diff options
Diffstat (limited to 'biology/ruby-bio/pkg-plist')
-rw-r--r-- | biology/ruby-bio/pkg-plist | 24 |
1 files changed, 23 insertions, 1 deletions
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%% |