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authorAkinori MUSHA <knu@FreeBSD.org>2004-12-25 17:52:46 +0000
committerAkinori MUSHA <knu@FreeBSD.org>2004-12-25 17:52:46 +0000
commitad31ad2bd2925b4c80bd3c7014b0286c0fd3d7e9 (patch)
treea128dc16913fdd178465eb5b0b48196a66a1587c /biology
parentf813070cb5219d98cec4963af0224b7ad3bd3f0d (diff)
downloadports-ad31ad2bd2925b4c80bd3c7014b0286c0fd3d7e9.tar.gz
ports-ad31ad2bd2925b4c80bd3c7014b0286c0fd3d7e9.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/ruby-bio/Makefile2
-rw-r--r--biology/ruby-bio/distinfo4
-rw-r--r--biology/ruby-bio/pkg-plist27
3 files changed, 26 insertions, 7 deletions
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index d39eba7529ed..ce6f343a3a22 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= bio
-PORTVERSION= 0.5.3
+PORTVERSION= 0.6.2
CATEGORIES= biology ruby
MASTER_SITES= http://bioruby.org/archive/
PKGNAMEPREFIX= ${RUBY_PKGNAMEPREFIX}
diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
index 024ab729e312..9bb3f6ecf73a 100644
--- a/biology/ruby-bio/distinfo
+++ b/biology/ruby-bio/distinfo
@@ -1,2 +1,2 @@
-MD5 (ruby/bioruby-0.5.3.tar.gz) = 44079bb50a88315af81ef589d001ca2e
-SIZE (ruby/bioruby-0.5.3.tar.gz) = 223811
+MD5 (ruby/bioruby-0.6.2.tar.gz) = 68c7ae5aa8562bfe1021d9a5201a9581
+SIZE (ruby/bioruby-0.6.2.tar.gz) = 270444
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index ed4ca2b76847..7a61592cf7a2 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -1,6 +1,7 @@
-bin/biofetch
-bin/bioflat
-bin/biogetseq
+bin/br_biofetch.rb
+bin/br_bioflat.rb
+bin/br_biogetseq.rb
+bin/br_pmfetch.rb
@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
@@ -15,6 +16,7 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/wublast.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/xmlparser.rb
+%%RUBY_SITELIBDIR%%/bio/appl/blat/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/clustalw.rb
%%RUBY_SITELIBDIR%%/bio/appl/clustalw/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/emboss.rb
@@ -28,16 +30,19 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/psort.rb
%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/sim4.rb
+%%RUBY_SITELIBDIR%%/bio/appl/sim4/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/sosui/report.rb
+%%RUBY_SITELIBDIR%%/bio/appl/spidey/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/targetp/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/tmhmm/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/embl.rb
+%%RUBY_SITELIBDIR%%/bio/db/embl/common.rb
%%RUBY_SITELIBDIR%%/bio/db/embl/embl.rb
%%RUBY_SITELIBDIR%%/bio/db/embl/sptr.rb
%%RUBY_SITELIBDIR%%/bio/db/embl/swissprot.rb
@@ -45,6 +50,7 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/db/fantom.rb
%%RUBY_SITELIBDIR%%/bio/db/fasta.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank/common.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/ddbj.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/genbank.rb
%%RUBY_SITELIBDIR%%/bio/db/genbank/genpept.rb
@@ -57,13 +63,21 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/glycan.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/keggtab.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/ko.rb
%%RUBY_SITELIBDIR%%/bio/db/kegg/microarray.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/reaction.rb
%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
%%RUBY_SITELIBDIR%%/bio/db/medline.rb
%%RUBY_SITELIBDIR%%/bio/db/nbrf.rb
%%RUBY_SITELIBDIR%%/bio/db/pdb.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/atom.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/chain.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/model.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/pdb.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/residue.rb
+%%RUBY_SITELIBDIR%%/bio/db/pdb/utils.rb
%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
%%RUBY_SITELIBDIR%%/bio/extend.rb
@@ -80,6 +94,7 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/io/keggapi.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/location.rb
%%RUBY_SITELIBDIR%%/bio/pathway.rb
@@ -87,6 +102,7 @@ etc/bioinformatics/seqdatabase.ini.sample
%%RUBY_SITELIBDIR%%/bio/sequence.rb
@dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
@dirrm %%RUBY_SITELIBDIR%%/bio/io
+@dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
@@ -94,13 +110,16 @@ etc/bioinformatics/seqdatabase.ini.sample
@dirrm %%RUBY_SITELIBDIR%%/bio/data
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/spidey
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
+@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
@dirrm %%RUBY_SITELIBDIR%%/bio/appl
@dirrm %%RUBY_SITELIBDIR%%/bio