/usr/share/rubygems-integration/1.9.1/specifications/bio-1.4.2.gemspec is in ruby-bio 1.4.2-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | # -*- encoding: utf-8 -*-
Gem::Specification.new do |s|
s.name = "bio"
s.version = "1.4.2"
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
s.authors = ["BioRuby project"]
s.autorequire = "bio"
s.date = "2011-08-26"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.email = "staff@bioruby.org"
s.executables = ["bioruby", "br_biofetch.rb", "br_bioflat.rb", "br_biogetseq.rb", "br_pmfetch.rb"]
s.extra_rdoc_files = ["ChangeLog", "KNOWN_ISSUES.rdoc", "README.rdoc", "README_DEV.rdoc", "RELEASE_NOTES.rdoc", "doc/Changes-1.3.rdoc", "doc/RELEASE_NOTES-1.4.0.rdoc", "doc/RELEASE_NOTES-1.4.1.rdoc"]
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/RELEASE_NOTES-1.4.1.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", 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"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/ddbjrest.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", 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"sample/pmfetch.rb", "sample/pmsearch.rb", "sample/psortplot_html.rb", "sample/ssearch2tab.rb", "sample/tdiary.rb", "sample/test_phyloxml_big.rb", "sample/test_restriction_enzyme_long.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", "test/data/KEGG/T00070.genome", "test/data/KEGG/b0529.gene", "test/data/KEGG/ec00072.pathway", "test/data/KEGG/hsa00790.pathway", "test/data/KEGG/ko00312.pathway", "test/data/KEGG/map00030.pathway", "test/data/KEGG/map00052.pathway", "test/data/KEGG/rn00250.pathway", "test/data/SOSUI/sample.report", "test/data/TMHMM/sample.report", 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