- Update to 1.5.0

PR:		208351
Submitted by:	wen@FreeBSD.org
Approved by:	mauricio@arareko.net (maintainer)

3 files changed, 11 insertions, 23 deletions

diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index fabba5c99e92..1f06ce5f639d 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bio
-PORTVERSION=	1.4.1
+PORTVERSION=	1.5.0
 CATEGORIES=	biology ruby
 MASTER_SITES=	http://bioruby.org/archive/
 PKGNAMEPREFIX=	${RUBY_PKGNAMEPREFIX}
@@ -23,7 +23,7 @@ XMLPARSER_DESC=	xmlparser support for faster Blast processing
 BDB4_DESC=	bdb4 support for faster flat file indexing
 
 NO_ARCH=	yes
-USES=	shebangfix
+USES=		shebangfix
 USE_RUBY=	yes
 USE_RUBY_SETUP=	yes
 SHEBANG_FILES=	sample/biofetch.rb
diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
index aeb00ae3e5da..0c477906ffcd 100644
--- a/biology/ruby-bio/distinfo
+++ b/biology/ruby-bio/distinfo
@@ -1,2 +1,2 @@
-SHA256 (ruby/bioruby-1.4.1.tar.gz) = 4610997ef0350b4d17ccd67a76a1712c2d986168523256eb6de395bfc8a3f15d
-SIZE (ruby/bioruby-1.4.1.tar.gz) = 1340224
+SHA256 (ruby/bioruby-1.5.0.tar.gz) = b920dd27374d5f9443986f4184bfc34d79a54d927b16a8ce23caf1ce116f7026
+SIZE (ruby/bioruby-1.5.0.tar.gz) = 1475866
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 73749a266504..ebb6100098e7 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,21 +1,17 @@
 %%RUBY_DOCDIR%%/bio/ChangeLog
 %%RUBY_DOCDIR%%/bio/Changes-0.7.rd
-%%RUBY_DOCDIR%%/bio/KEGG_API.rd
 %%RUBY_DOCDIR%%/bio/README.rdoc
 %%RUBY_DOCDIR%%/bio/Tutorial.rd
-%%RUBY_DOCDIR%%/bio/ja/KEGG_API.rd.ja
 %%RUBY_DOCDIR%%/bio/ja/Tutorial.rd.ja
 %%RUBY_EXAMPLESDIR%%/bio/any2fasta.rb
 %%RUBY_EXAMPLESDIR%%/bio/biofetch.rb
 %%RUBY_EXAMPLESDIR%%/bio/color_scheme_na.rb
-%%RUBY_EXAMPLESDIR%%/bio/dbget
 %%RUBY_EXAMPLESDIR%%/bio/demo_aaindex.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_aminoacid.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_bl2seq_report.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_blast_report.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_codontable.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_das.rb
-%%RUBY_EXAMPLESDIR%%/bio/demo_ddbjxml.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_fasta_remote.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_fastaformat.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_genbank.rb
@@ -29,8 +25,6 @@
 %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_glycan.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_orthology.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_kegg_reaction.rb
-%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_taxonomy.rb
-%%RUBY_EXAMPLESDIR%%/bio/demo_keggapi.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_litdb.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_locations.rb
 %%RUBY_EXAMPLESDIR%%/bio/demo_ncbi_rest.rb
@@ -63,17 +57,18 @@
 %%RUBY_EXAMPLESDIR%%/bio/na2aa.rb
 %%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
 %%RUBY_EXAMPLESDIR%%/bio/pmsearch.rb
-%%RUBY_EXAMPLESDIR%%/bio/psortplot_html.rb
 %%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
 %%RUBY_EXAMPLESDIR%%/bio/tdiary.rb
 %%RUBY_EXAMPLESDIR%%/bio/test_phyloxml_big.rb
 %%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
 %%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb
+%%RUBY_MODEXAMPLESDIR%%/benchmark_clustalw_report.rb
+%%RUBY_MODEXAMPLESDIR%%/seqdatabase.ini
+%%RUBY_MODEXAMPLESDIR%%/test_restriction_enzyme_long.rb
 %%RUBY_SITELIBDIR%%/bio.rb
 %%RUBY_SITELIBDIR%%/bio/alignment.rb
 %%RUBY_SITELIBDIR%%/bio/appl/bl2seq/report.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast.rb
-%%RUBY_SITELIBDIR%%/bio/appl/blast/ddbj.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/format0.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
 %%RUBY_SITELIBDIR%%/bio/appl/blast/genomenet.rb
@@ -142,6 +137,7 @@
 %%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb
 %%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb
 %%RUBY_SITELIBDIR%%/bio/db/embl/uniprot.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/uniprotkb.rb
 %%RUBY_SITELIBDIR%%/bio/db/fantom.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta.rb
 %%RUBY_SITELIBDIR%%/bio/db/fasta/defline.rb
@@ -177,7 +173,6 @@
 %%RUBY_SITELIBDIR%%/bio/db/kegg/orthology.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/pathway.rb
 %%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
-%%RUBY_SITELIBDIR%%/bio/db/kegg/taxonomy.rb
 %%RUBY_SITELIBDIR%%/bio/db/lasergene.rb
 %%RUBY_SITELIBDIR%%/bio/db/litdb.rb
 %%RUBY_SITELIBDIR%%/bio/db/medline.rb
@@ -209,10 +204,6 @@
 %%RUBY_SITELIBDIR%%/bio/io/biosql/biosql.rb
 %%RUBY_SITELIBDIR%%/bio/io/biosql/config/database.yml
 %%RUBY_SITELIBDIR%%/bio/io/das.rb
-%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
-%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.rb
-%%RUBY_SITELIBDIR%%/bio/io/ebisoap.rb
-%%RUBY_SITELIBDIR%%/bio/io/ensembl.rb
 %%RUBY_SITELIBDIR%%/bio/io/fastacmd.rb
 %%RUBY_SITELIBDIR%%/bio/io/fetch.rb
 %%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
@@ -222,14 +213,10 @@
 %%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
 %%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
 %%RUBY_SITELIBDIR%%/bio/io/flatfile/splitter.rb
-%%RUBY_SITELIBDIR%%/bio/io/higet.rb
 %%RUBY_SITELIBDIR%%/bio/io/hinv.rb
-%%RUBY_SITELIBDIR%%/bio/io/keggapi.rb
 %%RUBY_SITELIBDIR%%/bio/io/ncbirest.rb
-%%RUBY_SITELIBDIR%%/bio/io/ncbisoap.rb
 %%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
 %%RUBY_SITELIBDIR%%/bio/io/registry.rb
-%%RUBY_SITELIBDIR%%/bio/io/soapwsdl.rb
 %%RUBY_SITELIBDIR%%/bio/io/sql.rb
 %%RUBY_SITELIBDIR%%/bio/io/togows.rb
 %%RUBY_SITELIBDIR%%/bio/location.rb
@@ -260,13 +247,11 @@
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/emboss.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/entry.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/flatfile.rb
-%%RUBY_SITELIBDIR%%/bio/shell/plugin/keggapi.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/midi.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/ncbirest.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/obda.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/psort.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/seq.rb
-%%RUBY_SITELIBDIR%%/bio/shell/plugin/soap.rb
 %%RUBY_SITELIBDIR%%/bio/shell/plugin/togows.rb
 %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
 %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
@@ -289,6 +274,7 @@
 %%RUBY_SITELIBDIR%%/bio/shell/setup.rb
 %%RUBY_SITELIBDIR%%/bio/shell/web.rb
 %%RUBY_SITELIBDIR%%/bio/tree.rb
+%%RUBY_SITELIBDIR%%/bio/tree/output.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme/buried.rb
 %%RUBY_SITELIBDIR%%/bio/util/color_scheme/helix.rb
@@ -303,6 +289,7 @@
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/analysis_basic.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/cut_symbol.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/dense_int_array.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
@@ -321,6 +308,7 @@
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand_complement.rb
+%%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/sorted_num_array.rb
 %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/string_formatting.rb
 %%RUBY_SITELIBDIR%%/bio/util/sirna.rb
 %%RUBY_SITELIBDIR%%/bio/version.rb