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finishm.gemspec
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# Generated by jeweler
# DO NOT EDIT THIS FILE DIRECTLY
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
# -*- encoding: utf-8 -*-
# stub: finishm 0.0.9 ruby lib
# stub: ext/mkrf_conf.rb
Gem::Specification.new do |s|
s.name = "finishm"
s.version = "0.0.9"
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 = "2016-08-21"
s.description = "De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies."
s.email = "donttrustben near gmail.com"
s.executables = ["finishm"]
s.extensions = ["ext/mkrf_conf.rb"]
s.extra_rdoc_files = [
"LICENSE.txt",
"README.md"
]
s.files = [
".document",
".gitmodules",
".rspec",
"Gemfile",
"LICENSE.txt",
"README.md",
"Rakefile",
"VERSION",
"bin/finishm",
"ext/mkrf_conf.rb",
"ext/src/Makefile",
"ext/src/src/allocArray.c",
"ext/src/src/allocArray.h",
"ext/src/src/autoOpen.c",
"ext/src/src/autoOpen.h",
"ext/src/src/binarySequences.c",
"ext/src/src/binarySequences.h",
"ext/src/src/concatenatedGraph.c",
"ext/src/src/concatenatedGraph.h",
"ext/src/src/concatenatedPreGraph.c",
"ext/src/src/concatenatedPreGraph.h",
"ext/src/src/correctedGraph.c",
"ext/src/src/correctedGraph.h",
"ext/src/src/dfib.c",
"ext/src/src/dfib.h",
"ext/src/src/dfibHeap.c",
"ext/src/src/dfibHeap.h",
"ext/src/src/dfibpriv.h",
"ext/src/src/fib.c",
"ext/src/src/fib.h",
"ext/src/src/fibHeap.c",
"ext/src/src/fibHeap.h",
"ext/src/src/fibpriv.h",
"ext/src/src/globals.h",
"ext/src/src/graph.c",
"ext/src/src/graph.h",
"ext/src/src/graphReConstruction.c",
"ext/src/src/graphReConstruction.h",
"ext/src/src/graphStats.c",
"ext/src/src/graphStats.h",
"ext/src/src/graphStructures.h",
"ext/src/src/kmer.c",
"ext/src/src/kmer.h",
"ext/src/src/kmerOccurenceTable.c",
"ext/src/src/kmerOccurenceTable.h",
"ext/src/src/kseq.h",
"ext/src/src/locallyCorrectedGraph.c",
"ext/src/src/locallyCorrectedGraph.h",
"ext/src/src/passageMarker.c",
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"ext/src/src/tightString.c",
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"finishm.gemspec",
"lib/assembly/a_b_visualiser.rb",
"lib/assembly/acyclic_connection_finder.rb",
"lib/assembly/all_orfs.rb",
"lib/assembly/bad_format_writer.rb",
"lib/assembly/bam_probe_read_selector.rb",
"lib/assembly/bubbly_assembler.rb",
"lib/assembly/c_probe_node_finder.rb",
"lib/assembly/connection_interpreter.rb",
"lib/assembly/contig_printer.rb",
"lib/assembly/coverage_based_graph_filter.rb",
"lib/assembly/depth_first_search.rb",
"lib/assembly/dijkstra.rb",
"lib/assembly/fluffer.rb",
"lib/assembly/graph_explorer.rb",
"lib/assembly/graph_generator.rb",
"lib/assembly/height_finder.rb",
"lib/assembly/hybrid_velvet_graph.rb",
"lib/assembly/input_genome.rb",
"lib/assembly/kmer_coverage_based_path_filter.rb",
"lib/assembly/node_finder.rb",
"lib/assembly/oriented_node_trail.rb",
"lib/assembly/paired_end_assembler.rb",
"lib/assembly/paired_end_neighbour_finder.rb",
"lib/assembly/probed_graph.rb",
"lib/assembly/read_input.rb",
"lib/assembly/read_to_node.rb",
"lib/assembly/scaffold_breaker.rb",
"lib/assembly/sequence_hasher.rb",
"lib/assembly/single_coherent_paths_between_nodes.rb",
"lib/assembly/single_coherent_wanderer.rb",
"lib/assembly/single_ended_assembler.rb",
"lib/assembly/velvet_c_binding.rb",
"lib/assembly/velvet_graph_sequence_extractor.rb",
"lib/external/VERSION",
"lib/finishm/assemble.rb",
"lib/finishm/connect.rb",
"lib/finishm/explore.rb",
"lib/finishm/finisher.rb",
"lib/finishm/fluff.rb",
"lib/finishm/gapfiller.rb",
"lib/finishm/orfs_finder.rb",
"lib/finishm/path_counter.rb",
"lib/finishm/primers.rb",
"lib/finishm/primers_check.rb",
"lib/finishm/roundup.rb",
"lib/finishm/sequence.rb",
"lib/finishm/visualise.rb",
"lib/finishm/wander.rb",
"lib/kmer_abundance_pattern.rb",
"lib/kmer_multi_abundance_file.rb",
"lib/oligo_designer.rb",
"lib/priner.rb",
"spec/acyclic_connection_finder_spec.rb",
"spec/all_orfs_spec.rb",
"spec/assemble_spec.rb",
"spec/bubbly_assembler_spec.rb",
"spec/c_node_finder_spec.rb",
"spec/connection_interpreter_spec.rb",
"spec/contig_printer_spec.rb",
"spec/coverage_based_graph_filter_spec.rb",
"spec/data/6_3e4e5e6e.1vANME.bam",
"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",
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"spec/data/fluff/1/2seqs.sammy.fa",
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"spec/data/fluff/1/seq1.fa",
"spec/data/fluff/1/seq2.fa",
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"spec/data/gapfilling/1/trail_with_Ns.fa",
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"spec/data/gapfilling/1/velvetAssembly/PreGraph",
"spec/data/gapfilling/1/velvetAssembly/Roadmaps",
"spec/data/gapfilling/1/velvetAssembly/Sequences",
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"spec/data/gapfilling/5/reads.fa",
"spec/data/gapfilling/5/reads.faVanswer.bam",
"spec/data/gapfilling/5/reads.faVanswer.bam.bai",
"spec/data/gapfilling/5/reads2.fa",
"spec/data/gapfilling/5/to_gapfill.fa",
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"spec/data/gapfilling/5/velvet23_3.5/Roadmaps",
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"spec/data/gapfilling/6/random2.fa",
"spec/data/gapfilling/6/random_sequence_length_2000",
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"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",
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"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",
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"spec/data/velvet_test_trails/Assem/PreGraph",
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"spec/data/wander/1/reference_reads.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-3.0+"]
s.required_ruby_version = Gem::Requirement.new("~> 2.3")
s.rubygems_version = "2.5.1"
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<bio-ipcress>, ["~> 0.0"])
s.add_runtime_dependency(%q<bio-logger>, ["~> 1.0"])
s.add_runtime_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
s.add_runtime_dependency(%q<progressbar>, ["~> 0.21"])
s.add_runtime_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
s.add_runtime_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
s.add_runtime_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
s.add_runtime_dependency(%q<bio-velvet>, ["~> 0.6"])
s.add_runtime_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
s.add_runtime_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
s.add_runtime_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
s.add_runtime_dependency(%q<pry>, ["~> 0.10"])
s.add_development_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
s.add_development_dependency(%q<yard>, ["~> 0.7"])
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
s.add_development_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
s.add_development_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
s.add_development_dependency(%q<bio-commandeer>, ["~> 0.1"])
else
s.add_dependency(%q<bio-ipcress>, ["~> 0.0"])
s.add_dependency(%q<bio-logger>, ["~> 1.0"])
s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
s.add_dependency(%q<progressbar>, ["~> 0.21"])
s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
s.add_dependency(%q<bio-velvet>, ["~> 0.6"])
s.add_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
s.add_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
s.add_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
s.add_dependency(%q<pry>, ["~> 0.10"])
s.add_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
s.add_dependency(%q<yard>, ["~> 0.7"])
s.add_dependency(%q<rdoc>, ["~> 3.12"])
s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
s.add_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
end
else
s.add_dependency(%q<bio-ipcress>, ["~> 0.0"])
s.add_dependency(%q<bio-logger>, ["~> 1.0"])
s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
s.add_dependency(%q<progressbar>, ["~> 0.21"])
s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
s.add_dependency(%q<bio-velvet>, ["~> 0.6"])
s.add_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
s.add_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
s.add_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
s.add_dependency(%q<pry>, ["~> 0.10"])
s.add_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
s.add_dependency(%q<yard>, ["~> 0.7"])
s.add_dependency(%q<rdoc>, ["~> 3.12"])
s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
s.add_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
end
end