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authorAkinori MUSHA <knu@FreeBSD.org>2003-01-29 10:45:59 +0000
committerAkinori MUSHA <knu@FreeBSD.org>2003-01-29 10:45:59 +0000
commit4dce26edf6286f6eba911ee551c24bfd9f69f074 (patch)
tree4b4d50cb29239fe4b6d4451ed809ebf14cc16e8c /biology
parent2f692e4645a28be8e471a9541b626fa0f3d49fc3 (diff)
downloadports-4dce26edf6286f6eba911ee551c24bfd9f69f074.tar.gz
ports-4dce26edf6286f6eba911ee551c24bfd9f69f074.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/ruby-bio/Makefile2
-rw-r--r--biology/ruby-bio/distinfo2
-rw-r--r--biology/ruby-bio/pkg-plist36
3 files changed, 26 insertions, 14 deletions
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index e7d87f012542..d0830646b68e 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= bio
-PORTVERSION= 0.3.9
+PORTVERSION= 0.4.0
CATEGORIES= biology ruby
MASTER_SITES= ftp://ftp.bioruby.org/bioruby/
MASTER_SITE_SUBDIR= knu
diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
index e1a271443086..5e292a0e9b23 100644
--- a/biology/ruby-bio/distinfo
+++ b/biology/ruby-bio/distinfo
@@ -1 +1 @@
-MD5 (ruby/bioruby-0.3.9.tar.gz) = 00a78b1897e864f04094fa423d54a02c
+MD5 (ruby/bioruby-0.4.0.tar.gz) = 6c0eb08df96c376ab5a2ad93ff5ce34e
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 440a3fc7afdb..95761fdbd961 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,4 +1,5 @@
bin/biofetch
+bin/bioflat
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
@@ -9,20 +10,29 @@ etc/bioinformatics/seqdatabase.ini.sample
%%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/emboss.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta/format6.rb
+%%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb
+%%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb
%%RUBY_SITELIBDIR%%/bio/data/aa.rb
%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
%%RUBY_SITELIBDIR%%/bio/data/keggorg.rb
%%RUBY_SITELIBDIR%%/bio/data/na.rb
%%RUBY_SITELIBDIR%%/bio/db.rb
%%RUBY_SITELIBDIR%%/bio/db/aaindex.rb
-%%RUBY_SITELIBDIR%%/bio/db/ddbj.rb
%%RUBY_SITELIBDIR%%/bio/db/embl.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/trembl.rb
%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
-%%RUBY_SITELIBDIR%%/bio/db/genpept.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank/refseq.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
@@ -34,32 +44,34 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
%%RUBY_SITELIBDIR%%/bio/db/medline.rb
%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
-%%RUBY_SITELIBDIR%%/bio/db/refseq.rb
-%%RUBY_SITELIBDIR%%/bio/db/sptr.rb
-%%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/io/brdb.rb
%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
%%RUBY_SITELIBDIR%%/bio/io/fetch.rb
%%RUBY_SITELIBDIR%%/bio/io/flatfile.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/bdb.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/index.rb
+%%RUBY_SITELIBDIR%%/bio/io/flatfile/indexer.rb
%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
%%RUBY_SITELIBDIR%%/bio/io/registry.rb
%%RUBY_SITELIBDIR%%/bio/io/sql.rb
%%RUBY_SITELIBDIR%%/bio/location.rb
-%%RUBY_SITELIBDIR%%/bio/matrix.rb
%%RUBY_SITELIBDIR%%/bio/pathway.rb
%%RUBY_SITELIBDIR%%/bio/reference.rb
%%RUBY_SITELIBDIR%%/bio/sequence.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/io/flatfile
+@dirrm %%RUBY_SITELIBDIR%%/bio/io
@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
+@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
+@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
@dirrm %%RUBY_SITELIBDIR%%/bio/db
-@dirrm %%RUBY_SITELIBDIR%%/bio/io
+@dirrm %%RUBY_SITELIBDIR%%/bio/data
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl
@dirrm %%RUBY_SITELIBDIR%%/bio
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/biofetch.rb
%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb