[gentoo-commits] gentoo-x86 commit in sci-biology/consed: metadata.xml ChangeLog consed-19.ebuild

[gentoo-commits] gentoo-x86 commit in sci-biology/consed: metadata.xml ChangeLog consed-19.ebuild

[Andrey Kislyuk (weaver)]

weaver      09/02/18 16:21:44

  Added:                metadata.xml ChangeLog consed-19.ebuild
  Log:
  New package sci-biology/consed, bug 253451
  (Portage version: 2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64)

Revision  Changes    Path
1.1                  sci-biology/consed/metadata.xml

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/metadata.xml?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/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>
	<maintainer>
		<email>weaver@gentoo.org</email>
		<name>Andrey Kislyuk</name>
	</maintainer>
	<herd>sci-biology</herd>
</pkgmetadata>



1.1                  sci-biology/consed/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.1&content-type=text/plain

Index: ChangeLog
===================================================================
# ChangeLog for sci-biology/consed
# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.1 2009/02/18 16:21:44 weaver Exp $

*consed-19 (18 Feb 2009)

  18 Feb 2009; weaver <weaver@gentoo.org> +metadata.xml, +consed-19.ebuild:
  New package sci-biology/consed, bug 253451. Ebuild written by Martin Mokrejs
  <mmokrejs@ribosome.natur.cuni.cz> and me.




1.1                  sci-biology/consed/consed-19.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/consed-19.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/consed/consed-19.ebuild?rev=1.1&content-type=text/plain

Index: consed-19.ebuild
===================================================================
# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19.ebuild,v 1.1 2009/02/18 16:21:44 weaver Exp $

inherit toolchain-funcs

DESCRIPTION="Consed: a genome sequence finishing program"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
SRC_URI="consed-19-sources.tar.gz
	consed-19-linux.tar.gz"

LICENSE="phrap"
SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""

DEPEND="x11-libs/openmotif"
RDEPEND="${DEPEND}
	>=sci-biology/phrap-1.080721"

S="${WORKDIR}"

RESTRICT="fetch"

pkg_nofetch() {
	einfo "Please visit ${HOMEPAGE} and obtain the file"
	einfo "\"sources.tar.gz\", then rename it to \"consed-${PV}-sources.tar.gz\""
	einfo "and place it in ${DISTDIR},"
	einfo "obtain the file"
	einfo "\"consed_linux.tar.gz\", then rename it to \"consed-${PV}-linux.tar.gz\""
	einfo "and place it in ${DISTDIR}"
}

src_unpack() {
	unpack ${A}
	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
	sed -i -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
}

src_compile() {
	emake || die
	emake -C misc/mktrace || die
	emake -C misc/phd2fasta || die
	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
}

src_install() {
	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
	dobin scripts/* || die
	insinto /usr/share/${PN}/examples
	doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions selectRegionsAnswer || die
	echo 'CONSED_HOME=/usr' > "${S}/99consed"
	doenvd "${S}/99consed" || die
	dodoc README.txt *_announcement.txt
}