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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 DOCS
XMLPARSER_DESC= xmlparser support for faster Blast processing
BDB4_DESC= bdb4 support for faster flat file indexing
OPTIONSFILE= ${PORT_DBDIR}/ruby-${PORTNAME}/options
USES= shebangfix
USE_RUBY= yes
USE_RUBY_SETUP= yes
SHEBANG_FILES= sample/biofetch.rb
ruby_OLD_CMD= /usr/proj/bioruby/bin/ruby
XML_PARSER_RUN_DEPENDS= ${RUBY_SITEARCHLIBDIR}/xmlparser.so:${PORTSDIR}/textproc/ruby-xmlparser
BDB4_RUN_DEPENDS= ${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb
MYSQL_RUN_DEPENDS= rubygem-dbd-mysql>=0:${PORTSDIR}/databases/rubygem-dbd-mysql
PGSQL_RUN_DEPENDS= rubygem-dbd-pg>=0:${PORTSDIR}/databases/rubygem-dbd-pg
post-patch:
${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
${WRKSRC}/doc/Tutorial.rd \
${WRKSRC}/lib/bio/io/registry.rb
do-install:
@${MKDIR} ${STAGEDIR}${PREFIX}/etc/bioinformatics
.for f in etc/bioinformatics/seqdatabase.ini
${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/${f}.sample
.endfor
@${MKDIR} ${STAGEDIR}${RUBY_MODEXAMPLESDIR}
${CP} -R ${WRKSRC}/sample/ ${STAGEDIR}${RUBY_MODEXAMPLESDIR}/
@${MKDIR} ${STAGEDIR}${RUBY_MODDOCDIR}/ja
${INSTALL_DATA} ${WRKSRC}/ChangeLog ${WRKSRC}/README.rdoc ${STAGEDIR}${RUBY_MODDOCDIR}/
${INSTALL_DATA} ${WRKSRC}/doc/*.rd ${STAGEDIR}${RUBY_MODDOCDIR}/
${INSTALL_DATA} ${WRKSRC}/doc/*.rd.ja ${STAGEDIR}${RUBY_MODDOCDIR}/ja/
.include <bsd.port.pre.mk>
.if ${RUBY_VER} >= 2.2
BROKEN= Does not build
.endif
.include <bsd.port.post.mk>
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