[gentoo-commits] gentoo-x86 commit in sci-biology/cd-hit: metadata.xml ChangeLog cd-hit-4.5.1.ebuild

[Justin Lecher (jlec)]

jlec        11/02/01 09:06:35

  Added:                metadata.xml ChangeLog cd-hit-4.5.1.ebuild
  Log:
  New addition, written by me
  
  (Portage version: 2.2.0_alpha19/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/cd-hit/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/metadata.xml?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/metadata.xml?rev=1.1&content-type=text/plain

Index: metadata.xml
===================================================================
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
  <email>jlec@g.o</email>
</maintainer>
<longdescription>
CD-HIT is a very widely used program for clustering and comparing large sets 
of protein or nucleotide sequences. CD-HIT is very fast and can handle 
extremely large databases. CD-HIT helps to significantly reduce the 
computational and manual efforts in many sequence analysis tasks and aids in 
understanding the data structure and correct the bias within a dataset.

The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
datasets and identifies the sequences in db2 that are similar to db1 above 
a threshold. CD-HIT-454 is a program to identify natural and artificial 
duplicates from pyrosequencing reads. The usage of other programs and 
scripts can be found in CD-HIT user's guide.
</longdescription>
</pkgmetadata>



1.1                  sci-biology/cd-hit/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/ChangeLog?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/ChangeLog?rev=1.1&content-type=text/plain

Index: ChangeLog
===================================================================
# ChangeLog for sci-biology/cd-hit
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.1 2011/02/01 09:06:35 jlec Exp $

*cd-hit-4.5.1 (01 Feb 2011)

  01 Feb 2011; Justin Lecher <jlec@g.o> +files/4.5.1-gentoo.patch,
  +cd-hit-4.5.1.ebuild, +metadata.xml:
  New addition, written by me




1.1                  sci-biology/cd-hit/cd-hit-4.5.1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild?rev=1.1&content-type=text/plain

Index: cd-hit-4.5.1.ebuild
===================================================================
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild,v 1.1 2011/02/01 09:06:35 jlec Exp $

EAPI="3"

inherit flag-o-matic toolchain-funcs

RELDATE="2011-01-31"
RELEASE="${PN}-v${PV}-${RELDATE}"

DESCRIPTION="Clustering Database at High Identity with Tolerance"
HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit"
SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"

SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
LICENSE="GPL-2"
IUSE="openmp"

S="${WORKDIR}"/${RELEASE}

pkg_setup() {
	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
}

src_prepare() {
	tc-export CXX
	use openmp || append-flags -DNO_OPENMP
	epatch "${FILESDIR}"/${PV}-gentoo.patch
}

src_compile() {
	if use openmp; then
		emake openmp=yes || die
	else
		emake || die
	fi
}

src_install() {
	dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die
	dodoc ChangeLog cdhit-user-guide.pdf || die
}