Update to 0.3.8.

3 files changed, 29 insertions, 6 deletions

diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index 67890bead319..c7931810a7a1 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	bio
-PORTVERSION=	0.3.6
+PORTVERSION=	0.3.8
 CATEGORIES=	biology ruby
 MASTER_SITES=	ftp://ftp.bioruby.org/bioruby/
 MASTER_SITE_SUBDIR=	knu
@@ -22,7 +22,19 @@ RUBY_SETUP=	install.rb
 
 RUBY_SHEBANG_FILES=	${WRKSRC}/bin/dbget
 
+post-patch:
+	${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
+		${WRKSRC}/doc/Tutorial.rd.ja \
+		${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 !defined(NOPORTDOCS)
 	${MKDIR} ${RUBY_EXAMPLESDIR}/${PORTNAME}
 	${CP} -R ${WRKSRC}/sample/ ${RUBY_EXAMPLESDIR}/${PORTNAME}/
diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
index 70abb2d374c3..533cb2aaf898 100644
--- a/biology/ruby-bio/distinfo
+++ b/biology/ruby-bio/distinfo
@@ -1 +1 @@
-MD5 (ruby/bioruby-0.3.6.tar.gz) = 8a446e6c2bfaa6155a9e9a14e316a146
+MD5 (ruby/bioruby-0.3.8.tar.gz) = 9a35773cf2bd8f5e622d9b259ace28a9
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 5b2b13b51ef3..77ea42459ca6 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,8 +1,17 @@
 bin/biofetch
 bin/dbget
+@unexec if cmp -s %D/etc/bioinformatics/seqdatabase.ini %D/etc/bioinformatics/seqdatabase.ini.sample; then rm -f %D/etc/bioinformatics/seqdatabase.ini; fi
+etc/bioinformatics/seqdatabase.ini.sample
+@exec [ ! -f %B/etc/bioinformatics/seqdatabase.ini ] && cp %B/%f %B/etc/bioinformatics/seqdatabase.ini
+@dirrm etc/bioinformatics
 %%RUBY_SITELIBDIR%%/bio.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast.rb
+%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
+%%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb
+%%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb
 %%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
+%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
+%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
 %%RUBY_SITELIBDIR%%/bio/data/aa.rb
 %%RUBY_SITELIBDIR%%/bio/data/codontable.rb
 %%RUBY_SITELIBDIR%%/bio/data/keggorg.rb
@@ -29,8 +38,8 @@ bin/dbget
 %%RUBY_SITELIBDIR%%/bio/db/swissprot.rb
 %%RUBY_SITELIBDIR%%/bio/db/transfac.rb
 %%RUBY_SITELIBDIR%%/bio/db/trembl.rb
+%%RUBY_SITELIBDIR%%/bio/extend.rb
 %%RUBY_SITELIBDIR%%/bio/feature.rb
-%%RUBY_SITELIBDIR%%/bio/id.rb
 %%RUBY_SITELIBDIR%%/bio/io/brdb.rb
 %%RUBY_SITELIBDIR%%/bio/io/dbget.rb
 %%RUBY_SITELIBDIR%%/bio/io/fetch.rb
@@ -43,26 +52,28 @@ bin/dbget
 %%RUBY_SITELIBDIR%%/bio/pathway.rb
 %%RUBY_SITELIBDIR%%/bio/reference.rb
 %%RUBY_SITELIBDIR%%/bio/sequence.rb
-%%RUBY_SITELIBDIR%%/bio/util/fold.rb
-%%RUBY_SITELIBDIR%%/bio/util/hoge.rb
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
 @dirrm %%RUBY_SITELIBDIR%%/bio/appl
 @dirrm %%RUBY_SITELIBDIR%%/bio/data
 @dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
 @dirrm %%RUBY_SITELIBDIR%%/bio/db
 @dirrm %%RUBY_SITELIBDIR%%/bio/io
-@dirrm %%RUBY_SITELIBDIR%%/bio/util
 @dirrm %%RUBY_SITELIBDIR%%/bio
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/biofetch.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gbtab2mysql.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2rb.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
 %%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb