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4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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1 # This file is automatically generated from bioruby.gemspec.erb and
2 # should NOT be edited by hand.
3 #
4 Gem::Specification.new do |s|
5 s.name = 'bio'
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6 s.version = "1.3.9.9901"
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7
8 s.author = "BioRuby project"
9 s.email = "staff@bioruby.org"
10 s.homepage = "http://bioruby.org/"
11 s.rubyforge_project = "bioruby"
12 s.summary = "Bioinformatics library"
13 s.description = "BioRuby is a library for bioinformatics (biology + information science)."
14
15 s.platform = Gem::Platform::RUBY
16 s.files = [
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17 "COPYING",
18 "COPYING.ja",
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19 "ChangeLog",
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20 "GPL",
06b1026 Naohisa Goto KNOWN_ISSUES.rdoc describes known issues and bugs in current BioRuby
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21 "KNOWN_ISSUES.rdoc",
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22 "LEGAL",
23 "LGPL",
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24 "README.rdoc",
25 "README_DEV.rdoc",
26 "Rakefile",
27 "bin/bioruby",
28 "bin/br_biofetch.rb",
29 "bin/br_bioflat.rb",
30 "bin/br_biogetseq.rb",
31 "bin/br_pmfetch.rb",
32 "bioruby.gemspec",
33 "bioruby.gemspec.erb",
34 "doc/Changes-0.7.rd",
35 "doc/Changes-1.3.rdoc",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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36 "doc/Changes-1.4.rdoc",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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37 "doc/KEGG_API.rd",
38 "doc/KEGG_API.rd.ja",
39 "doc/Tutorial.rd",
e8cb0db Naohisa Goto bioruby.gemspec is regenerated
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40 "doc/Tutorial.rd.html",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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41 "doc/Tutorial.rd.ja",
e8cb0db Naohisa Goto bioruby.gemspec is regenerated
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42 "doc/Tutorial.rd.ja.html",
43 "doc/bioruby.css",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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44 "etc/bioinformatics/seqdatabase.ini",
45 "extconf.rb",
46 "lib/bio.rb",
47 "lib/bio/alignment.rb",
48 "lib/bio/appl/bl2seq/report.rb",
49 "lib/bio/appl/blast.rb",
50 "lib/bio/appl/blast/ddbj.rb",
51 "lib/bio/appl/blast/format0.rb",
52 "lib/bio/appl/blast/format8.rb",
53 "lib/bio/appl/blast/genomenet.rb",
54 "lib/bio/appl/blast/ncbioptions.rb",
55 "lib/bio/appl/blast/remote.rb",
56 "lib/bio/appl/blast/report.rb",
57 "lib/bio/appl/blast/rexml.rb",
58 "lib/bio/appl/blast/rpsblast.rb",
59 "lib/bio/appl/blast/wublast.rb",
60 "lib/bio/appl/blast/xmlparser.rb",
61 "lib/bio/appl/blat/report.rb",
62 "lib/bio/appl/clustalw.rb",
63 "lib/bio/appl/clustalw/report.rb",
64 "lib/bio/appl/emboss.rb",
65 "lib/bio/appl/fasta.rb",
66 "lib/bio/appl/fasta/format10.rb",
67 "lib/bio/appl/gcg/msf.rb",
68 "lib/bio/appl/gcg/seq.rb",
69 "lib/bio/appl/genscan/report.rb",
70 "lib/bio/appl/hmmer.rb",
71 "lib/bio/appl/hmmer/report.rb",
72 "lib/bio/appl/iprscan/report.rb",
73 "lib/bio/appl/mafft.rb",
74 "lib/bio/appl/mafft/report.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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75 "lib/bio/appl/meme/mast.rb",
76 "lib/bio/appl/meme/mast/report.rb",
77 "lib/bio/appl/meme/motif.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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78 "lib/bio/appl/muscle.rb",
79 "lib/bio/appl/paml/baseml.rb",
80 "lib/bio/appl/paml/baseml/report.rb",
81 "lib/bio/appl/paml/codeml.rb",
82 "lib/bio/appl/paml/codeml/rates.rb",
83 "lib/bio/appl/paml/codeml/report.rb",
84 "lib/bio/appl/paml/common.rb",
85 "lib/bio/appl/paml/common_report.rb",
86 "lib/bio/appl/paml/yn00.rb",
87 "lib/bio/appl/paml/yn00/report.rb",
88 "lib/bio/appl/phylip/alignment.rb",
89 "lib/bio/appl/phylip/distance_matrix.rb",
90 "lib/bio/appl/probcons.rb",
91 "lib/bio/appl/psort.rb",
92 "lib/bio/appl/psort/report.rb",
93 "lib/bio/appl/pts1.rb",
94 "lib/bio/appl/sim4.rb",
95 "lib/bio/appl/sim4/report.rb",
96 "lib/bio/appl/sosui/report.rb",
97 "lib/bio/appl/spidey/report.rb",
98 "lib/bio/appl/targetp/report.rb",
99 "lib/bio/appl/tcoffee.rb",
100 "lib/bio/appl/tmhmm/report.rb",
101 "lib/bio/command.rb",
102 "lib/bio/compat/features.rb",
103 "lib/bio/compat/references.rb",
104 "lib/bio/data/aa.rb",
105 "lib/bio/data/codontable.rb",
106 "lib/bio/data/na.rb",
107 "lib/bio/db.rb",
108 "lib/bio/db/aaindex.rb",
109 "lib/bio/db/biosql/biosql_to_biosequence.rb",
110 "lib/bio/db/biosql/sequence.rb",
111 "lib/bio/db/embl/common.rb",
112 "lib/bio/db/embl/embl.rb",
113 "lib/bio/db/embl/embl_to_biosequence.rb",
114 "lib/bio/db/embl/format_embl.rb",
115 "lib/bio/db/embl/sptr.rb",
116 "lib/bio/db/embl/swissprot.rb",
117 "lib/bio/db/embl/trembl.rb",
118 "lib/bio/db/embl/uniprot.rb",
119 "lib/bio/db/fantom.rb",
120 "lib/bio/db/fasta.rb",
121 "lib/bio/db/fasta/defline.rb",
122 "lib/bio/db/fasta/fasta_to_biosequence.rb",
123 "lib/bio/db/fasta/format_fasta.rb",
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124 "lib/bio/db/fasta/format_qual.rb",
125 "lib/bio/db/fasta/qual.rb",
126 "lib/bio/db/fastq.rb",
127 "lib/bio/db/fastq/fastq_to_biosequence.rb",
128 "lib/bio/db/fastq/format_fastq.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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129 "lib/bio/db/genbank/common.rb",
130 "lib/bio/db/genbank/ddbj.rb",
131 "lib/bio/db/genbank/format_genbank.rb",
132 "lib/bio/db/genbank/genbank.rb",
133 "lib/bio/db/genbank/genbank_to_biosequence.rb",
134 "lib/bio/db/genbank/genpept.rb",
135 "lib/bio/db/genbank/refseq.rb",
136 "lib/bio/db/gff.rb",
137 "lib/bio/db/go.rb",
138 "lib/bio/db/kegg/brite.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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139 "lib/bio/db/kegg/common.rb",
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140 "lib/bio/db/kegg/compound.rb",
141 "lib/bio/db/kegg/drug.rb",
142 "lib/bio/db/kegg/enzyme.rb",
143 "lib/bio/db/kegg/expression.rb",
144 "lib/bio/db/kegg/genes.rb",
145 "lib/bio/db/kegg/genome.rb",
146 "lib/bio/db/kegg/glycan.rb",
147 "lib/bio/db/kegg/keggtab.rb",
148 "lib/bio/db/kegg/kgml.rb",
149 "lib/bio/db/kegg/orthology.rb",
150 "lib/bio/db/kegg/reaction.rb",
151 "lib/bio/db/kegg/taxonomy.rb",
152 "lib/bio/db/lasergene.rb",
153 "lib/bio/db/litdb.rb",
154 "lib/bio/db/medline.rb",
155 "lib/bio/db/nbrf.rb",
156 "lib/bio/db/newick.rb",
157 "lib/bio/db/nexus.rb",
158 "lib/bio/db/pdb.rb",
159 "lib/bio/db/pdb/atom.rb",
160 "lib/bio/db/pdb/chain.rb",
161 "lib/bio/db/pdb/chemicalcomponent.rb",
162 "lib/bio/db/pdb/model.rb",
163 "lib/bio/db/pdb/pdb.rb",
164 "lib/bio/db/pdb/residue.rb",
165 "lib/bio/db/pdb/utils.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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166 "lib/bio/db/phyloxml/phyloxml.xsd",
167 "lib/bio/db/phyloxml/phyloxml_elements.rb",
168 "lib/bio/db/phyloxml/phyloxml_parser.rb",
169 "lib/bio/db/phyloxml/phyloxml_writer.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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170 "lib/bio/db/prosite.rb",
171 "lib/bio/db/rebase.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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172 "lib/bio/db/sanger_chromatogram/abif.rb",
173 "lib/bio/db/sanger_chromatogram/chromatogram.rb",
174 "lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
175 "lib/bio/db/sanger_chromatogram/scf.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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176 "lib/bio/db/soft.rb",
177 "lib/bio/db/transfac.rb",
178 "lib/bio/feature.rb",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
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179 "lib/bio/io/biosql/ar-biosql.rb",
180 "lib/bio/io/biosql/biosql.rb",
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181 "lib/bio/io/biosql/config/database.yml",
182 "lib/bio/io/das.rb",
183 "lib/bio/io/dbget.rb",
184 "lib/bio/io/ddbjxml.rb",
185 "lib/bio/io/ebisoap.rb",
186 "lib/bio/io/ensembl.rb",
187 "lib/bio/io/fastacmd.rb",
188 "lib/bio/io/fetch.rb",
189 "lib/bio/io/flatfile.rb",
190 "lib/bio/io/flatfile/autodetection.rb",
191 "lib/bio/io/flatfile/bdb.rb",
192 "lib/bio/io/flatfile/buffer.rb",
193 "lib/bio/io/flatfile/index.rb",
194 "lib/bio/io/flatfile/indexer.rb",
195 "lib/bio/io/flatfile/splitter.rb",
196 "lib/bio/io/higet.rb",
197 "lib/bio/io/hinv.rb",
198 "lib/bio/io/keggapi.rb",
199 "lib/bio/io/ncbirest.rb",
200 "lib/bio/io/ncbisoap.rb",
201 "lib/bio/io/pubmed.rb",
202 "lib/bio/io/registry.rb",
203 "lib/bio/io/soapwsdl.rb",
204 "lib/bio/io/sql.rb",
21333cd Naohisa Goto bioruby.gemspec is regenerated
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205 "lib/bio/io/togows.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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206 "lib/bio/location.rb",
207 "lib/bio/map.rb",
208 "lib/bio/pathway.rb",
209 "lib/bio/reference.rb",
210 "lib/bio/sequence.rb",
211 "lib/bio/sequence/aa.rb",
212 "lib/bio/sequence/adapter.rb",
213 "lib/bio/sequence/common.rb",
214 "lib/bio/sequence/compat.rb",
215 "lib/bio/sequence/dblink.rb",
216 "lib/bio/sequence/format.rb",
217 "lib/bio/sequence/format_raw.rb",
218 "lib/bio/sequence/generic.rb",
219 "lib/bio/sequence/na.rb",
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220 "lib/bio/sequence/quality_score.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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221 "lib/bio/shell.rb",
222 "lib/bio/shell/core.rb",
223 "lib/bio/shell/demo.rb",
224 "lib/bio/shell/interface.rb",
225 "lib/bio/shell/irb.rb",
226 "lib/bio/shell/object.rb",
227 "lib/bio/shell/plugin/blast.rb",
228 "lib/bio/shell/plugin/codon.rb",
229 "lib/bio/shell/plugin/das.rb",
230 "lib/bio/shell/plugin/emboss.rb",
231 "lib/bio/shell/plugin/entry.rb",
232 "lib/bio/shell/plugin/flatfile.rb",
233 "lib/bio/shell/plugin/keggapi.rb",
234 "lib/bio/shell/plugin/midi.rb",
06b1026 Naohisa Goto KNOWN_ISSUES.rdoc describes known issues and bugs in current BioRuby
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235 "lib/bio/shell/plugin/ncbirest.rb",
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236 "lib/bio/shell/plugin/obda.rb",
237 "lib/bio/shell/plugin/psort.rb",
238 "lib/bio/shell/plugin/seq.rb",
239 "lib/bio/shell/plugin/soap.rb",
21333cd Naohisa Goto bioruby.gemspec is regenerated
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240 "lib/bio/shell/plugin/togows.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
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241 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
242 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
243 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
244 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
245 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
246 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
247 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
248 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
249 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
250 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
251 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
252 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
253 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
254 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
255 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
256 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
257 "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
258 "lib/bio/shell/script.rb",
259 "lib/bio/shell/setup.rb",
260 "lib/bio/shell/web.rb",
261 "lib/bio/tree.rb",
262 "lib/bio/util/color_scheme.rb",
263 "lib/bio/util/color_scheme/buried.rb",
264 "lib/bio/util/color_scheme/helix.rb",
265 "lib/bio/util/color_scheme/hydropathy.rb",
266 "lib/bio/util/color_scheme/nucleotide.rb",
267 "lib/bio/util/color_scheme/strand.rb",
268 "lib/bio/util/color_scheme/taylor.rb",
269 "lib/bio/util/color_scheme/turn.rb",
270 "lib/bio/util/color_scheme/zappo.rb",
271 "lib/bio/util/contingency_table.rb",
272 "lib/bio/util/restriction_enzyme.rb",
273 "lib/bio/util/restriction_enzyme/analysis.rb",
274 "lib/bio/util/restriction_enzyme/analysis_basic.rb",
275 "lib/bio/util/restriction_enzyme/cut_symbol.rb",
276 "lib/bio/util/restriction_enzyme/double_stranded.rb",
277 "lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb",
278 "lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb",
279 "lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb",
280 "lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb",
281 "lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb",
282 "lib/bio/util/restriction_enzyme/enzymes.yaml",
283 "lib/bio/util/restriction_enzyme/range/cut_range.rb",
284 "lib/bio/util/restriction_enzyme/range/cut_ranges.rb",
285 "lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb",
286 "lib/bio/util/restriction_enzyme/range/sequence_range.rb",
287 "lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb",
288 "lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb",
289 "lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb",
290 "lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb",
291 "lib/bio/util/restriction_enzyme/single_strand.rb",
292 "lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb",
293 "lib/bio/util/restriction_enzyme/single_strand_complement.rb",
294 "lib/bio/util/restriction_enzyme/string_formatting.rb",
295 "lib/bio/util/sirna.rb",
21333cd Naohisa Goto bioruby.gemspec is regenerated
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296 "lib/bio/version.rb",
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297 "rdoc.zsh",
298 "sample/any2fasta.rb",
299 "sample/biofetch.rb",
300 "sample/color_scheme_na.rb",
301 "sample/dbget",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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302 "sample/demo_aaindex.rb",
303 "sample/demo_aminoacid.rb",
304 "sample/demo_bl2seq_report.rb",
305 "sample/demo_blast_report.rb",
306 "sample/demo_codontable.rb",
307 "sample/demo_das.rb",
308 "sample/demo_ddbjxml.rb",
309 "sample/demo_fasta_remote.rb",
310 "sample/demo_fastaformat.rb",
311 "sample/demo_genbank.rb",
312 "sample/demo_genscan_report.rb",
313 "sample/demo_gff1.rb",
314 "sample/demo_go.rb",
315 "sample/demo_hmmer_report.rb",
316 "sample/demo_kegg_compound.rb",
317 "sample/demo_kegg_drug.rb",
318 "sample/demo_kegg_genome.rb",
319 "sample/demo_kegg_glycan.rb",
320 "sample/demo_kegg_orthology.rb",
321 "sample/demo_kegg_reaction.rb",
322 "sample/demo_kegg_taxonomy.rb",
323 "sample/demo_keggapi.rb",
324 "sample/demo_litdb.rb",
325 "sample/demo_locations.rb",
326 "sample/demo_ncbi_rest.rb",
327 "sample/demo_nucleicacid.rb",
328 "sample/demo_pathway.rb",
329 "sample/demo_prosite.rb",
330 "sample/demo_psort.rb",
331 "sample/demo_psort_report.rb",
332 "sample/demo_pubmed.rb",
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333 "sample/demo_sequence.rb",
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334 "sample/demo_sirna.rb",
335 "sample/demo_sosui_report.rb",
336 "sample/demo_targetp_report.rb",
337 "sample/demo_tmhmm_report.rb",
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338 "sample/enzymes.rb",
339 "sample/fasta2tab.rb",
340 "sample/fastagrep.rb",
341 "sample/fastasort.rb",
342 "sample/fsplit.rb",
343 "sample/gb2fasta.rb",
344 "sample/gb2tab.rb",
345 "sample/gbtab2mysql.rb",
346 "sample/genes2nuc.rb",
347 "sample/genes2pep.rb",
348 "sample/genes2tab.rb",
349 "sample/genome2rb.rb",
350 "sample/genome2tab.rb",
351 "sample/goslim.rb",
352 "sample/gt2fasta.rb",
353 "sample/na2aa.rb",
354 "sample/pmfetch.rb",
355 "sample/pmsearch.rb",
356 "sample/psortplot_html.rb",
357 "sample/ssearch2tab.rb",
358 "sample/tdiary.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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359 "sample/test_phyloxml_big.rb",
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360 "sample/tfastx2tab.rb",
361 "sample/vs-genes.rb",
362 "setup.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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363 "test/bioruby_test_helper.rb",
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364 "test/data/HMMER/hmmpfam.out",
365 "test/data/HMMER/hmmsearch.out",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
366 "test/data/KEGG/1.1.1.1.enzyme",
367 "test/data/KEGG/C00025.compound",
aeacbbd Naohisa Goto bioruby.gemspec is regenerated
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368 "test/data/KEGG/D00063.drug",
369 "test/data/KEGG/G00024.glycan",
370 "test/data/KEGG/G01366.glycan",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
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371 "test/data/KEGG/K02338.orthology",
372 "test/data/KEGG/R00006.reaction",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
373 "test/data/SOSUI/sample.report",
374 "test/data/TMHMM/sample.report",
375 "test/data/aaindex/DAYM780301",
376 "test/data/aaindex/PRAM900102",
377 "test/data/bl2seq/cd8a_cd8b_blastp.bl2seq",
378 "test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq",
379 "test/data/blast/2.2.15.blastp.m7",
380 "test/data/blast/b0002.faa",
381 "test/data/blast/b0002.faa.m0",
382 "test/data/blast/b0002.faa.m7",
383 "test/data/blast/b0002.faa.m8",
384 "test/data/blast/blastp-multi.m7",
385 "test/data/command/echoarg2.bat",
386 "test/data/embl/AB090716.embl",
387 "test/data/embl/AB090716.embl.rel89",
388 "test/data/fasta/example1.txt",
389 "test/data/fasta/example2.txt",
aeacbbd Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
390 "test/data/fastq/README.txt",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
391 "test/data/fastq/error_diff_ids.fastq",
392 "test/data/fastq/error_double_qual.fastq",
393 "test/data/fastq/error_double_seq.fastq",
394 "test/data/fastq/error_long_qual.fastq",
395 "test/data/fastq/error_no_qual.fastq",
396 "test/data/fastq/error_qual_del.fastq",
397 "test/data/fastq/error_qual_escape.fastq",
398 "test/data/fastq/error_qual_null.fastq",
399 "test/data/fastq/error_qual_space.fastq",
400 "test/data/fastq/error_qual_tab.fastq",
401 "test/data/fastq/error_qual_unit_sep.fastq",
402 "test/data/fastq/error_qual_vtab.fastq",
403 "test/data/fastq/error_short_qual.fastq",
404 "test/data/fastq/error_spaces.fastq",
405 "test/data/fastq/error_tabs.fastq",
406 "test/data/fastq/error_trunc_at_plus.fastq",
407 "test/data/fastq/error_trunc_at_qual.fastq",
408 "test/data/fastq/error_trunc_at_seq.fastq",
409 "test/data/fastq/error_trunc_in_plus.fastq",
410 "test/data/fastq/error_trunc_in_qual.fastq",
411 "test/data/fastq/error_trunc_in_seq.fastq",
412 "test/data/fastq/error_trunc_in_title.fastq",
413 "test/data/fastq/illumina_full_range_as_illumina.fastq",
414 "test/data/fastq/illumina_full_range_as_sanger.fastq",
415 "test/data/fastq/illumina_full_range_as_solexa.fastq",
416 "test/data/fastq/illumina_full_range_original_illumina.fastq",
417 "test/data/fastq/longreads_as_illumina.fastq",
418 "test/data/fastq/longreads_as_sanger.fastq",
419 "test/data/fastq/longreads_as_solexa.fastq",
420 "test/data/fastq/longreads_original_sanger.fastq",
421 "test/data/fastq/misc_dna_as_illumina.fastq",
422 "test/data/fastq/misc_dna_as_sanger.fastq",
423 "test/data/fastq/misc_dna_as_solexa.fastq",
424 "test/data/fastq/misc_dna_original_sanger.fastq",
425 "test/data/fastq/misc_rna_as_illumina.fastq",
426 "test/data/fastq/misc_rna_as_sanger.fastq",
427 "test/data/fastq/misc_rna_as_solexa.fastq",
428 "test/data/fastq/misc_rna_original_sanger.fastq",
429 "test/data/fastq/sanger_full_range_as_illumina.fastq",
430 "test/data/fastq/sanger_full_range_as_sanger.fastq",
431 "test/data/fastq/sanger_full_range_as_solexa.fastq",
432 "test/data/fastq/sanger_full_range_original_sanger.fastq",
433 "test/data/fastq/solexa_full_range_as_illumina.fastq",
434 "test/data/fastq/solexa_full_range_as_sanger.fastq",
435 "test/data/fastq/solexa_full_range_as_solexa.fastq",
436 "test/data/fastq/solexa_full_range_original_solexa.fastq",
437 "test/data/fastq/wrapping_as_illumina.fastq",
438 "test/data/fastq/wrapping_as_sanger.fastq",
439 "test/data/fastq/wrapping_as_solexa.fastq",
440 "test/data/fastq/wrapping_original_sanger.fastq",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
441 "test/data/gcg/pileup-aa.msf",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
442 "test/data/genscan/sample.report",
443 "test/data/iprscan/merged.raw",
444 "test/data/iprscan/merged.txt",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
445 "test/data/meme/db",
446 "test/data/meme/mast",
447 "test/data/meme/mast.out",
448 "test/data/meme/meme.out",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
449 "test/data/paml/codeml/control_file.txt",
450 "test/data/paml/codeml/output.txt",
451 "test/data/paml/codeml/rates",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
452 "test/data/phyloxml/apaf.xml",
453 "test/data/phyloxml/bcl_2.xml",
454 "test/data/phyloxml/made_up.xml",
455 "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
456 "test/data/phyloxml/phyloxml_examples.xml",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
457 "test/data/prosite/prosite.dat",
458 "test/data/refseq/nm_126355.entret",
459 "test/data/rpsblast/misc.rpsblast",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
460 "test/data/sanger_chromatogram/test_chromatogram_abif.ab1",
461 "test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf",
462 "test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
463 "test/data/sim4/complement-A4.sim4",
464 "test/data/sim4/simple-A4.sim4",
465 "test/data/sim4/simple2-A4.sim4",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
466 "test/data/soft/GDS100_partial.soft",
467 "test/data/soft/GSE3457_family_partial.soft",
468 "test/data/uniprot/p53_human.uniprot",
469 "test/functional/bio/appl/test_pts1.rb",
470 "test/functional/bio/io/test_ensembl.rb",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
471 "test/functional/bio/io/test_pubmed.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
472 "test/functional/bio/io/test_soapwsdl.rb",
21333cd Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
473 "test/functional/bio/io/test_togows.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
474 "test/functional/bio/sequence/test_output_embl.rb",
475 "test/functional/bio/test_command.rb",
476 "test/runner.rb",
477 "test/unit/bio/appl/bl2seq/test_report.rb",
478 "test/unit/bio/appl/blast/test_ncbioptions.rb",
479 "test/unit/bio/appl/blast/test_report.rb",
480 "test/unit/bio/appl/blast/test_rpsblast.rb",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
481 "test/unit/bio/appl/gcg/test_msf.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
482 "test/unit/bio/appl/genscan/test_report.rb",
483 "test/unit/bio/appl/hmmer/test_report.rb",
484 "test/unit/bio/appl/iprscan/test_report.rb",
485 "test/unit/bio/appl/mafft/test_report.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
486 "test/unit/bio/appl/meme/mast/test_report.rb",
487 "test/unit/bio/appl/meme/test_mast.rb",
488 "test/unit/bio/appl/meme/test_motif.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
489 "test/unit/bio/appl/paml/codeml/test_rates.rb",
490 "test/unit/bio/appl/paml/codeml/test_report.rb",
491 "test/unit/bio/appl/paml/test_codeml.rb",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
492 "test/unit/bio/appl/sim4/test_report.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
493 "test/unit/bio/appl/sosui/test_report.rb",
494 "test/unit/bio/appl/targetp/test_report.rb",
495 "test/unit/bio/appl/test_blast.rb",
496 "test/unit/bio/appl/test_fasta.rb",
497 "test/unit/bio/appl/test_pts1.rb",
498 "test/unit/bio/appl/tmhmm/test_report.rb",
499 "test/unit/bio/data/test_aa.rb",
500 "test/unit/bio/data/test_codontable.rb",
501 "test/unit/bio/data/test_na.rb",
2af5ef1 Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
502 "test/unit/bio/db/biosql/tc_biosql.rb",
503 "test/unit/bio/db/biosql/ts_suite_biosql.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
504 "test/unit/bio/db/embl/test_common.rb",
505 "test/unit/bio/db/embl/test_embl.rb",
506 "test/unit/bio/db/embl/test_embl_rel89.rb",
507 "test/unit/bio/db/embl/test_embl_to_bioseq.rb",
508 "test/unit/bio/db/embl/test_sptr.rb",
509 "test/unit/bio/db/embl/test_uniprot.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
510 "test/unit/bio/db/fasta/test_format_qual.rb",
511 "test/unit/bio/db/kegg/test_compound.rb",
aeacbbd Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
512 "test/unit/bio/db/kegg/test_drug.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
513 "test/unit/bio/db/kegg/test_enzyme.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
514 "test/unit/bio/db/kegg/test_genes.rb",
aeacbbd Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
515 "test/unit/bio/db/kegg/test_glycan.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
516 "test/unit/bio/db/kegg/test_orthology.rb",
517 "test/unit/bio/db/kegg/test_reaction.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
518 "test/unit/bio/db/pdb/test_pdb.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
519 "test/unit/bio/db/sanger_chromatogram/test_abif.rb",
520 "test/unit/bio/db/sanger_chromatogram/test_scf.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
521 "test/unit/bio/db/test_aaindex.rb",
522 "test/unit/bio/db/test_fasta.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
523 "test/unit/bio/db/test_fastq.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
524 "test/unit/bio/db/test_gff.rb",
525 "test/unit/bio/db/test_lasergene.rb",
526 "test/unit/bio/db/test_medline.rb",
527 "test/unit/bio/db/test_newick.rb",
528 "test/unit/bio/db/test_nexus.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
529 "test/unit/bio/db/test_phyloxml.rb",
530 "test/unit/bio/db/test_phyloxml_writer.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
531 "test/unit/bio/db/test_prosite.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
532 "test/unit/bio/db/test_qual.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
533 "test/unit/bio/db/test_rebase.rb",
534 "test/unit/bio/db/test_soft.rb",
535 "test/unit/bio/io/flatfile/test_autodetection.rb",
536 "test/unit/bio/io/flatfile/test_buffer.rb",
537 "test/unit/bio/io/flatfile/test_splitter.rb",
538 "test/unit/bio/io/test_ddbjxml.rb",
539 "test/unit/bio/io/test_ensembl.rb",
540 "test/unit/bio/io/test_fastacmd.rb",
541 "test/unit/bio/io/test_flatfile.rb",
542 "test/unit/bio/io/test_soapwsdl.rb",
21333cd Naohisa Goto bioruby.gemspec is regenerated
ngoto authored
543 "test/unit/bio/io/test_togows.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
544 "test/unit/bio/sequence/test_aa.rb",
545 "test/unit/bio/sequence/test_common.rb",
546 "test/unit/bio/sequence/test_compat.rb",
547 "test/unit/bio/sequence/test_dblink.rb",
548 "test/unit/bio/sequence/test_na.rb",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
549 "test/unit/bio/sequence/test_quality_score.rb",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
550 "test/unit/bio/shell/plugin/test_seq.rb",
551 "test/unit/bio/test_alignment.rb",
552 "test/unit/bio/test_command.rb",
553 "test/unit/bio/test_db.rb",
554 "test/unit/bio/test_feature.rb",
555 "test/unit/bio/test_location.rb",
556 "test/unit/bio/test_map.rb",
557 "test/unit/bio/test_pathway.rb",
558 "test/unit/bio/test_reference.rb",
559 "test/unit/bio/test_sequence.rb",
560 "test/unit/bio/test_shell.rb",
561 "test/unit/bio/test_tree.rb",
562 "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
563 "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
564 "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb",
565 "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb",
566 "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb",
567 "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb",
568 "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb",
569 "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb",
570 "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb",
571 "test/unit/bio/util/restriction_enzyme/test_analysis.rb",
572 "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb",
573 "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb",
574 "test/unit/bio/util/restriction_enzyme/test_single_strand.rb",
575 "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb",
576 "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb",
577 "test/unit/bio/util/test_color_scheme.rb",
578 "test/unit/bio/util/test_contingency_table.rb",
579 "test/unit/bio/util/test_restriction_enzyme.rb",
580 "test/unit/bio/util/test_sirna.rb"
581 ]
582
583 s.has_rdoc = true
584 s.extra_rdoc_files = [
e04da7a Naohisa Goto BioRuby 1.3.0 is released.
ngoto authored
585 "ChangeLog",
06b1026 Naohisa Goto KNOWN_ISSUES.rdoc describes known issues and bugs in current BioRuby
ngoto authored
586 "KNOWN_ISSUES.rdoc",
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
587 "README.rdoc",
588 "README_DEV.rdoc",
f364ea6 Naohisa Goto Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
ngoto authored
589 "doc/Changes-1.3.rdoc",
590 "doc/Changes-1.4.rdoc"
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
591 ]
592 s.rdoc_options << '--main' << 'README.rdoc'
4e1cd3b Naohisa Goto Automatically gemerated bioruby.gemspec from bioruby.gemsepc.erb
ngoto authored
593 s.rdoc_options << '--title' << 'BioRuby API documentation'
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
594 s.rdoc_options << '--exclude' << '\.yaml\z'
4e1cd3b Naohisa Goto Automatically gemerated bioruby.gemspec from bioruby.gemsepc.erb
ngoto authored
595 s.rdoc_options << '--line-numbers' << '--inline-source'
4c54597 Naohisa Goto Added bioruby.gemspec created from bioruby.gemspec.erb
ngoto authored
596
597 s.require_path = 'lib'
598 s.autorequire = 'bio'
599
600 s.bindir = "bin"
601 s.executables = [
602 "bioruby",
603 "br_biofetch.rb",
604 "br_bioflat.rb",
605 "br_biogetseq.rb",
606 "br_pmfetch.rb"
607 ]
608 s.default_executable = "bioruby"
609 end
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