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# Copyright 1999-2005 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-pipeline/bioperl-pipeline-0.1.ebuild,v 1.4 2005/07/09 17:59:22 swegener Exp $
inherit perl-module
CATEGORY="sci-biology"
DESCRIPTION="A collection of tools for bioinformatics, genomics and life science research: Biopipe"
HOMEPAGE="http://www.biopipe.org/"
SRC_URI="mirror://gentoo/$P.tar.gz"
LICENSE="Artistic GPL-2"
SLOT="0"
KEYWORDS="~x86 ~ppc"
IUSE=""
RDEPEND="
dev-db/mysql
>=sci-biology/ncbi-tools-20031103
>=sci-biology/bioperl-1.2.3
>=sci-biology/bioperl-run-1.2.2
dev-perl/XML-SimpleObject
dev-perl/XML-Parser
dev-perl/Data-ShowTable"
DEPEND=""
src_unpack() {
unpack ${A}
cd ${S}
}
src_compile() {
# there's a test to run for BioGFFDB if using mysql
perl-module_src_compile || die "compile failed"
# make test
## perl-module_src_test || die "src test failed"
ewarn
ewarn "Tests skipped since they will fail unless"
ewarn "mysql root user has no password"
ewarn
}
src_install() {
mydoc="AUTHORS README LICENSE INSTALL FAQ database_schema.doc database_tables.txt"
perl-module_src_install
# bioperl scripts and examples
einfo "Adding bioperl-pipeline scripts, sql and xml directories to /usr/share/${PF}..."
dodir /usr/share/${PF}/scripts
cd ${S}/scripts/
tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
dodir /usr/share/${PF}/sql
cd ${S}/sql/
tar cf - ./ | ( cd ${D}/usr/share/${PF}/sql; tar xf -)
dodir /usr/share/${PF}/xml
cd ${S}/xml/
tar cf - ./ | ( cd ${D}/usr/share/${PF}/xml; tar xf -)
dodir /usr/share/doc/${PF}/
cd ${S}/doc/
tar cf - ./ | ( cd ${D}/usr/share/doc/${PF}; tar xf -)
cd ${S}
}
pkg_postinst() {
einfo
einfo "You will need to modify Bio/Pipeline/PipeConf.pm"
einfo "with mysql user and batch job software information"
einfo "Read the docs in /usr/share/docs/${PF}"
einfo "for more information"
einfo
}
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