# Generated by jeweler # DO NOT EDIT THIS FILE DIRECTLY # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec' # -*- encoding: utf-8 -*- # stub: finishm 0.0.4 ruby lib # stub: ext/mkrf_conf.rb Gem::Specification.new do |s| s.name = "finishm" s.version = "0.0.4" s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.require_paths = ["lib"] s.authors = ["Ben J. Woodcroft"] s.date = "2015-08-30" s.description = "De-novo assemblies generally only provide draft genomes. 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"spec/data/6_3e4e5e6e.1vANME.bam.bai", "spec/data/acyclic_connection_finder/1/probes.fa", "spec/data/acyclic_connection_finder/1/random1.fa", "spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz", "spec/data/acyclic_connection_finder/1/random2.fa", "spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz", "spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa", "spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa", "spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz", "spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31", "spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31", "spec/data/assembly_visualiser/Graph", "spec/data/assembly_visualiser/start_kmers1", "spec/data/bands.csv", "spec/data/c_probe_node_finder/1/CnyUnifiedSeq", "spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names", "spec/data/c_probe_node_finder/1/Graph2", "spec/data/c_probe_node_finder/1/LastGraph", "spec/data/c_probe_node_finder/1/Log", "spec/data/c_probe_node_finder/1/PreGraph", "spec/data/c_probe_node_finder/1/Roadmaps", "spec/data/c_probe_node_finder/1/contigs.fa", "spec/data/c_probe_node_finder/1/stats.txt", "spec/data/contig_printer/1/HOWTO_RECREATE", "spec/data/contig_printer/1/contigs.fa", "spec/data/contig_printer/1/seq.fa", "spec/data/contig_printer/1/seq.fa.svg", "spec/data/contig_printer/1/seq.fa.velvet/Graph2", "spec/data/contig_printer/1/seq.fa.velvet/LastGraph", "spec/data/contig_printer/1/seq.fa.velvet/Log", "spec/data/contig_printer/1/seq.fa.velvet/PreGraph", "spec/data/contig_printer/1/seq.fa.velvet/Roadmaps", "spec/data/contig_printer/1/seq.fa.velvet/Sequences", "spec/data/contig_printer/1/seq.fa.velvet/contigs.fa", "spec/data/contig_printer/1/seq.fa.velvet/stats.txt", "spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam", "spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai", "spec/data/contig_printer/1/seq.node12.fa", "spec/data/contig_printer/1/seq1_1to550.fa", "spec/data/contig_printer/1/seq2_1to550.fa", "spec/data/contig_printer/1/seq2_1to550.fa.fai", "spec/data/explore/1/2seqs.sammy.fa", "spec/data/explore/1/HOWTO_RECREATE.txt", "spec/data/explore/1/a.fa", "spec/data/explore/1/seq1_and_a.fa", "spec/data/explore/1/seq2.fa", "spec/data/fluff/1/2seqs.sammy.fa", "spec/data/fluff/1/HOWTO_RECREATE.txt", "spec/data/fluff/1/seq1.fa", "spec/data/fluff/1/seq2.fa", "spec/data/gapfilling/1/reads.fa", "spec/data/gapfilling/1/trail_with_Ns.fa", "spec/data/gapfilling/1/velvetAssembly/Graph2", "spec/data/gapfilling/1/velvetAssembly/LastGraph", "spec/data/gapfilling/1/velvetAssembly/Log", "spec/data/gapfilling/1/velvetAssembly/PreGraph", "spec/data/gapfilling/1/velvetAssembly/Roadmaps", "spec/data/gapfilling/1/velvetAssembly/Sequences", "spec/data/gapfilling/1/velvetAssembly/contigs.fa", "spec/data/gapfilling/1/velvetAssembly/stats.txt", "spec/data/gapfilling/2/HOWTO_recreate", "spec/data/gapfilling/2/reference.fa", "spec/data/gapfilling/2/reference_part1.fa", "spec/data/gapfilling/2/reference_part2.fa", "spec/data/gapfilling/2/sammy_reads.fa.gz", "spec/data/gapfilling/2/with_gaps.fa", "spec/data/gapfilling/3/HOWTO_recreate", "spec/data/gapfilling/3/reads.fa.gz", "spec/data/gapfilling/3/reference_part1.fa", "spec/data/gapfilling/3/reference_part2.fa", "spec/data/gapfilling/3/with_gaps.fa", "spec/data/gapfilling/4/HOWTO_recreate", "spec/data/gapfilling/4/reads.fa.gz", "spec/data/gapfilling/5/HOWTO_RECREATE", "spec/data/gapfilling/5/answer.fna", "spec/data/gapfilling/5/gappy.fna", "spec/data/gapfilling/5/reads.fa", "spec/data/gapfilling/5/velvet51_3.5/LastGraph", "spec/data/gapfilling/5/velvet51_3.5/Sequences", "spec/data/gapfilling/6/random1.fa", "spec/data/gapfilling/6/random2.fa", "spec/data/gapfilling/6/random_sequence_length_2000", "spec/data/gapfilling/6/reads.random1.fa.gz", "spec/data/gapfilling/6/reads.random2.fa.gz", "spec/data/gapfilling/6/to_gapfill.fa", "spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv", "spec/data/kmers_count1.csv", "spec/data/kmers_count2.csv", "spec/data/out", "spec/data/positive_latching_pair.fa", "spec/data/primers.csv", "spec/data/read_selection_by_kmer/blacklist1.txt", "spec/data/read_selection_by_kmer/input.fasta", "spec/data/read_selection_by_kmer/whitelist1.txt", "spec/data/read_selection_by_kmer/whitelist2.txt", "spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt", "spec/data/read_to_node/1_a_graph/LastGraph", "spec/data/read_to_node/1_a_graph/ReadToNode.bin", "spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt", "spec/data/read_to_node/2_no_read256_or_259/LastGraph", "spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin", "spec/data/read_to_node/3_no_last_read/LastGraph", "spec/data/read_to_node/3_no_last_read/ReadToNode.bin", "spec/data/t/details.txt", "spec/data/t/details.txt.srt", "spec/data/t/location.txt", "spec/data/t/location.txt.srt", "spec/data/tweak/1_gap_then_unscaffolded/answer.fa", "spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz", "spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa", "spec/data/tweak/2_second_genome/answer2.fa", "spec/data/tweak/2_second_genome/reads.fa.gz", "spec/data/tweak/3_variant/answer.fa", "spec/data/tweak/3_variant/lesser_answer.fa", "spec/data/tweak/3_variant/reads.fa.gz", "spec/data/tweak/3_variant/with_gaps.fa", "spec/data/velvet_test_trails/Assem/Graph", "spec/data/velvet_test_trails/Assem/Graph2", "spec/data/velvet_test_trails/Assem/LastGraph", "spec/data/velvet_test_trails/Assem/Log", "spec/data/velvet_test_trails/Assem/PreGraph", "spec/data/velvet_test_trails/Assem/Roadmaps", "spec/data/velvet_test_trails/Assem/Sequences", "spec/data/velvet_test_trails/Assem/a.svg", "spec/data/velvet_test_trails/Assem/contigs.fa", "spec/data/velvet_test_trails/Assem/stats.txt", "spec/data/velvet_test_trails/node_fwds.fa", "spec/data/velvet_test_trails/node_seqs.fa", "spec/data/velvet_test_trails/nodes_fwd_rev.fa", "spec/data/velvet_test_trails/read1.fa", "spec/data/velvet_test_trails/reads.fa", "spec/data/velvet_test_trails_reverse/Assem/LastGraph", "spec/data/velvet_test_trails_reverse/Assem/a.svg", "spec/data/velvet_test_trails_reverse/reads_reversed.fa", "spec/data/visualise/1/LastGraph", "spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt", "spec/data/visualise/2_paired_end/rand1.fa", "spec/data/visualise/2_paired_end/rand2.fa", "spec/data/visualise/2_paired_end/with_gaps.fa", "spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz", "spec/data/wander/1/random1.fa", "spec/data/wander/1/random1.sammy.fa", "spec/depth_first_search_spec.rb", "spec/dijkstra_spec.rb", "spec/explore_spec.rb", "spec/fluffer_spec.rb", "spec/gapfiller_spec.rb", "spec/graph_explorer_spec.rb", "spec/graph_generator_spec.rb", "spec/height_finder_spec.rb", "spec/kmer_abundance_pattern_spec.rb", "spec/kmer_coverage_based_path_filter_spec.rb", "spec/kmer_profile_finder_spec.rb", "spec/kmers_count_tabulate_spec.rb", "spec/oriented_node_trail_spec.rb", "spec/paired_end_neighbours_spec.rb", "spec/paths_between_nodes_spec.rb", "spec/priner_spec.rb", "spec/read_input_spec.rb", "spec/read_selection_by_kmer_spec.rb", "spec/read_to_node_spec.rb", "spec/roundup_spec.rb", "spec/scaffold_breaker_spec.rb", "spec/sequence_spec.rb", "spec/single_coherent_paths_between_nodes_spec.rb", "spec/single_coherent_wanderer_spec.rb", "spec/single_ended_assembler_spec.rb", "spec/spec_helper.rb", "spec/velvet_graph_sequence_extractor_spec.rb", "spec/visualise_spec.rb", "spec/wander_spec.rb", "spec/watch_for_changes.sh", "validation/fasta_compare.rb", "validation/gapfill_simulate_perfect.rb" ] s.homepage = "http://github.com/wwood/finishm" s.licenses = ["GPL"] s.rubygems_version = "2.2.2" s.summary = "Genome improvement and finishing with or without further sequencing effort" if s.respond_to? :specification_version then s.specification_version = 4 if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then s.add_runtime_dependency(%q, ["~> 0.0"]) s.add_runtime_dependency(%q, ["~> 1.0"]) s.add_runtime_dependency(%q, [">= 1.4.3", "~> 1.4"]) s.add_runtime_dependency(%q, ["~> 0.21"]) s.add_runtime_dependency(%q, ["~> 0.6"]) s.add_runtime_dependency(%q, [">= 1.0.9", "~> 1.0"]) s.add_runtime_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_runtime_dependency(%q, [">= 0.4.3", "~> 0.4"]) s.add_runtime_dependency(%q, ["~> 0.6"]) s.add_runtime_dependency(%q, ["~> 0.3"]) s.add_runtime_dependency(%q, [">= 1.4.2", "~> 1.4"]) s.add_runtime_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_runtime_dependency(%q, ["~> 0.10"]) s.add_development_dependency(%q, [">= 2.8.0", "~> 2.8"]) s.add_development_dependency(%q, ["~> 0.7"]) s.add_development_dependency(%q, ["~> 3.12"]) s.add_development_dependency(%q, [">= 1.6.2", "~> 1.6"]) s.add_development_dependency(%q, [">= 2.0.1", "~> 2.0"]) s.add_development_dependency(%q, ["~> 0.1"]) else s.add_dependency(%q, ["~> 0.0"]) s.add_dependency(%q, ["~> 1.0"]) s.add_dependency(%q, [">= 1.4.3", "~> 1.4"]) s.add_dependency(%q, ["~> 0.21"]) s.add_dependency(%q, ["~> 0.6"]) s.add_dependency(%q, [">= 1.0.9", "~> 1.0"]) s.add_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_dependency(%q, [">= 0.4.3", "~> 0.4"]) s.add_dependency(%q, ["~> 0.6"]) s.add_dependency(%q, ["~> 0.3"]) s.add_dependency(%q, [">= 1.4.2", "~> 1.4"]) s.add_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_dependency(%q, ["~> 0.10"]) s.add_dependency(%q, [">= 2.8.0", "~> 2.8"]) s.add_dependency(%q, ["~> 0.7"]) s.add_dependency(%q, ["~> 3.12"]) s.add_dependency(%q, [">= 1.6.2", "~> 1.6"]) s.add_dependency(%q, [">= 2.0.1", "~> 2.0"]) s.add_dependency(%q, ["~> 0.1"]) end else s.add_dependency(%q, ["~> 0.0"]) s.add_dependency(%q, ["~> 1.0"]) s.add_dependency(%q, [">= 1.4.3", "~> 1.4"]) s.add_dependency(%q, ["~> 0.21"]) s.add_dependency(%q, ["~> 0.6"]) s.add_dependency(%q, [">= 1.0.9", "~> 1.0"]) s.add_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_dependency(%q, [">= 0.4.3", "~> 0.4"]) s.add_dependency(%q, ["~> 0.6"]) s.add_dependency(%q, ["~> 0.3"]) s.add_dependency(%q, [">= 1.4.2", "~> 1.4"]) s.add_dependency(%q, [">= 0.0.4", "~> 0.0"]) s.add_dependency(%q, ["~> 0.10"]) s.add_dependency(%q, [">= 2.8.0", "~> 2.8"]) s.add_dependency(%q, ["~> 0.7"]) s.add_dependency(%q, ["~> 3.12"]) s.add_dependency(%q, [">= 1.6.2", "~> 1.6"]) s.add_dependency(%q, [">= 2.0.1", "~> 2.0"]) s.add_dependency(%q, ["~> 0.1"]) end end