diff options
-rw-r--r-- | biology/ruby-bio/Makefile | 4 | ||||
-rw-r--r-- | biology/ruby-bio/distinfo | 2 | ||||
-rw-r--r-- | biology/ruby-bio/pkg-plist | 24 |
3 files changed, 25 insertions, 5 deletions
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile index 440c1d7818d2..e4be577b546b 100644 --- a/biology/ruby-bio/Makefile +++ b/biology/ruby-bio/Makefile @@ -6,7 +6,7 @@ # PORTNAME= bio -PORTVERSION= 0.4.0 +PORTVERSION= 0.5.0 CATEGORIES= biology ruby MASTER_SITES= ftp://ftp.bioruby.org/bioruby/ MASTER_SITE_SUBDIR= knu @@ -21,8 +21,6 @@ USE_RUBY= yes USE_RUBY_SETUP= yes 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 \ diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo index 5e292a0e9b23..891fa1161643 100644 --- a/biology/ruby-bio/distinfo +++ b/biology/ruby-bio/distinfo @@ -1 +1 @@ -MD5 (ruby/bioruby-0.4.0.tar.gz) = 6c0eb08df96c376ab5a2ad93ff5ce34e +MD5 (ruby/bioruby-0.5.0.tar.gz) = 22f0ef196b4e364bb468a2806c4d321f diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist index 95761fdbd961..38c98bc22f06 100644 --- a/biology/ruby-bio/pkg-plist +++ b/biology/ruby-bio/pkg-plist @@ -1,6 +1,6 @@ bin/biofetch bin/bioflat -bin/dbget +bin/biogetseq @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 @@ -8,14 +8,21 @@ etc/bioinformatics/seqdatabase.ini.sample %%RUBY_SITELIBDIR%%/bio.rb %%RUBY_SITELIBDIR%%/bio/appl/blast.rb %%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb +%%RUBY_SITELIBDIR%%/bio/appl/blast/report.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/genscan/report.rb %%RUBY_SITELIBDIR%%/bio/appl/hmmer.rb %%RUBY_SITELIBDIR%%/bio/appl/hmmer/report.rb +%%RUBY_SITELIBDIR%%/bio/appl/psort.rb +%%RUBY_SITELIBDIR%%/bio/appl/psort/report.rb +%%RUBY_SITELIBDIR%%/bio/appl/sosui/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 @@ -27,12 +34,15 @@ etc/bioinformatics/seqdatabase.ini.sample %%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/fantom.rb %%RUBY_SITELIBDIR%%/bio/db/fasta.rb %%RUBY_SITELIBDIR%%/bio/db/genbank.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/gff.rb +%%RUBY_SITELIBDIR%%/bio/db/go.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb @@ -40,6 +50,7 @@ etc/bioinformatics/seqdatabase.ini.sample %%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb %%RUBY_SITELIBDIR%%/bio/db/kegg/genome.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/litdb.rb %%RUBY_SITELIBDIR%%/bio/db/medline.rb @@ -48,12 +59,15 @@ etc/bioinformatics/seqdatabase.ini.sample %%RUBY_SITELIBDIR%%/bio/extend.rb %%RUBY_SITELIBDIR%%/bio/feature.rb %%RUBY_SITELIBDIR%%/bio/io/brdb.rb +%%RUBY_SITELIBDIR%%/bio/io/das.rb %%RUBY_SITELIBDIR%%/bio/io/dbget.rb +%%RUBY_SITELIBDIR%%/bio/io/ddbjxml.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/keggapi.rb %%RUBY_SITELIBDIR%%/bio/io/pubmed.rb %%RUBY_SITELIBDIR%%/bio/io/registry.rb %%RUBY_SITELIBDIR%%/bio/io/sql.rb @@ -68,12 +82,18 @@ etc/bioinformatics/seqdatabase.ini.sample @dirrm %%RUBY_SITELIBDIR%%/bio/db/embl @dirrm %%RUBY_SITELIBDIR%%/bio/db @dirrm %%RUBY_SITELIBDIR%%/bio/data +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort @dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer +@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan @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%%/dbget %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fasta2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/fsplit.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gb2fasta.rb @@ -84,10 +104,12 @@ etc/bioinformatics/seqdatabase.ini.sample %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genes2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genome2rb.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/genome2tab.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/goslim.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/gt2fasta.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmfetch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/pmsearch.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/ssearch2tab.rb +%%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tdiary.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/tfastx2tab.rb %%PORTDOCS%%%%RUBY_MODEXAMPLESDIR%%/vs-genes.rb %%PORTDOCS%%@dirrm %%RUBY_MODEXAMPLESDIR%% |