diff options
| author | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-04-07 13:01:26 +0000 |
|---|---|---|
| committer | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-04-07 13:01:26 +0000 |
| commit | 8086bfab37dcaa9aec522c6ec8d92d1266b5e605 (patch) | |
| tree | e6899578292f623b27b4078f1b4b79008fb3d182 /biology | |
| parent | 864901d96847664ed8615d900672c337f7547343 (diff) | |
| download | ports-8086bfab37dcaa9aec522c6ec8d92d1266b5e605.tar.gz ports-8086bfab37dcaa9aec522c6ec8d92d1266b5e605.zip | |
Notes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/ruby-bio/Makefile | 47 | ||||
| -rw-r--r-- | biology/ruby-bio/pkg-plist | 1 |
2 files changed, 16 insertions, 32 deletions
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile index 616ed926fce4..54503ea6f71e 100644 --- a/biology/ruby-bio/Makefile +++ b/biology/ruby-bio/Makefile @@ -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> diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist index 45398963167e..76edcc355b9f 100644 --- a/biology/ruby-bio/pkg-plist +++ b/biology/ruby-bio/pkg-plist @@ -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 |