BSD Portsbiology/ruby-bio 1.5.1 FreeBSD
Integrated environment for Bioinformatics written in Ruby
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv2, RUBY
- Categories
- biology, ruby
- Package size
- 530.5 KiB, 2658.3 KiB installed
Description
BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/ruby-bio | 1.5.1 |
| DragonFly | biology/ruby-bio | 1.5.1 |
| MidnightBSD | biology/ruby-bio | 1.5.1 |
Install
Binary package:
pkg install ruby34-bioFrom the ports tree:
cd /usr/ports/biology/ruby-bio/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= ruby34-bio>0:biology/ruby-bioPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 1.5.1 | 1.5.1 | 1.5.1 | 1.5.1 | 1.5.1 |
| FreeBSD:14:quarterly | 1.5.1 | 1.5.1 | n/a | 1.5.1 | 1.5.1 |
| FreeBSD:15:latest | 1.5.1 | 1.5.1 | n/a | 1.5.1 | 1.5.1 |
| FreeBSD:15:quarterly | 1.5.1 | 1.5.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.5.1 | 1.5.1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
The Makefile names none itself; they come from USES and USE_*.
The full lists below include those, and their dependencies in turn.
Build dependencies 5
Run dependencies 5
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 | Build and/or install documentation |
| MYSQL | off | MySQL database support |
| PGSQL | off | PostgreSQL database support |
- 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/
Commit history 0
No commits in the history this site was built from.