Moved from app-sci/bioperl to sci-biology/bioperl.

1 files changed, 76 insertions, 0 deletions

diff --git a/sci-biology/bioperl/bioperl-1.2.2.ebuild b/sci-biology/bioperl/bioperl-1.2.2.ebuild
new file mode 100644
index 000000000000..653a27669cc8
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.2.2.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.2.2.ebuild,v 1.1 2004/12/23 22:05:32 ribosome Exp $
+
+inherit perl-module eutils
+CATEGORY="app-sci"
+
+DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
+HOMEPAGE="http://www.bioperl.org/"
+#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
+SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="x86"
+IUSE="mysql gd"
+
+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 )"
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	# remove interactiveness
+	use mysql && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
+	# want man pages in addition to perldoc documentation??
+	#epatch ${FILESDIR}/domanpages-${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 installed and executeable
+	dodir /usr/bin
+	dosym /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl /usr/bin/bptutorial.pl
+	fperms +x /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl
+
+	# bioperl scripts and examples
+	einfo 'Adding bioperl examples and scripts to /usr/share/...'
+	dodir /usr/share/${PF}/scripts
+	#insinto /usr/share/${PF}/scripts
+	cd ${S}/scripts/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+	dodir /usr/share/${PF}/examples
+	cd ${S}/examples/
+	tar cf - ./ | ( cd ${D}/usr/share/${PF}/examples; tar xf -)
+	cd ${S}
+
+	# some pods in maindir
+	eval `perl '-V:installsitelib'`
+	MY_SITE_LIB=${installsitelib}
+	insinto ${MY_SITE_LIB}
+	doins biodatabases.pod  biodesign.pod  bioperl.pod  bioscripts.pod
+}