(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm || die +} + +src_install() { + dobin ${PN} || die + dodoc README.* VERSION || die +} diff --git a/sci-biology/sim4/sim4-20030921.ebuild b/sci-biology/sim4/sim4-20030921.ebuild new file mode 100644 index 000000000000..12d5231aa120 --- /dev/null +++ b/sci-biology/sim4/sim4-20030921.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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_install() { + dobin sim4 || die + dodoc README.psublast README.sim4 VERSION || die +} |