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This commit is contained in:
Baptiste Daroussin 2014-04-07 13:01:26 +00:00
parent 864901d968
commit 8086bfab37
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=350461
2 changed files with 16 additions and 32 deletions
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47
biology/ruby-bio/Makefile
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@ -12,30 +12,22 @@ DIST_SUBDIR= ruby
MAINTAINER= mauricio@arareko.net
COMMENT= Integrated environment for Bioinformatics written in Ruby
OPTIONS_DEFINE= XMLPARSER BDB4 MYSQL PGSQL
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
NO_STAGE= yes
.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
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= ${RUBY_SITELIBDIR}/DBD/Mysql/Mysql.rb:${PORTSDIR}/databases/ruby-dbd_mysql
PGSQL_RUN_DEPENDS= ${RUBY_SITELIBDIR}/DBD/Pg/Pg.rb:${PORTSDIR}/databases/ruby-dbd_pg
post-patch:
${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
@ -43,22 +35,15 @@ post-patch:
${WRKSRC}/lib/bio/io/registry.rb
do-install:
${MKDIR} ${PREFIX}/etc/bioinformatics
@${MKDIR} ${STAGEDIR}${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
${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/${f}.sample
.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 ${RUBY_MODDOCDIR}/ja/
.endif
@${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.mk>

1
biology/ruby-bio/pkg-plist
View File

@ -329,7 +329,6 @@ bin/br_biofetch
bin/br_bioflat
bin/br_biogetseq
bin/br_pmfetch
etc/bioinformatics/seqdatabase.ini
etc/bioinformatics/seqdatabase.ini.sample
@dirrm etc/bioinformatics
@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand