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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs"
SRC_URI="
http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
LICENSE="Artistic-Manatee"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
>=dev-libs/expat-1.95.8
>=media-libs/gd-2.0.34
dev-perl/CGI
dev-perl/Bio-DB-Das-Chado
dev-perl/DBI
dev-perl/DBD-mysql
dev-perl/XML-Parser
dev-perl/XML-Twig
dev-perl/XML-Simple
dev-perl/XML-Writer
dev-perl/HTML-Template
dev-perl/Tree-DAG_Node
virtual/perl-File-Spec
virtual/perl-Data-Dumper
dev-perl/GD
dev-perl/GDTextUtil
dev-perl/GDGraph
virtual/perl-Storable
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
dev-perl/Date-Manip
dev-perl/IO-Tee
dev-perl/MLDBM
dev-perl/JSON
dev-perl/JSON-Any
sci-biology/bioperl"
RDEPEND="${DEPEND}
>=virtual/mysql-5:*
>=www-servers/apache-2.2"
S="${WORKDIR}"/manatee-"${PV}"_linux
src_prepare(){
find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
}
#src_configure(){
# there used to be manateee-="${PV}".tgz file which contained configure script in the past
# now the layout is different, temporarily commenting out untill we find the current full sources back again
# econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
#}
#
#src_compile(){
# default
#}
src_install(){
dodoc ${DISTDIR}"/README_Linux.txt"
dodir /var/www/localhost/cgi-bin
cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
dodir /var/www/localhost/htdocs/manatee
cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
einfo "You need to update it regularly."
einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
}
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