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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: 2023-01-14 23:08:33
Commit Hash: 18c6e18
Also Listed In: ruby
License: GPLv2 RUBY
WWW:
http://bioruby.org/
Description:
BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (327 items)
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  1. /usr/local/share/licenses/ruby30-bio-1.5.1/catalog.mk
  2. /usr/local/share/licenses/ruby30-bio-1.5.1/LICENSE
  3. /usr/local/share/licenses/ruby30-bio-1.5.1/GPLv2
  4. /usr/local/share/licenses/ruby30-bio-1.5.1/RUBY
  5. share/doc/ruby30/bio/ChangeLog
  6. share/doc/ruby30/bio/Changes-0.7.rd
  7. share/doc/ruby30/bio/README.rdoc
  8. share/doc/ruby30/bio/Tutorial.rd
  9. share/doc/ruby30/bio/ja/Tutorial.rd.ja
  10. share/examples/ruby30/bio/any2fasta.rb
  11. share/examples/ruby30/bio/biofetch.rb
  12. share/examples/ruby30/bio/color_scheme_na.rb
  13. share/examples/ruby30/bio/demo_aaindex.rb
  14. share/examples/ruby30/bio/demo_aminoacid.rb
  15. share/examples/ruby30/bio/demo_bl2seq_report.rb
  16. share/examples/ruby30/bio/demo_blast_report.rb
  17. share/examples/ruby30/bio/demo_codontable.rb
  18. share/examples/ruby30/bio/demo_das.rb
  19. share/examples/ruby30/bio/demo_fasta_remote.rb
  20. share/examples/ruby30/bio/demo_fastaformat.rb
  21. share/examples/ruby30/bio/demo_genbank.rb
  22. share/examples/ruby30/bio/demo_genscan_report.rb
  23. share/examples/ruby30/bio/demo_gff1.rb
  24. share/examples/ruby30/bio/demo_go.rb
  25. share/examples/ruby30/bio/demo_hmmer_report.rb
  26. share/examples/ruby30/bio/demo_kegg_compound.rb
  27. share/examples/ruby30/bio/demo_kegg_drug.rb
  28. share/examples/ruby30/bio/demo_kegg_genome.rb
  29. share/examples/ruby30/bio/demo_kegg_glycan.rb
  30. share/examples/ruby30/bio/demo_kegg_orthology.rb
  31. share/examples/ruby30/bio/demo_kegg_reaction.rb
  32. share/examples/ruby30/bio/demo_litdb.rb
  33. share/examples/ruby30/bio/demo_locations.rb
  34. share/examples/ruby30/bio/demo_ncbi_rest.rb
  35. share/examples/ruby30/bio/demo_nucleicacid.rb
  36. share/examples/ruby30/bio/demo_pathway.rb
  37. share/examples/ruby30/bio/demo_prosite.rb
  38. share/examples/ruby30/bio/demo_psort.rb
  39. share/examples/ruby30/bio/demo_psort_report.rb
  40. share/examples/ruby30/bio/demo_pubmed.rb
  41. share/examples/ruby30/bio/demo_sequence.rb
  42. share/examples/ruby30/bio/demo_sirna.rb
  43. share/examples/ruby30/bio/demo_sosui_report.rb
  44. share/examples/ruby30/bio/demo_targetp_report.rb
  45. share/examples/ruby30/bio/demo_tmhmm_report.rb
  46. share/examples/ruby30/bio/enzymes.rb
  47. share/examples/ruby30/bio/fasta2tab.rb
  48. share/examples/ruby30/bio/fastagrep.rb
  49. share/examples/ruby30/bio/fastasort.rb
  50. share/examples/ruby30/bio/fsplit.rb
  51. share/examples/ruby30/bio/gb2fasta.rb
  52. share/examples/ruby30/bio/gb2tab.rb
  53. share/examples/ruby30/bio/gbtab2mysql.rb
  54. share/examples/ruby30/bio/genes2nuc.rb
  55. share/examples/ruby30/bio/genes2pep.rb
  56. share/examples/ruby30/bio/genes2tab.rb
  57. share/examples/ruby30/bio/genome2rb.rb
  58. share/examples/ruby30/bio/genome2tab.rb
  59. share/examples/ruby30/bio/goslim.rb
  60. share/examples/ruby30/bio/gt2fasta.rb
  61. share/examples/ruby30/bio/na2aa.rb
  62. share/examples/ruby30/bio/pmfetch.rb
  63. share/examples/ruby30/bio/pmsearch.rb
  64. share/examples/ruby30/bio/ssearch2tab.rb
  65. share/examples/ruby30/bio/tdiary.rb
  66. share/examples/ruby30/bio/test_phyloxml_big.rb
  67. share/examples/ruby30/bio/tfastx2tab.rb
  68. share/examples/ruby30/bio/vs-genes.rb
  69. share/examples/ruby30/bio/benchmark_clustalw_report.rb
  70. share/examples/ruby30/bio/seqdatabase.ini
  71. share/examples/ruby30/bio/test_restriction_enzyme_long.rb
  72. lib/ruby/site_ruby/3.0/bio.rb
  73. lib/ruby/site_ruby/3.0/bio/alignment.rb
  74. lib/ruby/site_ruby/3.0/bio/appl/bl2seq/report.rb
  75. lib/ruby/site_ruby/3.0/bio/appl/blast.rb
  76. lib/ruby/site_ruby/3.0/bio/appl/blast/format0.rb
  77. lib/ruby/site_ruby/3.0/bio/appl/blast/format8.rb
  78. lib/ruby/site_ruby/3.0/bio/appl/blast/genomenet.rb
  79. lib/ruby/site_ruby/3.0/bio/appl/blast/ncbioptions.rb
  80. lib/ruby/site_ruby/3.0/bio/appl/blast/remote.rb
  81. lib/ruby/site_ruby/3.0/bio/appl/blast/report.rb
  82. lib/ruby/site_ruby/3.0/bio/appl/blast/rexml.rb
  83. lib/ruby/site_ruby/3.0/bio/appl/blast/rpsblast.rb
  84. lib/ruby/site_ruby/3.0/bio/appl/blast/wublast.rb
  85. lib/ruby/site_ruby/3.0/bio/appl/blast/xmlparser.rb
  86. lib/ruby/site_ruby/3.0/bio/appl/blat/report.rb
  87. lib/ruby/site_ruby/3.0/bio/appl/clustalw.rb
  88. lib/ruby/site_ruby/3.0/bio/appl/clustalw/report.rb
  89. lib/ruby/site_ruby/3.0/bio/appl/emboss.rb
  90. lib/ruby/site_ruby/3.0/bio/appl/fasta.rb
  91. lib/ruby/site_ruby/3.0/bio/appl/fasta/format10.rb
  92. lib/ruby/site_ruby/3.0/bio/appl/gcg/msf.rb
  93. lib/ruby/site_ruby/3.0/bio/appl/gcg/seq.rb
  94. lib/ruby/site_ruby/3.0/bio/appl/genscan/report.rb
  95. lib/ruby/site_ruby/3.0/bio/appl/hmmer.rb
  96. lib/ruby/site_ruby/3.0/bio/appl/hmmer/report.rb
  97. lib/ruby/site_ruby/3.0/bio/appl/iprscan/report.rb
  98. lib/ruby/site_ruby/3.0/bio/appl/mafft.rb
  99. lib/ruby/site_ruby/3.0/bio/appl/mafft/report.rb
  100. lib/ruby/site_ruby/3.0/bio/appl/meme/mast.rb
  101. lib/ruby/site_ruby/3.0/bio/appl/meme/mast/report.rb
  102. lib/ruby/site_ruby/3.0/bio/appl/meme/motif.rb
  103. lib/ruby/site_ruby/3.0/bio/appl/muscle.rb
  104. lib/ruby/site_ruby/3.0/bio/appl/paml/baseml.rb
  105. lib/ruby/site_ruby/3.0/bio/appl/paml/baseml/report.rb
  106. lib/ruby/site_ruby/3.0/bio/appl/paml/codeml.rb
  107. lib/ruby/site_ruby/3.0/bio/appl/paml/codeml/rates.rb
  108. lib/ruby/site_ruby/3.0/bio/appl/paml/codeml/report.rb
  109. lib/ruby/site_ruby/3.0/bio/appl/paml/common.rb
  110. lib/ruby/site_ruby/3.0/bio/appl/paml/common_report.rb
  111. lib/ruby/site_ruby/3.0/bio/appl/paml/yn00.rb
  112. lib/ruby/site_ruby/3.0/bio/appl/paml/yn00/report.rb
  113. lib/ruby/site_ruby/3.0/bio/appl/phylip/alignment.rb
  114. lib/ruby/site_ruby/3.0/bio/appl/phylip/distance_matrix.rb
  115. lib/ruby/site_ruby/3.0/bio/appl/probcons.rb
  116. lib/ruby/site_ruby/3.0/bio/appl/psort.rb
  117. lib/ruby/site_ruby/3.0/bio/appl/psort/report.rb
  118. lib/ruby/site_ruby/3.0/bio/appl/pts1.rb
  119. lib/ruby/site_ruby/3.0/bio/appl/sim4.rb
  120. lib/ruby/site_ruby/3.0/bio/appl/sim4/report.rb
  121. lib/ruby/site_ruby/3.0/bio/appl/sosui/report.rb
  122. lib/ruby/site_ruby/3.0/bio/appl/spidey/report.rb
  123. lib/ruby/site_ruby/3.0/bio/appl/targetp/report.rb
  124. lib/ruby/site_ruby/3.0/bio/appl/tcoffee.rb
  125. lib/ruby/site_ruby/3.0/bio/appl/tmhmm/report.rb
  126. lib/ruby/site_ruby/3.0/bio/command.rb
  127. lib/ruby/site_ruby/3.0/bio/compat/features.rb
  128. lib/ruby/site_ruby/3.0/bio/compat/references.rb
  129. lib/ruby/site_ruby/3.0/bio/data/aa.rb
  130. lib/ruby/site_ruby/3.0/bio/data/codontable.rb
  131. lib/ruby/site_ruby/3.0/bio/data/na.rb
  132. lib/ruby/site_ruby/3.0/bio/db.rb
  133. lib/ruby/site_ruby/3.0/bio/db/aaindex.rb
  134. lib/ruby/site_ruby/3.0/bio/db/biosql/biosql_to_biosequence.rb
  135. lib/ruby/site_ruby/3.0/bio/db/biosql/sequence.rb
  136. lib/ruby/site_ruby/3.0/bio/db/embl/common.rb
  137. lib/ruby/site_ruby/3.0/bio/db/embl/embl.rb
  138. lib/ruby/site_ruby/3.0/bio/db/embl/embl_to_biosequence.rb
  139. lib/ruby/site_ruby/3.0/bio/db/embl/format_embl.rb
  140. lib/ruby/site_ruby/3.0/bio/db/embl/sptr.rb
  141. lib/ruby/site_ruby/3.0/bio/db/embl/swissprot.rb
  142. lib/ruby/site_ruby/3.0/bio/db/embl/trembl.rb
  143. lib/ruby/site_ruby/3.0/bio/db/embl/uniprot.rb
  144. lib/ruby/site_ruby/3.0/bio/db/embl/uniprotkb.rb
  145. lib/ruby/site_ruby/3.0/bio/db/fantom.rb
  146. lib/ruby/site_ruby/3.0/bio/db/fasta.rb
  147. lib/ruby/site_ruby/3.0/bio/db/fasta/defline.rb
  148. lib/ruby/site_ruby/3.0/bio/db/fasta/fasta_to_biosequence.rb
  149. lib/ruby/site_ruby/3.0/bio/db/fasta/format_fasta.rb
  150. lib/ruby/site_ruby/3.0/bio/db/fasta/format_qual.rb
  151. lib/ruby/site_ruby/3.0/bio/db/fasta/qual.rb
  152. lib/ruby/site_ruby/3.0/bio/db/fasta/qual_to_biosequence.rb
  153. lib/ruby/site_ruby/3.0/bio/db/fastq.rb
  154. lib/ruby/site_ruby/3.0/bio/db/fastq/fastq_to_biosequence.rb
  155. lib/ruby/site_ruby/3.0/bio/db/fastq/format_fastq.rb
  156. lib/ruby/site_ruby/3.0/bio/db/genbank/common.rb
  157. lib/ruby/site_ruby/3.0/bio/db/genbank/ddbj.rb
  158. lib/ruby/site_ruby/3.0/bio/db/genbank/format_genbank.rb
  159. lib/ruby/site_ruby/3.0/bio/db/genbank/genbank.rb
  160. lib/ruby/site_ruby/3.0/bio/db/genbank/genbank_to_biosequence.rb
  161. lib/ruby/site_ruby/3.0/bio/db/genbank/genpept.rb
  162. lib/ruby/site_ruby/3.0/bio/db/genbank/refseq.rb
  163. lib/ruby/site_ruby/3.0/bio/db/gff.rb
  164. lib/ruby/site_ruby/3.0/bio/db/go.rb
  165. lib/ruby/site_ruby/3.0/bio/db/kegg/brite.rb
  166. lib/ruby/site_ruby/3.0/bio/db/kegg/common.rb
  167. lib/ruby/site_ruby/3.0/bio/db/kegg/compound.rb
  168. lib/ruby/site_ruby/3.0/bio/db/kegg/drug.rb
  169. lib/ruby/site_ruby/3.0/bio/db/kegg/enzyme.rb
  170. lib/ruby/site_ruby/3.0/bio/db/kegg/expression.rb
  171. lib/ruby/site_ruby/3.0/bio/db/kegg/genes.rb
  172. lib/ruby/site_ruby/3.0/bio/db/kegg/genome.rb
  173. lib/ruby/site_ruby/3.0/bio/db/kegg/glycan.rb
  174. lib/ruby/site_ruby/3.0/bio/db/kegg/keggtab.rb
  175. lib/ruby/site_ruby/3.0/bio/db/kegg/kgml.rb
  176. lib/ruby/site_ruby/3.0/bio/db/kegg/module.rb
  177. lib/ruby/site_ruby/3.0/bio/db/kegg/orthology.rb
  178. lib/ruby/site_ruby/3.0/bio/db/kegg/pathway.rb
  179. lib/ruby/site_ruby/3.0/bio/db/kegg/reaction.rb
  180. lib/ruby/site_ruby/3.0/bio/db/lasergene.rb
  181. lib/ruby/site_ruby/3.0/bio/db/litdb.rb
  182. lib/ruby/site_ruby/3.0/bio/db/medline.rb
  183. lib/ruby/site_ruby/3.0/bio/db/nbrf.rb
  184. lib/ruby/site_ruby/3.0/bio/db/newick.rb
  185. lib/ruby/site_ruby/3.0/bio/db/nexus.rb
  186. lib/ruby/site_ruby/3.0/bio/db/pdb.rb
  187. lib/ruby/site_ruby/3.0/bio/db/pdb/atom.rb
  188. lib/ruby/site_ruby/3.0/bio/db/pdb/chain.rb
  189. lib/ruby/site_ruby/3.0/bio/db/pdb/chemicalcomponent.rb
  190. lib/ruby/site_ruby/3.0/bio/db/pdb/model.rb
  191. lib/ruby/site_ruby/3.0/bio/db/pdb/pdb.rb
  192. lib/ruby/site_ruby/3.0/bio/db/pdb/residue.rb
  193. lib/ruby/site_ruby/3.0/bio/db/pdb/utils.rb
  194. lib/ruby/site_ruby/3.0/bio/db/phyloxml/phyloxml.xsd
  195. lib/ruby/site_ruby/3.0/bio/db/phyloxml/phyloxml_elements.rb
  196. lib/ruby/site_ruby/3.0/bio/db/phyloxml/phyloxml_parser.rb
  197. lib/ruby/site_ruby/3.0/bio/db/phyloxml/phyloxml_writer.rb
  198. lib/ruby/site_ruby/3.0/bio/db/prosite.rb
  199. lib/ruby/site_ruby/3.0/bio/db/rebase.rb
  200. lib/ruby/site_ruby/3.0/bio/db/sanger_chromatogram/abif.rb
  201. lib/ruby/site_ruby/3.0/bio/db/sanger_chromatogram/chromatogram.rb
  202. lib/ruby/site_ruby/3.0/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
  203. lib/ruby/site_ruby/3.0/bio/db/sanger_chromatogram/scf.rb
  204. lib/ruby/site_ruby/3.0/bio/db/soft.rb
  205. lib/ruby/site_ruby/3.0/bio/db/transfac.rb
  206. lib/ruby/site_ruby/3.0/bio/feature.rb
  207. lib/ruby/site_ruby/3.0/bio/io/biosql/ar-biosql.rb
  208. lib/ruby/site_ruby/3.0/bio/io/biosql/biosql.rb
  209. lib/ruby/site_ruby/3.0/bio/io/biosql/config/database.yml
  210. lib/ruby/site_ruby/3.0/bio/io/das.rb
  211. lib/ruby/site_ruby/3.0/bio/io/fastacmd.rb
  212. lib/ruby/site_ruby/3.0/bio/io/fetch.rb
  213. lib/ruby/site_ruby/3.0/bio/io/flatfile.rb
  214. lib/ruby/site_ruby/3.0/bio/io/flatfile/autodetection.rb
  215. lib/ruby/site_ruby/3.0/bio/io/flatfile/bdb.rb
  216. lib/ruby/site_ruby/3.0/bio/io/flatfile/buffer.rb
  217. lib/ruby/site_ruby/3.0/bio/io/flatfile/index.rb
  218. lib/ruby/site_ruby/3.0/bio/io/flatfile/indexer.rb
  219. lib/ruby/site_ruby/3.0/bio/io/flatfile/splitter.rb
  220. lib/ruby/site_ruby/3.0/bio/io/hinv.rb
  221. lib/ruby/site_ruby/3.0/bio/io/ncbirest.rb
  222. lib/ruby/site_ruby/3.0/bio/io/pubmed.rb
  223. lib/ruby/site_ruby/3.0/bio/io/registry.rb
  224. lib/ruby/site_ruby/3.0/bio/io/sql.rb
  225. lib/ruby/site_ruby/3.0/bio/io/togows.rb
  226. lib/ruby/site_ruby/3.0/bio/location.rb
  227. lib/ruby/site_ruby/3.0/bio/map.rb
  228. lib/ruby/site_ruby/3.0/bio/pathway.rb
  229. lib/ruby/site_ruby/3.0/bio/reference.rb
  230. lib/ruby/site_ruby/3.0/bio/sequence.rb
  231. lib/ruby/site_ruby/3.0/bio/sequence/aa.rb
  232. lib/ruby/site_ruby/3.0/bio/sequence/adapter.rb
  233. lib/ruby/site_ruby/3.0/bio/sequence/common.rb
  234. lib/ruby/site_ruby/3.0/bio/sequence/compat.rb
  235. lib/ruby/site_ruby/3.0/bio/sequence/dblink.rb
  236. lib/ruby/site_ruby/3.0/bio/sequence/format.rb
  237. lib/ruby/site_ruby/3.0/bio/sequence/format_raw.rb
  238. lib/ruby/site_ruby/3.0/bio/sequence/generic.rb
  239. lib/ruby/site_ruby/3.0/bio/sequence/na.rb
  240. lib/ruby/site_ruby/3.0/bio/sequence/quality_score.rb
  241. lib/ruby/site_ruby/3.0/bio/sequence/sequence_masker.rb
  242. lib/ruby/site_ruby/3.0/bio/shell.rb
  243. lib/ruby/site_ruby/3.0/bio/shell/core.rb
  244. lib/ruby/site_ruby/3.0/bio/shell/demo.rb
  245. lib/ruby/site_ruby/3.0/bio/shell/interface.rb
  246. lib/ruby/site_ruby/3.0/bio/shell/irb.rb
  247. lib/ruby/site_ruby/3.0/bio/shell/object.rb
  248. lib/ruby/site_ruby/3.0/bio/shell/plugin/blast.rb
  249. lib/ruby/site_ruby/3.0/bio/shell/plugin/codon.rb
  250. lib/ruby/site_ruby/3.0/bio/shell/plugin/das.rb
  251. lib/ruby/site_ruby/3.0/bio/shell/plugin/emboss.rb
  252. lib/ruby/site_ruby/3.0/bio/shell/plugin/entry.rb
  253. lib/ruby/site_ruby/3.0/bio/shell/plugin/flatfile.rb
  254. lib/ruby/site_ruby/3.0/bio/shell/plugin/midi.rb
  255. lib/ruby/site_ruby/3.0/bio/shell/plugin/ncbirest.rb
  256. lib/ruby/site_ruby/3.0/bio/shell/plugin/obda.rb
  257. lib/ruby/site_ruby/3.0/bio/shell/plugin/psort.rb
  258. lib/ruby/site_ruby/3.0/bio/shell/plugin/seq.rb
  259. lib/ruby/site_ruby/3.0/bio/shell/plugin/togows.rb
  260. lib/ruby/site_ruby/3.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
  261. lib/ruby/site_ruby/3.0/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
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  277. lib/ruby/site_ruby/3.0/bio/shell/script.rb
  278. lib/ruby/site_ruby/3.0/bio/shell/setup.rb
  279. lib/ruby/site_ruby/3.0/bio/shell/web.rb
  280. lib/ruby/site_ruby/3.0/bio/tree.rb
  281. lib/ruby/site_ruby/3.0/bio/tree/output.rb
  282. lib/ruby/site_ruby/3.0/bio/util/color_scheme.rb
  283. lib/ruby/site_ruby/3.0/bio/util/color_scheme/buried.rb
  284. lib/ruby/site_ruby/3.0/bio/util/color_scheme/helix.rb
  285. lib/ruby/site_ruby/3.0/bio/util/color_scheme/hydropathy.rb
  286. lib/ruby/site_ruby/3.0/bio/util/color_scheme/nucleotide.rb
  287. lib/ruby/site_ruby/3.0/bio/util/color_scheme/strand.rb
  288. lib/ruby/site_ruby/3.0/bio/util/color_scheme/taylor.rb
  289. lib/ruby/site_ruby/3.0/bio/util/color_scheme/turn.rb
  290. lib/ruby/site_ruby/3.0/bio/util/color_scheme/zappo.rb
  291. lib/ruby/site_ruby/3.0/bio/util/contingency_table.rb
  292. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme.rb
  293. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/analysis.rb
  294. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/analysis_basic.rb
  295. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/cut_symbol.rb
  296. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/dense_int_array.rb
  297. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded.rb
  298. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
  299. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
  300. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
  301. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
  302. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
  303. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/enzymes.yaml
  304. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/cut_range.rb
  305. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/cut_ranges.rb
  306. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
  307. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/sequence_range.rb
  308. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
  309. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
  310. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
  311. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/range/vertical_cut_range.rb
  312. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/single_strand.rb
  313. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
  314. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/single_strand_complement.rb
  315. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/sorted_num_array.rb
  316. lib/ruby/site_ruby/3.0/bio/util/restriction_enzyme/string_formatting.rb
  317. lib/ruby/site_ruby/3.0/bio/util/sirna.rb
  318. lib/ruby/site_ruby/3.0/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:
  • ruby30-bio>0:biology/ruby-bio
Conflicts:
CONFLICTS_INSTALL:
  • rubygem-bio-shell
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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 ruby30-bio
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ruby30-bio
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1494171635 SHA256 (ruby/bioruby-1.5.1.tar.gz) = 872435a811f2a02000c9a5a5da5ba91c33e4a221ab8b243a69bf737df9bfb75a SIZE (ruby/bioruby-1.5.1.tar.gz) = 1478155

Packages (timestamps in pop-ups are UTC):
ruby27-bio
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--1.5.1---1.5.1-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
 

ruby30-bio
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly--------
FreeBSD:14:latest--1.5.1-----
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
 

ruby31-bio
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.5.1--1.5.1----
FreeBSD:13:quarterly1.5.11.5.11.5.11.5.11.5.11.5.11.5.11.5.1
FreeBSD:14:latest1.5.1--1.5.1-1.5.1-1.5.1
FreeBSD:14:quarterly1.5.11.5.1-1.5.11.5.11.5.11.5.11.5.1
FreeBSD:15:latest1.5.1-n/a1.5.1n/a1.5.11.5.11.5.1
FreeBSD:15:quarterly--n/a-n/a---
 

ruby32-bio
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-1.5.1--1.5.1---
FreeBSD:13:quarterly--------
FreeBSD:14:latest-1.5.1--1.5.1---
FreeBSD:14:quarterly--------
FreeBSD:15:latest-1.5.1n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ruby30 : lang/ruby30
Runtime dependencies:
  1. ruby30 : lang/ruby30
Patch dependencies:
  1. ruby30 : lang/ruby30
Extract dependencies:
  1. ruby30 : lang/ruby30
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for ruby30-bio-1.5.1: BDB4=off: bdb4 support for faster flat file indexing DOCS=on: Build and/or install documentation MYSQL=off: MySQL database support PGSQL=off: PostgreSQL database support ===> Use 'make config' to modify these settings
Options name:
biology_ruby-bio
USES:
ruby:setup shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://bioruby.org/archive/
Collapse this list.

Number of commits found: 47

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.5.1
14 Jan 2023 23:08:33
commit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9ae files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby

Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk

Notable changes are.

- Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk.
- USE_RUBY=yes is replaced with USES=ruby.
- USE_RUBY_EXTCONF is replaced with USES=ruby:extconf.
- USE_RUBY_RDOC is replaced with USES=ruby:rdoc.
- USE_RUBY_SETUP is replaces with USES=ruby:setup.
- RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with
  USES=ruby:{build,none,run}.
- RUBY_REQUIRE isn't used anywhere, so removed.
- USES=gem now implies USES=ruby.

This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863

I have just made some cosmetic changes and ran exp-run to test that the
tree is not in a BROKEN state.

Approved by:	portmgr
Differential Revision:	https://reviews.freebsd.org/D37925
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.5.1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.5.1
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.5.1
10 Jan 2022 15:15:39
commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.5.1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.5.1
05 May 2020 14:22:09
Revision:534089Original commit files touched by this commit
rene search for other commits by this committer
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
1.5.1
07 May 2017 15:44:34
Revision:440343Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.5.1
1.5.0
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
1.5.0
31 Mar 2016 17:36:55
Revision:412278Original commit files touched by this commit
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)
1.4.1
17 Jan 2016 07:06:25
Revision:406285Original commit files touched by this commit
swills search for other commits by this committer
mark ports that don't work with Ruby 2.3

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

Approved by:	portmgr (blanket)
1.4.1
03 Sep 2015 16:23:37
Revision:395991Original commit files touched by this commit
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
1.4.1
17 Aug 2015 14:20:41
Revision:394508Original commit files touched by this commit
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
1.4.1
03 Apr 2015 13:50:39
Revision:383123Original commit files touched by this commit
swills search for other commits by this committer
biology/ruby-bio: mark broken with ruby 2.2
1.4.1
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.4.1
21 Sep 2014 13:44:59
Revision:368754Original commit files touched by this commit
dinoex search for other commits by this committer
- any version for RUN_DEPENDS
1.4.1
21 Sep 2014 09:51:18
Revision:368736Original commit files touched by this commit
dinoex search for other commits by this committer
- update RUN_DEPENDS for rubygems-dbi
1.4.1
07 Apr 2014 13:01:27
Revision:350461Original commit files touched by this commit
bapt search for other commits by this committer
Support stage
1.4.1
15 Jan 2014 22:52:28
Revision:339846Original commit files touched by this commit
bapt search for other commits by this committer
Reduce over inclusion of bsd.port.mk
1.4.1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.4.1
18 Mar 2013 06:55:42
Revision:314532Original commit files touched by this commit
jgh search for other commits by this committer
- adoption of optionsNG
- trim historical header

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

Reported by:    pointyhat via pav
1.4.1
27 Dec 2010 15:11:50
Original commit files touched by this commit
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
1.4.0
08 Jun 2010 00:18:54
Original commit files touched by this commit
pgollucci search for other commits by this committer
- Update to 1.4.0
- Sort pkg-plist
- seperate NOPORTDOCS and NOPORTEXAMPLES
1.1.0
24 Oct 2007 01:38:51
Original commit files touched by this commit
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)
1.0.0
25 Apr 2006 22:09:29
Original commit files touched by this commit
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>
0.6.2
24 Nov 2005 00:04:00
Original commit files touched by this commit
pav search for other commits by this committer
- Add SHA256
0.6.2
11 Nov 2005 01:18:01
Original commit files touched by this commit
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.
0.6.2
25 Dec 2004 17:52:46
Original commit files touched by this commit
knu search for other commits by this committer
Update to 0.6.2.
0.5.3
06 Jul 2004 14:31:55
Original commit files touched by this commit
vs search for other commits by this committer
Fix distsite

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

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

Number of commits found: 47