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# Created by: Akinori MUSHA aka knu <knu@idaemons.org>
# $FreeBSD$
PORTNAME= bio
PORTVERSION= 1.4.1
CATEGORIES= biology ruby
MASTER_SITES= http://bioruby.org/archive/
PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}
DISTNAME= ${PORTNAME}ruby-${PORTVERSION}
DIST_SUBDIR= ruby
MAINTAINER= mauricio@arareko.net
COMMENT= Integrated environment for Bioinformatics written in Ruby
OPTIONS_DEFINE= XMLPARSER BDB4 MYSQL PGSQL
XMLPARSER_DESC= xmlparser support for faster Blast processing
BDB4_DESC= bdb4 support for faster flat file indexing
OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNAME}/options
USE_RUBY= yes
USE_RUBY_SETUP= yes
.include <bsd.port.pre.mk>
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MXMLPARSER}
RUN_DEPENDS+= ${RUBY_SITEARCHLIBDIR}/xmlparser.so:${PORTSDIR}/textproc/ruby-xmlparser
.endif
.if ${PORT_OPTIONS:MBDB4}
RUN_DEPENDS+= ${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb
.endif
.if ${PORT_OPTIONS:MMYSQL}
RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Mysql/Mysql.rb:${PORTSDIR}/databases/ruby-dbd_mysql
.endif
.if ${PORT_OPTIONS:MPGSQL}
RUN_DEPENDS+= ${RUBY_SITELIBDIR}/DBD/Pg/Pg.rb:${PORTSDIR}/databases/ruby-dbd_pg
.endif
post-patch:
${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
${WRKSRC}/doc/Tutorial.rd \
${WRKSRC}/lib/bio/io/registry.rb
do-install:
${MKDIR} ${PREFIX}/etc/bioinformatics
.for f in etc/bioinformatics/seqdatabase.ini
${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${f}.sample
if [ ! -f ${PREFIX}/${f} ]; then \
${CP} -p ${PREFIX}/${f}.sample ${PREFIX}/${f}; \
fi
.endfor
.if ${PORT_OPTIONS:MEXAMPLES}
${MKDIR} ${RUBY_MODEXAMPLESDIR}
${CP} -R ${WRKSRC}/sample/ ${RUBY_MODEXAMPLESDIR}/
.endif
.if ${PORT_OPTIONS:MDOCS}
${MKDIR} ${RUBY_MODDOCDIR}/ja
${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README.rdoc ${RUBY_MODDOCDIR}/
${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${RUBY_MODDOCDIR}/
${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${RUBY_MODDOCDIR}/ja/
.endif
.include <bsd.port.post.mk>
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