forked from bioruby/bioruby
/
bioruby.gemspec
646 lines (641 loc) · 25.3 KB
/
bioruby.gemspec
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# This file is automatically generated from bioruby.gemspec.erb and
# should NOT be edited by hand.
#
Gem::Specification.new do |s|
s.name = 'bio'
s.version = "1.4.1.5000"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
s.rubyforge_project = "bioruby"
s.summary = "Bioinformatics library"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.platform = Gem::Platform::RUBY
s.files = [
"COPYING",
"COPYING.ja",
"ChangeLog",
"GPL",
"KNOWN_ISSUES.rdoc",
"LEGAL",
"LGPL",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"Rakefile",
"bin/bioruby",
"bin/br_biofetch.rb",
"bin/br_bioflat.rb",
"bin/br_biogetseq.rb",
"bin/br_pmfetch.rb",
"bioruby.gemspec",
"bioruby.gemspec.erb",
"doc/ChangeLog-before-1.3.1",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
"doc/KEGG_API.rd",
"doc/KEGG_API.rd.ja",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
"etc/bioinformatics/seqdatabase.ini",
"extconf.rb",
"lib/bio.rb",
"lib/bio/alignment.rb",
"lib/bio/appl/bl2seq/report.rb",
"lib/bio/appl/blast.rb",
"lib/bio/appl/blast/ddbj.rb",
"lib/bio/appl/blast/format0.rb",
"lib/bio/appl/blast/format8.rb",
"lib/bio/appl/blast/genomenet.rb",
"lib/bio/appl/blast/ncbioptions.rb",
"lib/bio/appl/blast/remote.rb",
"lib/bio/appl/blast/report.rb",
"lib/bio/appl/blast/rexml.rb",
"lib/bio/appl/blast/rpsblast.rb",
"lib/bio/appl/blast/wublast.rb",
"lib/bio/appl/blast/xmlparser.rb",
"lib/bio/appl/blat/report.rb",
"lib/bio/appl/clustalw.rb",
"lib/bio/appl/clustalw/report.rb",
"lib/bio/appl/emboss.rb",
"lib/bio/appl/fasta.rb",
"lib/bio/appl/fasta/format10.rb",
"lib/bio/appl/gcg/msf.rb",
"lib/bio/appl/gcg/seq.rb",
"lib/bio/appl/genscan/report.rb",
"lib/bio/appl/hmmer.rb",
"lib/bio/appl/hmmer/report.rb",
"lib/bio/appl/iprscan/report.rb",
"lib/bio/appl/mafft.rb",
"lib/bio/appl/mafft/report.rb",
"lib/bio/appl/meme/mast.rb",
"lib/bio/appl/meme/mast/report.rb",
"lib/bio/appl/meme/motif.rb",
"lib/bio/appl/muscle.rb",
"lib/bio/appl/paml/baseml.rb",
"lib/bio/appl/paml/baseml/report.rb",
"lib/bio/appl/paml/codeml.rb",
"lib/bio/appl/paml/codeml/rates.rb",
"lib/bio/appl/paml/codeml/report.rb",
"lib/bio/appl/paml/common.rb",
"lib/bio/appl/paml/common_report.rb",
"lib/bio/appl/paml/yn00.rb",
"lib/bio/appl/paml/yn00/report.rb",
"lib/bio/appl/phylip/alignment.rb",
"lib/bio/appl/phylip/distance_matrix.rb",
"lib/bio/appl/probcons.rb",
"lib/bio/appl/psort.rb",
"lib/bio/appl/psort/report.rb",
"lib/bio/appl/pts1.rb",
"lib/bio/appl/sim4.rb",
"lib/bio/appl/sim4/report.rb",
"lib/bio/appl/sosui/report.rb",
"lib/bio/appl/spidey/report.rb",
"lib/bio/appl/targetp/report.rb",
"lib/bio/appl/tcoffee.rb",
"lib/bio/appl/tmhmm/report.rb",
"lib/bio/command.rb",
"lib/bio/compat/features.rb",
"lib/bio/compat/references.rb",
"lib/bio/data/aa.rb",
"lib/bio/data/codontable.rb",
"lib/bio/data/na.rb",
"lib/bio/db.rb",
"lib/bio/db/aaindex.rb",
"lib/bio/db/biosql/biosql_to_biosequence.rb",
"lib/bio/db/biosql/sequence.rb",
"lib/bio/db/embl/common.rb",
"lib/bio/db/embl/embl.rb",
"lib/bio/db/embl/embl_to_biosequence.rb",
"lib/bio/db/embl/format_embl.rb",
"lib/bio/db/embl/sptr.rb",
"lib/bio/db/embl/swissprot.rb",
"lib/bio/db/embl/trembl.rb",
"lib/bio/db/embl/uniprot.rb",
"lib/bio/db/fantom.rb",
"lib/bio/db/fasta.rb",
"lib/bio/db/fasta/defline.rb",
"lib/bio/db/fasta/fasta_to_biosequence.rb",
"lib/bio/db/fasta/format_fasta.rb",
"lib/bio/db/fasta/format_qual.rb",
"lib/bio/db/fasta/qual.rb",
"lib/bio/db/fasta/qual_to_biosequence.rb",
"lib/bio/db/fastq.rb",
"lib/bio/db/fastq/fastq_to_biosequence.rb",
"lib/bio/db/fastq/format_fastq.rb",
"lib/bio/db/genbank/common.rb",
"lib/bio/db/genbank/ddbj.rb",
"lib/bio/db/genbank/format_genbank.rb",
"lib/bio/db/genbank/genbank.rb",
"lib/bio/db/genbank/genbank_to_biosequence.rb",
"lib/bio/db/genbank/genpept.rb",
"lib/bio/db/genbank/refseq.rb",
"lib/bio/db/gff.rb",
"lib/bio/db/go.rb",
"lib/bio/db/kegg/brite.rb",
"lib/bio/db/kegg/common.rb",
"lib/bio/db/kegg/compound.rb",
"lib/bio/db/kegg/drug.rb",
"lib/bio/db/kegg/enzyme.rb",
"lib/bio/db/kegg/expression.rb",
"lib/bio/db/kegg/genes.rb",
"lib/bio/db/kegg/genome.rb",
"lib/bio/db/kegg/glycan.rb",
"lib/bio/db/kegg/keggtab.rb",
"lib/bio/db/kegg/kgml.rb",
"lib/bio/db/kegg/module.rb",
"lib/bio/db/kegg/orthology.rb",
"lib/bio/db/kegg/pathway.rb",
"lib/bio/db/kegg/reaction.rb",
"lib/bio/db/kegg/taxonomy.rb",
"lib/bio/db/lasergene.rb",
"lib/bio/db/litdb.rb",
"lib/bio/db/medline.rb",
"lib/bio/db/nbrf.rb",
"lib/bio/db/newick.rb",
"lib/bio/db/nexus.rb",
"lib/bio/db/pdb.rb",
"lib/bio/db/pdb/atom.rb",
"lib/bio/db/pdb/chain.rb",
"lib/bio/db/pdb/chemicalcomponent.rb",
"lib/bio/db/pdb/model.rb",
"lib/bio/db/pdb/pdb.rb",
"lib/bio/db/pdb/residue.rb",
"lib/bio/db/pdb/utils.rb",
"lib/bio/db/phyloxml/phyloxml.xsd",
"lib/bio/db/phyloxml/phyloxml_elements.rb",
"lib/bio/db/phyloxml/phyloxml_parser.rb",
"lib/bio/db/phyloxml/phyloxml_writer.rb",
"lib/bio/db/prosite.rb",
"lib/bio/db/rebase.rb",
"lib/bio/db/sanger_chromatogram/abif.rb",
"lib/bio/db/sanger_chromatogram/chromatogram.rb",
"lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
"lib/bio/db/sanger_chromatogram/scf.rb",
"lib/bio/db/soft.rb",
"lib/bio/db/transfac.rb",
"lib/bio/feature.rb",
"lib/bio/io/biosql/ar-biosql.rb",
"lib/bio/io/biosql/biosql.rb",
"lib/bio/io/biosql/config/database.yml",
"lib/bio/io/das.rb",
"lib/bio/io/dbget.rb",
"lib/bio/io/ddbjxml.rb",
"lib/bio/io/ebisoap.rb",
"lib/bio/io/ensembl.rb",
"lib/bio/io/fastacmd.rb",
"lib/bio/io/fetch.rb",
"lib/bio/io/flatfile.rb",
"lib/bio/io/flatfile/autodetection.rb",
"lib/bio/io/flatfile/bdb.rb",
"lib/bio/io/flatfile/buffer.rb",
"lib/bio/io/flatfile/index.rb",
"lib/bio/io/flatfile/indexer.rb",
"lib/bio/io/flatfile/splitter.rb",
"lib/bio/io/higet.rb",
"lib/bio/io/hinv.rb",
"lib/bio/io/keggapi.rb",
"lib/bio/io/ncbirest.rb",
"lib/bio/io/ncbisoap.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
"lib/bio/io/soapwsdl.rb",
"lib/bio/io/sql.rb",
"lib/bio/io/togows.rb",
"lib/bio/location.rb",
"lib/bio/map.rb",
"lib/bio/pathway.rb",
"lib/bio/reference.rb",
"lib/bio/sequence.rb",
"lib/bio/sequence/aa.rb",
"lib/bio/sequence/adapter.rb",
"lib/bio/sequence/common.rb",
"lib/bio/sequence/compat.rb",
"lib/bio/sequence/dblink.rb",
"lib/bio/sequence/format.rb",
"lib/bio/sequence/format_raw.rb",
"lib/bio/sequence/generic.rb",
"lib/bio/sequence/na.rb",
"lib/bio/sequence/quality_score.rb",
"lib/bio/sequence/sequence_masker.rb",
"lib/bio/shell.rb",
"lib/bio/shell/core.rb",
"lib/bio/shell/demo.rb",
"lib/bio/shell/interface.rb",
"lib/bio/shell/irb.rb",
"lib/bio/shell/object.rb",
"lib/bio/shell/plugin/blast.rb",
"lib/bio/shell/plugin/codon.rb",
"lib/bio/shell/plugin/das.rb",
"lib/bio/shell/plugin/emboss.rb",
"lib/bio/shell/plugin/entry.rb",
"lib/bio/shell/plugin/flatfile.rb",
"lib/bio/shell/plugin/keggapi.rb",
"lib/bio/shell/plugin/midi.rb",
"lib/bio/shell/plugin/ncbirest.rb",
"lib/bio/shell/plugin/obda.rb",
"lib/bio/shell/plugin/psort.rb",
"lib/bio/shell/plugin/seq.rb",
"lib/bio/shell/plugin/soap.rb",
"lib/bio/shell/plugin/togows.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
"lib/bio/shell/script.rb",
"lib/bio/shell/setup.rb",
"lib/bio/shell/web.rb",
"lib/bio/tree.rb",
"lib/bio/util/color_scheme.rb",
"lib/bio/util/color_scheme/buried.rb",
"lib/bio/util/color_scheme/helix.rb",
"lib/bio/util/color_scheme/hydropathy.rb",
"lib/bio/util/color_scheme/nucleotide.rb",
"lib/bio/util/color_scheme/strand.rb",
"lib/bio/util/color_scheme/taylor.rb",
"lib/bio/util/color_scheme/turn.rb",
"lib/bio/util/color_scheme/zappo.rb",
"lib/bio/util/contingency_table.rb",
"lib/bio/util/restriction_enzyme.rb",
"lib/bio/util/restriction_enzyme/analysis.rb",
"lib/bio/util/restriction_enzyme/analysis_basic.rb",
"lib/bio/util/restriction_enzyme/cut_symbol.rb",
"lib/bio/util/restriction_enzyme/double_stranded.rb",
"lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb",
"lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/enzymes.yaml",
"lib/bio/util/restriction_enzyme/range/cut_range.rb",
"lib/bio/util/restriction_enzyme/range/cut_ranges.rb",
"lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb",
"lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb",
"lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb",
"lib/bio/util/restriction_enzyme/single_strand.rb",
"lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb",
"lib/bio/util/restriction_enzyme/single_strand_complement.rb",
"lib/bio/util/restriction_enzyme/string_formatting.rb",
"lib/bio/util/sirna.rb",
"lib/bio/version.rb",
"rdoc.zsh",
"sample/any2fasta.rb",
"sample/biofetch.rb",
"sample/color_scheme_na.rb",
"sample/dbget",
"sample/demo_aaindex.rb",
"sample/demo_aminoacid.rb",
"sample/demo_bl2seq_report.rb",
"sample/demo_blast_report.rb",
"sample/demo_codontable.rb",
"sample/demo_das.rb",
"sample/demo_ddbjxml.rb",
"sample/demo_fasta_remote.rb",
"sample/demo_fastaformat.rb",
"sample/demo_genbank.rb",
"sample/demo_genscan_report.rb",
"sample/demo_gff1.rb",
"sample/demo_go.rb",
"sample/demo_hmmer_report.rb",
"sample/demo_kegg_compound.rb",
"sample/demo_kegg_drug.rb",
"sample/demo_kegg_genome.rb",
"sample/demo_kegg_glycan.rb",
"sample/demo_kegg_orthology.rb",
"sample/demo_kegg_reaction.rb",
"sample/demo_kegg_taxonomy.rb",
"sample/demo_keggapi.rb",
"sample/demo_litdb.rb",
"sample/demo_locations.rb",
"sample/demo_ncbi_rest.rb",
"sample/demo_nucleicacid.rb",
"sample/demo_pathway.rb",
"sample/demo_prosite.rb",
"sample/demo_psort.rb",
"sample/demo_psort_report.rb",
"sample/demo_pubmed.rb",
"sample/demo_sequence.rb",
"sample/demo_sirna.rb",
"sample/demo_sosui_report.rb",
"sample/demo_targetp_report.rb",
"sample/demo_tmhmm_report.rb",
"sample/enzymes.rb",
"sample/fasta2tab.rb",
"sample/fastagrep.rb",
"sample/fastasort.rb",
"sample/fsplit.rb",
"sample/gb2fasta.rb",
"sample/gb2tab.rb",
"sample/gbtab2mysql.rb",
"sample/genes2nuc.rb",
"sample/genes2pep.rb",
"sample/genes2tab.rb",
"sample/genome2rb.rb",
"sample/genome2tab.rb",
"sample/goslim.rb",
"sample/gt2fasta.rb",
"sample/na2aa.rb",
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/psortplot_html.rb",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
"sample/test_phyloxml_big.rb",
"sample/tfastx2tab.rb",
"sample/vs-genes.rb",
"setup.rb",
"test/bioruby_test_helper.rb",
"test/data/HMMER/hmmpfam.out",
"test/data/HMMER/hmmsearch.out",
"test/data/KEGG/1.1.1.1.enzyme",
"test/data/KEGG/C00025.compound",
"test/data/KEGG/D00063.drug",
"test/data/KEGG/G00024.glycan",
"test/data/KEGG/G01366.glycan",
"test/data/KEGG/K02338.orthology",
"test/data/KEGG/M00118.module",
"test/data/KEGG/R00006.reaction",
"test/data/KEGG/T00005.genome",
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