bioperl-1.2.1.ebuild

bioperl-1.2.1.ebuild (text/plain), 2.25 KB, created by Gontran Zepeda on 2003-06-04 08:34:24 UTC

# Copyright 1999-2003 Gentoo Technologies, Inc.
# Distributed under the terms of the GNU General Public License v2
# $Header: $

IUSE="mysql gd"

inherit perl-module

S=${WORKDIR}/${P}
CATEGORY="app-sci"

DESCRIPTION="The Bioperl Project is a collection of tools for bioinformatics, genomics and life science research."
SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
HOMEPAGE="http://www.bioperl.org/"

SLOT="0"
LICENSE="Artistic GPL-2"
KEYWORDS="x86"

#DEPEND=${DEPEND}
DEPEND="${DEPEND}
	dev-perl/File-Temp
	dev-perl/HTML-Parser
	dev-perl/IO-String
	dev-perl/IO-stringy
	dev-perl/SOAP-Lite
	dev-perl/Storable
	dev-perl/XML-DOM
	dev-perl/XML-Parser
	dev-perl/XML-Writer
	dev-perl/XML-Twig
	dev-perl/libxml-perl
	dev-perl/libwww-perl
	dev-perl/Graph
	dev-perl/Text-Shellwords
	gd? ( >=dev-perl/GD-1.32-r1 )
	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
RDEPEND=${RDEPEND}

src_unpack() {
	unpack ${A}
	cd ${S}
	# remove interactiveness
	[ `use mysql` ] && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
}

src_compile() {
	# there's a test to run for BioGFFDB if using mysql
	perl-module_src_compile || die "compile failed"
	# make test
	perl-module_src_test || die "src test failed"
}

src_install() {
	mydoc="AUTHORS BUGS FAQ"
	perl-module_src_install
	# get the bptutorial
	dodir /usr/bin
	dosym /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl /usr/bin/bptutorial.pl
	fperm +x /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl

	# bioperl scripts
	dodir /usr/share/${PF}/scripts
	insinto /usr/share/${PF}/scripts
	dodoc "${S}/scripts/*.pl"

my_d="Bio-DB-GFF
das
structure
DB
exceptions
align
taxa
biblio
graphics
root_object
tk
biographics
index
searchio
tools
liveseq
seq
tree
cluster
utilities
contributed
seqstats"
	for _dir in ${my_d}; do
		dodir /usr/share/${PF}/scripts/${_dir}
		insinto /usr/share/${PF}/scripts/${_dir}
		doins `ls ${S}/scripts/${_dir}/?*`
	done

	# bioperl examples
	dodir /usr/share/${PF}/examples
my_d="biographics
ontology
searchio"
	for _dir in ${my_d}
	do
		dodir /usr/share/${PF}/examples/${_dir}
		insinto /usr/share/${PF}/examples/${_dir}
		doins `ls ${S}/examples/${_dir}/?*`
	done

	# some pods in maindir
	eval `perl '-V:installsitelib'`
	MY_SITE_LIB=${installsitelib}
	insinto ${MY_SITE_LIB}
	doins biodatabases.pod  biodesign.pod  bioperl.pod  bioscripts.pod
}