biology/ruby-bio 1.5.1 MidnightBSD

Integrated environment for Bioinformatics written in Ruby

System: MidnightBSD
Repository: mports
Maintainer: [email protected]
License: gpl2, ruby
Categories: biology, ruby

Description

BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby.

In the other systems

System

Port

Version

MidnightBSD

biology/ruby-bio

1.5.1

FreeBSD

biology/ruby-bio

1.5.1

DragonFly

biology/ruby-bio

1.5.1

HardenedBSD

biology/ruby-bio

1.5.1

GhostBSD

biology/ruby-bio

1.5.1

Install

Binary package:

mport install ${RUBY_PKGNAMEPREFIX}bio

From mports:

cd /usr/mports/biology/ruby-bio && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	${RUBY_PKGNAMEPREFIX}bio>0:biology/ruby-bio

Dependencies

No port depends on this one.

Configuration

Options name: biology_bio

Option

Default

Description

BDB4

off

bdb4 support for faster flat file indexing

DOCS

off

MYSQL

off

PGSQL

off

USES: ruby:setup shebangfix
Service scripts: none
Conflicts with: rubygem-bio-shell

Files

pkg-plist 320

%%RUBY_DOCDIR%%/bio/ChangeLog
%%RUBY_DOCDIR%%/bio/Changes-0.7.rd
%%RUBY_DOCDIR%%/bio/README.rdoc
%%RUBY_DOCDIR%%/bio/Tutorial.rd
%%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/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_fasta_remote.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_fastaformat.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_genbank.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_genscan_report.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_gff1.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_go.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_hmmer_report.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_compound.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_drug.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_kegg_genome.rb
%%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_litdb.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_locations.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_ncbi_rest.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_nucleicacid.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_pathway.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_prosite.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_psort.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_psort_report.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_pubmed.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_sequence.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_sirna.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_sosui_report.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_targetp_report.rb
%%RUBY_EXAMPLESDIR%%/bio/demo_tmhmm_report.rb
%%RUBY_EXAMPLESDIR%%/bio/enzymes.rb
%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
%%RUBY_EXAMPLESDIR%%/bio/fastagrep.rb
%%RUBY_EXAMPLESDIR%%/bio/fastasort.rb
%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
%%RUBY_EXAMPLESDIR%%/bio/gbtab2mysql.rb
%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
%%RUBY_EXAMPLESDIR%%/bio/genome2rb.rb
%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
%%RUBY_EXAMPLESDIR%%/bio/goslim.rb
%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
%%RUBY_EXAMPLESDIR%%/bio/na2aa.rb
%%RUBY_EXAMPLESDIR%%/bio/pmfetch.rb
%%RUBY_EXAMPLESDIR%%/bio/pmsearch.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/format0.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/format8.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/genomenet.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/ncbioptions.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/remote.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/rexml.rb
%%RUBY_SITELIBDIR%%/bio/appl/blast/rpsblast.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
%%RUBY_SITELIBDIR%%/bio/appl/fasta.rb
%%RUBY_SITELIBDIR%%/bio/appl/fasta/format10.rb
%%RUBY_SITELIBDIR%%/bio/appl/gcg/msf.rb
%%RUBY_SITELIBDIR%%/bio/appl/gcg/seq.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/iprscan/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft.rb
%%RUBY_SITELIBDIR%%/bio/appl/mafft/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/meme/mast.rb
%%RUBY_SITELIBDIR%%/bio/appl/meme/mast/report.rb
%%RUBY_SITELIBDIR%%/bio/appl/meme/motif.rb
%%RUBY_SITELIBDIR%%/bio/appl/muscle.rb
%%RUBY_SITELIBDIR%%/bio/appl/paml/baseml.rb

The first 100 are listed.

distinfo 1

File

Size

SHA256

ruby/bioruby-1.5.1.tar.gz

1.478155e+06

872435a811f2a02000c9a5a5da5ba91c33e4a221ab8b243a69bf737df9bfb75a

Master sites 1

http://bioruby.org/archive/