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Port details
ruby-bio Integrated environment for Bioinformatics written in Ruby
1.5.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.5.1Version of this port present on the latest quarterly branch.
Maintainer: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 2001-10-24 03:21:52
Last Update: 2021-04-06 14:31:07
Commit Hash: 305f148
Also Listed In: ruby
License: GPLv2 RUBY
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (327 items)
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  1. /usr/local/share/licenses/ruby27-bio-1.5.1/catalog.mk
  2. /usr/local/share/licenses/ruby27-bio-1.5.1/LICENSE
  3. /usr/local/share/licenses/ruby27-bio-1.5.1/GPLv2
  4. /usr/local/share/licenses/ruby27-bio-1.5.1/RUBY
  5. share/doc/ruby27/bio/ChangeLog
  6. share/doc/ruby27/bio/Changes-0.7.rd
  7. share/doc/ruby27/bio/README.rdoc
  8. share/doc/ruby27/bio/Tutorial.rd
  9. share/doc/ruby27/bio/ja/Tutorial.rd.ja
  10. share/examples/ruby27/bio/any2fasta.rb
  11. share/examples/ruby27/bio/biofetch.rb
  12. share/examples/ruby27/bio/color_scheme_na.rb
  13. share/examples/ruby27/bio/demo_aaindex.rb
  14. share/examples/ruby27/bio/demo_aminoacid.rb
  15. share/examples/ruby27/bio/demo_bl2seq_report.rb
  16. share/examples/ruby27/bio/demo_blast_report.rb
  17. share/examples/ruby27/bio/demo_codontable.rb
  18. share/examples/ruby27/bio/demo_das.rb
  19. share/examples/ruby27/bio/demo_fasta_remote.rb
  20. share/examples/ruby27/bio/demo_fastaformat.rb
  21. share/examples/ruby27/bio/demo_genbank.rb
  22. share/examples/ruby27/bio/demo_genscan_report.rb
  23. share/examples/ruby27/bio/demo_gff1.rb
  24. share/examples/ruby27/bio/demo_go.rb
  25. share/examples/ruby27/bio/demo_hmmer_report.rb
  26. share/examples/ruby27/bio/demo_kegg_compound.rb
  27. share/examples/ruby27/bio/demo_kegg_drug.rb
  28. share/examples/ruby27/bio/demo_kegg_genome.rb
  29. share/examples/ruby27/bio/demo_kegg_glycan.rb
  30. share/examples/ruby27/bio/demo_kegg_orthology.rb
  31. share/examples/ruby27/bio/demo_kegg_reaction.rb
  32. share/examples/ruby27/bio/demo_litdb.rb
  33. share/examples/ruby27/bio/demo_locations.rb
  34. share/examples/ruby27/bio/demo_ncbi_rest.rb
  35. share/examples/ruby27/bio/demo_nucleicacid.rb
  36. share/examples/ruby27/bio/demo_pathway.rb
  37. share/examples/ruby27/bio/demo_prosite.rb
  38. share/examples/ruby27/bio/demo_psort.rb
  39. share/examples/ruby27/bio/demo_psort_report.rb
  40. share/examples/ruby27/bio/demo_pubmed.rb
  41. share/examples/ruby27/bio/demo_sequence.rb
  42. share/examples/ruby27/bio/demo_sirna.rb
  43. share/examples/ruby27/bio/demo_sosui_report.rb
  44. share/examples/ruby27/bio/demo_targetp_report.rb
  45. share/examples/ruby27/bio/demo_tmhmm_report.rb
  46. share/examples/ruby27/bio/enzymes.rb
  47. share/examples/ruby27/bio/fasta2tab.rb
  48. share/examples/ruby27/bio/fastagrep.rb
  49. share/examples/ruby27/bio/fastasort.rb
  50. share/examples/ruby27/bio/fsplit.rb
  51. share/examples/ruby27/bio/gb2fasta.rb
  52. share/examples/ruby27/bio/gb2tab.rb
  53. share/examples/ruby27/bio/gbtab2mysql.rb
  54. share/examples/ruby27/bio/genes2nuc.rb
  55. share/examples/ruby27/bio/genes2pep.rb
  56. share/examples/ruby27/bio/genes2tab.rb
  57. share/examples/ruby27/bio/genome2rb.rb
  58. share/examples/ruby27/bio/genome2tab.rb
  59. share/examples/ruby27/bio/goslim.rb
  60. share/examples/ruby27/bio/gt2fasta.rb
  61. share/examples/ruby27/bio/na2aa.rb
  62. share/examples/ruby27/bio/pmfetch.rb
  63. share/examples/ruby27/bio/pmsearch.rb
  64. share/examples/ruby27/bio/ssearch2tab.rb
  65. share/examples/ruby27/bio/tdiary.rb
  66. share/examples/ruby27/bio/test_phyloxml_big.rb
  67. share/examples/ruby27/bio/tfastx2tab.rb
  68. share/examples/ruby27/bio/vs-genes.rb
  69. share/examples/ruby27/bio/benchmark_clustalw_report.rb
  70. share/examples/ruby27/bio/seqdatabase.ini
  71. share/examples/ruby27/bio/test_restriction_enzyme_long.rb
  72. lib/ruby/site_ruby/2.7/bio.rb
  73. lib/ruby/site_ruby/2.7/bio/alignment.rb
  74. lib/ruby/site_ruby/2.7/bio/appl/bl2seq/report.rb
  75. lib/ruby/site_ruby/2.7/bio/appl/blast.rb
  76. lib/ruby/site_ruby/2.7/bio/appl/blast/format0.rb
  77. lib/ruby/site_ruby/2.7/bio/appl/blast/format8.rb
  78. lib/ruby/site_ruby/2.7/bio/appl/blast/genomenet.rb
  79. lib/ruby/site_ruby/2.7/bio/appl/blast/ncbioptions.rb
  80. lib/ruby/site_ruby/2.7/bio/appl/blast/remote.rb
  81. lib/ruby/site_ruby/2.7/bio/appl/blast/report.rb
  82. lib/ruby/site_ruby/2.7/bio/appl/blast/rexml.rb
  83. lib/ruby/site_ruby/2.7/bio/appl/blast/rpsblast.rb
  84. lib/ruby/site_ruby/2.7/bio/appl/blast/wublast.rb
  85. lib/ruby/site_ruby/2.7/bio/appl/blast/xmlparser.rb
  86. lib/ruby/site_ruby/2.7/bio/appl/blat/report.rb
  87. lib/ruby/site_ruby/2.7/bio/appl/clustalw.rb
  88. lib/ruby/site_ruby/2.7/bio/appl/clustalw/report.rb
  89. lib/ruby/site_ruby/2.7/bio/appl/emboss.rb
  90. lib/ruby/site_ruby/2.7/bio/appl/fasta.rb
  91. lib/ruby/site_ruby/2.7/bio/appl/fasta/format10.rb
  92. lib/ruby/site_ruby/2.7/bio/appl/gcg/msf.rb
  93. lib/ruby/site_ruby/2.7/bio/appl/gcg/seq.rb
  94. lib/ruby/site_ruby/2.7/bio/appl/genscan/report.rb
  95. lib/ruby/site_ruby/2.7/bio/appl/hmmer.rb
  96. lib/ruby/site_ruby/2.7/bio/appl/hmmer/report.rb
  97. lib/ruby/site_ruby/2.7/bio/appl/iprscan/report.rb
  98. lib/ruby/site_ruby/2.7/bio/appl/mafft.rb
  99. lib/ruby/site_ruby/2.7/bio/appl/mafft/report.rb
  100. lib/ruby/site_ruby/2.7/bio/appl/meme/mast.rb
  101. lib/ruby/site_ruby/2.7/bio/appl/meme/mast/report.rb
  102. lib/ruby/site_ruby/2.7/bio/appl/meme/motif.rb
  103. lib/ruby/site_ruby/2.7/bio/appl/muscle.rb
  104. lib/ruby/site_ruby/2.7/bio/appl/paml/baseml.rb
  105. lib/ruby/site_ruby/2.7/bio/appl/paml/baseml/report.rb
  106. lib/ruby/site_ruby/2.7/bio/appl/paml/codeml.rb
  107. lib/ruby/site_ruby/2.7/bio/appl/paml/codeml/rates.rb
  108. lib/ruby/site_ruby/2.7/bio/appl/paml/codeml/report.rb
  109. lib/ruby/site_ruby/2.7/bio/appl/paml/common.rb
  110. lib/ruby/site_ruby/2.7/bio/appl/paml/common_report.rb
  111. lib/ruby/site_ruby/2.7/bio/appl/paml/yn00.rb
  112. lib/ruby/site_ruby/2.7/bio/appl/paml/yn00/report.rb
  113. lib/ruby/site_ruby/2.7/bio/appl/phylip/alignment.rb
  114. lib/ruby/site_ruby/2.7/bio/appl/phylip/distance_matrix.rb
  115. lib/ruby/site_ruby/2.7/bio/appl/probcons.rb
  116. lib/ruby/site_ruby/2.7/bio/appl/psort.rb
  117. lib/ruby/site_ruby/2.7/bio/appl/psort/report.rb
  118. lib/ruby/site_ruby/2.7/bio/appl/pts1.rb
  119. lib/ruby/site_ruby/2.7/bio/appl/sim4.rb
  120. lib/ruby/site_ruby/2.7/bio/appl/sim4/report.rb
  121. lib/ruby/site_ruby/2.7/bio/appl/sosui/report.rb
  122. lib/ruby/site_ruby/2.7/bio/appl/spidey/report.rb
  123. lib/ruby/site_ruby/2.7/bio/appl/targetp/report.rb
  124. lib/ruby/site_ruby/2.7/bio/appl/tcoffee.rb
  125. lib/ruby/site_ruby/2.7/bio/appl/tmhmm/report.rb
  126. lib/ruby/site_ruby/2.7/bio/command.rb
  127. lib/ruby/site_ruby/2.7/bio/compat/features.rb
  128. lib/ruby/site_ruby/2.7/bio/compat/references.rb
  129. lib/ruby/site_ruby/2.7/bio/data/aa.rb
  130. lib/ruby/site_ruby/2.7/bio/data/codontable.rb
  131. lib/ruby/site_ruby/2.7/bio/data/na.rb
  132. lib/ruby/site_ruby/2.7/bio/db.rb
  133. lib/ruby/site_ruby/2.7/bio/db/aaindex.rb
  134. lib/ruby/site_ruby/2.7/bio/db/biosql/biosql_to_biosequence.rb
  135. lib/ruby/site_ruby/2.7/bio/db/biosql/sequence.rb
  136. lib/ruby/site_ruby/2.7/bio/db/embl/common.rb
  137. lib/ruby/site_ruby/2.7/bio/db/embl/embl.rb
  138. lib/ruby/site_ruby/2.7/bio/db/embl/embl_to_biosequence.rb
  139. lib/ruby/site_ruby/2.7/bio/db/embl/format_embl.rb
  140. lib/ruby/site_ruby/2.7/bio/db/embl/sptr.rb
  141. lib/ruby/site_ruby/2.7/bio/db/embl/swissprot.rb
  142. lib/ruby/site_ruby/2.7/bio/db/embl/trembl.rb
  143. lib/ruby/site_ruby/2.7/bio/db/embl/uniprot.rb
  144. lib/ruby/site_ruby/2.7/bio/db/embl/uniprotkb.rb
  145. lib/ruby/site_ruby/2.7/bio/db/fantom.rb
  146. lib/ruby/site_ruby/2.7/bio/db/fasta.rb
  147. lib/ruby/site_ruby/2.7/bio/db/fasta/defline.rb
  148. lib/ruby/site_ruby/2.7/bio/db/fasta/fasta_to_biosequence.rb
  149. lib/ruby/site_ruby/2.7/bio/db/fasta/format_fasta.rb
  150. lib/ruby/site_ruby/2.7/bio/db/fasta/format_qual.rb
  151. lib/ruby/site_ruby/2.7/bio/db/fasta/qual.rb
  152. lib/ruby/site_ruby/2.7/bio/db/fasta/qual_to_biosequence.rb
  153. lib/ruby/site_ruby/2.7/bio/db/fastq.rb
  154. lib/ruby/site_ruby/2.7/bio/db/fastq/fastq_to_biosequence.rb
  155. lib/ruby/site_ruby/2.7/bio/db/fastq/format_fastq.rb
  156. lib/ruby/site_ruby/2.7/bio/db/genbank/common.rb
  157. lib/ruby/site_ruby/2.7/bio/db/genbank/ddbj.rb
  158. lib/ruby/site_ruby/2.7/bio/db/genbank/format_genbank.rb
  159. lib/ruby/site_ruby/2.7/bio/db/genbank/genbank.rb
  160. lib/ruby/site_ruby/2.7/bio/db/genbank/genbank_to_biosequence.rb
  161. lib/ruby/site_ruby/2.7/bio/db/genbank/genpept.rb
  162. lib/ruby/site_ruby/2.7/bio/db/genbank/refseq.rb
  163. lib/ruby/site_ruby/2.7/bio/db/gff.rb
  164. lib/ruby/site_ruby/2.7/bio/db/go.rb
  165. lib/ruby/site_ruby/2.7/bio/db/kegg/brite.rb
  166. lib/ruby/site_ruby/2.7/bio/db/kegg/common.rb
  167. lib/ruby/site_ruby/2.7/bio/db/kegg/compound.rb
  168. lib/ruby/site_ruby/2.7/bio/db/kegg/drug.rb
  169. lib/ruby/site_ruby/2.7/bio/db/kegg/enzyme.rb
  170. lib/ruby/site_ruby/2.7/bio/db/kegg/expression.rb
  171. lib/ruby/site_ruby/2.7/bio/db/kegg/genes.rb
  172. lib/ruby/site_ruby/2.7/bio/db/kegg/genome.rb
  173. lib/ruby/site_ruby/2.7/bio/db/kegg/glycan.rb
  174. lib/ruby/site_ruby/2.7/bio/db/kegg/keggtab.rb
  175. lib/ruby/site_ruby/2.7/bio/db/kegg/kgml.rb
  176. lib/ruby/site_ruby/2.7/bio/db/kegg/module.rb
  177. lib/ruby/site_ruby/2.7/bio/db/kegg/orthology.rb
  178. lib/ruby/site_ruby/2.7/bio/db/kegg/pathway.rb
  179. lib/ruby/site_ruby/2.7/bio/db/kegg/reaction.rb
  180. lib/ruby/site_ruby/2.7/bio/db/lasergene.rb
  181. lib/ruby/site_ruby/2.7/bio/db/litdb.rb
  182. lib/ruby/site_ruby/2.7/bio/db/medline.rb
  183. lib/ruby/site_ruby/2.7/bio/db/nbrf.rb
  184. lib/ruby/site_ruby/2.7/bio/db/newick.rb
  185. lib/ruby/site_ruby/2.7/bio/db/nexus.rb
  186. lib/ruby/site_ruby/2.7/bio/db/pdb.rb
  187. lib/ruby/site_ruby/2.7/bio/db/pdb/atom.rb
  188. lib/ruby/site_ruby/2.7/bio/db/pdb/chain.rb
  189. lib/ruby/site_ruby/2.7/bio/db/pdb/chemicalcomponent.rb
  190. lib/ruby/site_ruby/2.7/bio/db/pdb/model.rb
  191. lib/ruby/site_ruby/2.7/bio/db/pdb/pdb.rb
  192. lib/ruby/site_ruby/2.7/bio/db/pdb/residue.rb
  193. lib/ruby/site_ruby/2.7/bio/db/pdb/utils.rb
  194. lib/ruby/site_ruby/2.7/bio/db/phyloxml/phyloxml.xsd
  195. lib/ruby/site_ruby/2.7/bio/db/phyloxml/phyloxml_elements.rb
  196. lib/ruby/site_ruby/2.7/bio/db/phyloxml/phyloxml_parser.rb
  197. lib/ruby/site_ruby/2.7/bio/db/phyloxml/phyloxml_writer.rb
  198. lib/ruby/site_ruby/2.7/bio/db/prosite.rb
  199. lib/ruby/site_ruby/2.7/bio/db/rebase.rb
  200. lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram/abif.rb
  201. lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram/chromatogram.rb
  202. lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
  203. lib/ruby/site_ruby/2.7/bio/db/sanger_chromatogram/scf.rb
  204. lib/ruby/site_ruby/2.7/bio/db/soft.rb
  205. lib/ruby/site_ruby/2.7/bio/db/transfac.rb
  206. lib/ruby/site_ruby/2.7/bio/feature.rb
  207. lib/ruby/site_ruby/2.7/bio/io/biosql/ar-biosql.rb
  208. lib/ruby/site_ruby/2.7/bio/io/biosql/biosql.rb
  209. lib/ruby/site_ruby/2.7/bio/io/biosql/config/database.yml
  210. lib/ruby/site_ruby/2.7/bio/io/das.rb
  211. lib/ruby/site_ruby/2.7/bio/io/fastacmd.rb
  212. lib/ruby/site_ruby/2.7/bio/io/fetch.rb
  213. lib/ruby/site_ruby/2.7/bio/io/flatfile.rb
  214. lib/ruby/site_ruby/2.7/bio/io/flatfile/autodetection.rb
  215. lib/ruby/site_ruby/2.7/bio/io/flatfile/bdb.rb
  216. lib/ruby/site_ruby/2.7/bio/io/flatfile/buffer.rb
  217. lib/ruby/site_ruby/2.7/bio/io/flatfile/index.rb
  218. lib/ruby/site_ruby/2.7/bio/io/flatfile/indexer.rb
  219. lib/ruby/site_ruby/2.7/bio/io/flatfile/splitter.rb
  220. lib/ruby/site_ruby/2.7/bio/io/hinv.rb
  221. lib/ruby/site_ruby/2.7/bio/io/ncbirest.rb
  222. lib/ruby/site_ruby/2.7/bio/io/pubmed.rb
  223. lib/ruby/site_ruby/2.7/bio/io/registry.rb
  224. lib/ruby/site_ruby/2.7/bio/io/sql.rb
  225. lib/ruby/site_ruby/2.7/bio/io/togows.rb
  226. lib/ruby/site_ruby/2.7/bio/location.rb
  227. lib/ruby/site_ruby/2.7/bio/map.rb
  228. lib/ruby/site_ruby/2.7/bio/pathway.rb
  229. lib/ruby/site_ruby/2.7/bio/reference.rb
  230. lib/ruby/site_ruby/2.7/bio/sequence.rb
  231. lib/ruby/site_ruby/2.7/bio/sequence/aa.rb
  232. lib/ruby/site_ruby/2.7/bio/sequence/adapter.rb
  233. lib/ruby/site_ruby/2.7/bio/sequence/common.rb
  234. lib/ruby/site_ruby/2.7/bio/sequence/compat.rb
  235. lib/ruby/site_ruby/2.7/bio/sequence/dblink.rb
  236. lib/ruby/site_ruby/2.7/bio/sequence/format.rb
  237. lib/ruby/site_ruby/2.7/bio/sequence/format_raw.rb
  238. lib/ruby/site_ruby/2.7/bio/sequence/generic.rb
  239. lib/ruby/site_ruby/2.7/bio/sequence/na.rb
  240. lib/ruby/site_ruby/2.7/bio/sequence/quality_score.rb
  241. lib/ruby/site_ruby/2.7/bio/sequence/sequence_masker.rb
  242. lib/ruby/site_ruby/2.7/bio/shell.rb
  243. lib/ruby/site_ruby/2.7/bio/shell/core.rb
  244. lib/ruby/site_ruby/2.7/bio/shell/demo.rb
  245. lib/ruby/site_ruby/2.7/bio/shell/interface.rb
  246. lib/ruby/site_ruby/2.7/bio/shell/irb.rb
  247. lib/ruby/site_ruby/2.7/bio/shell/object.rb
  248. lib/ruby/site_ruby/2.7/bio/shell/plugin/blast.rb
  249. lib/ruby/site_ruby/2.7/bio/shell/plugin/codon.rb
  250. lib/ruby/site_ruby/2.7/bio/shell/plugin/das.rb
  251. lib/ruby/site_ruby/2.7/bio/shell/plugin/emboss.rb
  252. lib/ruby/site_ruby/2.7/bio/shell/plugin/entry.rb
  253. lib/ruby/site_ruby/2.7/bio/shell/plugin/flatfile.rb
  254. lib/ruby/site_ruby/2.7/bio/shell/plugin/midi.rb
  255. lib/ruby/site_ruby/2.7/bio/shell/plugin/ncbirest.rb
  256. lib/ruby/site_ruby/2.7/bio/shell/plugin/obda.rb
  257. lib/ruby/site_ruby/2.7/bio/shell/plugin/psort.rb
  258. lib/ruby/site_ruby/2.7/bio/shell/plugin/seq.rb
  259. lib/ruby/site_ruby/2.7/bio/shell/plugin/togows.rb
  260. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
  261. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
  262. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
  263. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
  264. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
  265. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
  266. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
  267. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
  268. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
  269. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
  270. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
  271. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
  272. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
  273. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
  274. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
  275. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
  276. lib/ruby/site_ruby/2.7/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
  277. lib/ruby/site_ruby/2.7/bio/shell/script.rb
  278. lib/ruby/site_ruby/2.7/bio/shell/setup.rb
  279. lib/ruby/site_ruby/2.7/bio/shell/web.rb
  280. lib/ruby/site_ruby/2.7/bio/tree.rb
  281. lib/ruby/site_ruby/2.7/bio/tree/output.rb
  282. lib/ruby/site_ruby/2.7/bio/util/color_scheme.rb
  283. lib/ruby/site_ruby/2.7/bio/util/color_scheme/buried.rb
  284. lib/ruby/site_ruby/2.7/bio/util/color_scheme/helix.rb
  285. lib/ruby/site_ruby/2.7/bio/util/color_scheme/hydropathy.rb
  286. lib/ruby/site_ruby/2.7/bio/util/color_scheme/nucleotide.rb
  287. lib/ruby/site_ruby/2.7/bio/util/color_scheme/strand.rb
  288. lib/ruby/site_ruby/2.7/bio/util/color_scheme/taylor.rb
  289. lib/ruby/site_ruby/2.7/bio/util/color_scheme/turn.rb
  290. lib/ruby/site_ruby/2.7/bio/util/color_scheme/zappo.rb
  291. lib/ruby/site_ruby/2.7/bio/util/contingency_table.rb
  292. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme.rb
  293. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/analysis.rb
  294. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/analysis_basic.rb
  295. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/cut_symbol.rb
  296. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/dense_int_array.rb
  297. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded.rb
  298. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
  299. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
  300. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
  301. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
  302. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
  303. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/enzymes.yaml
  304. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/cut_range.rb
  305. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/cut_ranges.rb
  306. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
  307. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range.rb
  308. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
  309. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
  310. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
  311. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/range/vertical_cut_range.rb
  312. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/single_strand.rb
  313. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
  314. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/single_strand_complement.rb
  315. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/sorted_num_array.rb
  316. lib/ruby/site_ruby/2.7/bio/util/restriction_enzyme/string_formatting.rb
  317. lib/ruby/site_ruby/2.7/bio/util/sirna.rb
  318. lib/ruby/site_ruby/2.7/bio/version.rb
  319. bin/bioruby
  320. bin/br_biofetch
  321. bin/br_bioflat
  322. bin/br_biogetseq
  323. bin/br_pmfetch
  324. etc/bioinformatics/seqdatabase.ini.sample
  325. @owner
  326. @group
  327. @mode
Collapse this list.
Dependency lines:
  • ruby27-bio>0:biology/ruby-bio
To install the port: cd /usr/ports/biology/ruby-bio/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ruby-bio
  • pkg install ruby27-bio
PKGNAME: ruby27-bio
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
ruby24-bio
ABIlatestquarterly
FreeBSD:11:aarch641.5.1-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch641.5.1-
FreeBSD:12:amd64--
FreeBSD:12:armv61.5.1-
FreeBSD:12:armv71.5.1-
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
ruby26-bio
ABIlatestquarterly
FreeBSD:11:aarch64-1.5.1
FreeBSD:11:amd64--
FreeBSD:11:armv6-1.5.1
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6-1.5.1
FreeBSD:12:armv7-1.5.1
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
ruby27-bio
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd641.5.11.5.1
FreeBSD:11:armv6--
FreeBSD:11:i3861.5.11.5.1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-1.5.1
FreeBSD:12:amd641.5.11.5.1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3861.5.11.5.1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-1.5.1
FreeBSD:13:aarch641.5.11.5.1
FreeBSD:13:amd641.5.11.5.1
FreeBSD:13:armv61.5.11.5.1
FreeBSD:13:armv71.5.11.5.1
FreeBSD:13:i3861.5.11.5.1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc641.5.11.5.1
FreeBSD:14:aarch641.5.1-
FreeBSD:14:amd641.5.1-
FreeBSD:14:armv61.5.1-
FreeBSD:14:armv71.5.1-
FreeBSD:14:i3861.5.1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc641.5.1-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ruby27 : lang/ruby27
Runtime dependencies:
  1. ruby27 : lang/ruby27
Patch dependencies:
  1. ruby27 : lang/ruby27
Extract dependencies:
  1. ruby27 : lang/ruby27
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://bioruby.org/archive/
Collapse this list.

Number of commits found: 42

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.5.1
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
05 May 2020 14:22:09
Original commit files touched by this commit Revision:534089  1.5.1
rene search for other commits by this committer
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
07 May 2017 15:44:34
Original commit files touched by this commit Revision:440343  1.5.1
miwi search for other commits by this committer
- Update to 1.5.1
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  1.5.0
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
31 Mar 2016 17:36:55
Original commit files touched by this commit Revision:412278  1.5.0
amdmi3 search for other commits by this committer
- Update to 1.5.0

PR:		208351
Submitted by:	wen@FreeBSD.org
Approved by:	mauricio@arareko.net (maintainer)
17 Jan 2016 07:06:25
Original commit files touched by this commit Revision:406285  1.4.1
swills search for other commits by this committer
mark ports that don't work with Ruby 2.3

PR:		205774
10 Oct 2015 23:15:16
Original commit files touched by this commit Revision:399072  1.4.1
sunpoet search for other commits by this committer
- Fix typo

Approved by:	portmgr (blanket)
03 Sep 2015 16:23:37
Original commit files touched by this commit Revision:395991  1.4.1
sunpoet search for other commits by this committer
- Add LICENSE
- Add NO_ARCH
- Use BROKEN_RUBY22
- While I'm here, use single space after WWW:

Approved by:	portmgr (blanket)
With hat:	ruby
17 Aug 2015 14:20:41
Original commit files touched by this commit Revision:394508  1.4.1
mat search for other commits by this committer
Remove UNIQUENAME and LATEST_LINK.

UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now,
we won't have conflicts there.

Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer
is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel
has the correct PKGNAME anyway.

Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called
OPTIONS_FILE now.)

Reviewed by:	antoine, bapt
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3336
03 Apr 2015 13:50:39
Original commit files touched by this commit Revision:383123  1.4.1
swills search for other commits by this committer
biology/ruby-bio: mark broken with ruby 2.2
20 Oct 2014 07:10:48
Original commit files touched by this commit Revision:371237  1.4.1
bapt search for other commits by this committer
Cleanup plist
21 Sep 2014 13:44:59
Original commit files touched by this commit Revision:368754  1.4.1
dinoex search for other commits by this committer
- any version for RUN_DEPENDS
21 Sep 2014 09:51:18
Original commit files touched by this commit Revision:368736  1.4.1
dinoex search for other commits by this committer
- update RUN_DEPENDS for rubygems-dbi
07 Apr 2014 13:01:27
Original commit files touched by this commit Revision:350461  1.4.1
bapt search for other commits by this committer
Support stage
15 Jan 2014 22:52:28
Original commit files touched by this commit Revision:339846  1.4.1
bapt search for other commits by this committer
Reduce over inclusion of bsd.port.mk
20 Sep 2013 15:55:44
Original commit files touched by this commit Revision:327709  1.4.1
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
18 Mar 2013 06:55:42
Original commit files touched by this commit Revision:314532  1.4.1
jgh search for other commits by this committer
- adoption of optionsNG
- trim historical header

Approved by:	portmgr (miwi)
30 Dec 2010 23:08:47
Original commit files touched by this commit   1.4.1
pgollucci search for other commits by this committer
- Fix pkg-plist, got the wrong version before

Reported by:    pointyhat via pav
27 Dec 2010 15:11:50
Original commit files touched by this commit   1.4.1
pgollucci search for other commits by this committer
- Update to 1.4.1
- Remove MD5

PR:             ports/153394
Submitted by:   myself (pgollucci)
Approved by:    mauricio@arareko.net (maintainer)
Sponsored by:   RideCharge Inc. / TaxiMagic
08 Jun 2010 00:18:54
Original commit files touched by this commit   1.4.0
pgollucci search for other commits by this committer
- Update to 1.4.0
- Sort pkg-plist
- seperate NOPORTDOCS and NOPORTEXAMPLES
24 Oct 2007 01:38:51
Original commit files touched by this commit   1.1.0
clsung search for other commits by this committer
- Update to 1.1.0

PR:             ports/117369
Submitted by:   Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp>
Approved by:    maintainer (Mauricio Herrera Cuadra)
25 Apr 2006 22:09:29
Original commit files touched by this commit   1.0.0
pav search for other commits by this committer
- Update to 1.0.0
- Provide OPTIONS
- Take maintainership

PR:             ports/94123
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
24 Nov 2005 00:04:00
Original commit files touched by this commit   0.6.2
pav search for other commits by this committer
- Add SHA256
11 Nov 2005 01:18:01
Original commit files touched by this commit   0.6.2
linimon search for other commits by this committer
With portmgr hat on, reset maintainership of knu's ports since he has
been inactive more than 6 months.  We hope to see him back sometime.
25 Dec 2004 17:52:46
Original commit files touched by this commit   0.6.2
knu search for other commits by this committer
Update to 0.6.2.
06 Jul 2004 14:31:55
Original commit files touched by this commit   0.5.3
vs search for other commits by this committer
Fix distsite

PR:             ports/67473
Submitted by:   Roman Neuhauser
Approved by:    maintainer timeout
29 May 2004 23:03:53
Original commit files touched by this commit   0.5.3
pav search for other commits by this committer
- Update WWW
22 Mar 2004 15:05:32
Original commit files touched by this commit   0.5.3
knu search for other commits by this committer
Add SIZE data.

Submitted by:   trevor
14 Oct 2003 22:25:59
Original commit files touched by this commit   0.5.3
knu search for other commits by this committer
Update to 0.5.3.
22 Aug 2003 22:53:54
Original commit files touched by this commit   0.5.2
knu search for other commits by this committer
Update to 0.5.2.
29 Jul 2003 06:44:28
Original commit files touched by this commit   0.5.1
knu search for other commits by this committer
Update to 0.5.1.
26 Jun 2003 03:34:44
Original commit files touched by this commit   0.5.0
knu search for other commits by this committer
Update to 0.5.0.
18 Feb 2003 04:22:03
Original commit files touched by this commit   0.4.0
knu search for other commits by this committer
De-pkg-comment.
29 Jan 2003 10:45:59
Original commit files touched by this commit   0.4.0
knu search for other commits by this committer
Update to 0.4.0.
06 Oct 2002 20:59:13
Original commit files touched by this commit   0.3.9
knu search for other commits by this committer
Use RUBY_MOD*.
03 Aug 2002 07:02:10
Original commit files touched by this commit   0.3.9
knu search for other commits by this committer
Update to 0.3.9.
07 Jul 2002 18:21:43
Original commit files touched by this commit   0.3.8
knu search for other commits by this committer
Update to 0.3.8.
10 Apr 2002 18:37:18
Original commit files touched by this commit   0.3.6
knu search for other commits by this committer
Update to 0.3.6.
12 Mar 2002 23:12:04
Original commit files touched by this commit 
knu search for other commits by this committer
Update to 0.3.5.
21 Dec 2001 21:25:16
 files touched by this commit commit hash:fp1.22349@dev.null.freshports.org
knu search for other commits by this committer
Update to 0.3.3.    
28 Nov 2001 13:46:31
 files touched by this commit commit hash:fp1.21322@dev.null.freshports.org
knu search for other commits by this committer
Update to 0.3.2.    
24 Oct 2001 07:21:52
 files touched by this commit commit hash:fp1.20038@dev.null.freshports.org
knu search for other commits by this committer
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics   written
in Ruby.    

Number of commits found: 42