# Generated by juwelier # DO NOT EDIT THIS FILE DIRECTLY # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec' # -*- encoding: utf-8 -*- # stub: bio-polyploid-tools 0.8.5 ruby lib Gem::Specification.new do |s| s.name = "bio-polyploid-tools".freeze s.version = "0.8.5" s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version= s.require_paths = ["lib".freeze] s.authors = ["Ricardo H. Ramirez-Gonzalez".freeze] s.date = "2018-07-31" s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze] s.extra_rdoc_files = [ "README", "README.md" ] s.files = [ ".travis.yml", "Gemfile", "README", "README.md", "Rakefile", "VERSION", "bin/bfr.rb", "bin/blast_triads.rb", "bin/blast_triads_promoters.rb", "bin/count_variations.rb", "bin/filter_blat_by_target_coverage.rb", "bin/filter_exonerate_by_identity.rb", "bin/find_best_blat_hit.rb", "bin/find_best_exonerate.rb", "bin/find_homoeologue_variations.rb", "bin/get_longest_hsp_blastx_triads.rb", "bin/hexaploid_primers.rb", "bin/homokaryot_primers.rb", "bin/mafft_triads.rb", "bin/mafft_triads_promoters.rb", "bin/map_markers_to_contigs.rb", "bin/markers_in_region.rb", "bin/mask_triads.rb", "bin/polymarker.rb", "bin/polymarker_capillary.rb", "bin/snp_position_to_polymarker.rb", "bin/snps_between_bams.rb", "bin/tag_stats.rb", "bin/vcfLineToTable.rb", "bio-polyploid-tools.gemspec", "conf/defaults.rb", "conf/primer3_config/dangle.dh", "conf/primer3_config/dangle.ds", "conf/primer3_config/interpretations/dangle_i.dh", "conf/primer3_config/interpretations/dangle_i.ds", "conf/primer3_config/interpretations/loops_i.dh", "conf/primer3_config/interpretations/loops_i.ds", "conf/primer3_config/interpretations/stack_i.dh", "conf/primer3_config/interpretations/stack_i.ds", "conf/primer3_config/interpretations/stackmm_i_mm.dh", "conf/primer3_config/interpretations/stackmm_i_mm.ds", "conf/primer3_config/interpretations/tetraloop_i.dh", "conf/primer3_config/interpretations/tetraloop_i.ds", "conf/primer3_config/interpretations/triloop_i.dh", "conf/primer3_config/interpretations/triloop_i.ds", "conf/primer3_config/interpretations/tstack2_i.dh", "conf/primer3_config/interpretations/tstack2_i.ds", "conf/primer3_config/interpretations/tstack_i.dh", "conf/primer3_config/interpretations/tstack_i.ds", "conf/primer3_config/interpretations/tstack_tm_inf_i.dh", "conf/primer3_config/interpretations/tstack_tm_inf_i.ds", "conf/primer3_config/loops.dh", "conf/primer3_config/loops.ds", "conf/primer3_config/stack.dh", "conf/primer3_config/stack.ds", "conf/primer3_config/stackmm.dh", "conf/primer3_config/stackmm.ds", "conf/primer3_config/tetraloop.dh", "conf/primer3_config/tetraloop.ds", "conf/primer3_config/triloop.dh", "conf/primer3_config/triloop.ds", "conf/primer3_config/tstack.dh", "conf/primer3_config/tstack2.dh", "conf/primer3_config/tstack2.ds", "conf/primer3_config/tstack_tm_inf.ds", "lib/bio/BFRTools.rb", "lib/bio/BIOExtensions.rb", "lib/bio/PolyploidTools/ChromosomeArm.rb", "lib/bio/PolyploidTools/ExonContainer.rb", "lib/bio/PolyploidTools/Marker.rb", "lib/bio/PolyploidTools/Mask.rb", "lib/bio/PolyploidTools/NoSNPSequence.rb", "lib/bio/PolyploidTools/PrimerRegion.rb", "lib/bio/PolyploidTools/SNP.rb", "lib/bio/PolyploidTools/SNPMutant.rb", "lib/bio/PolyploidTools/SNPSequence.rb", "lib/bio/db/blast.rb", "lib/bio/db/exonerate.rb", "lib/bio/db/primer3.rb", "lib/bioruby-polyploid-tools.rb", "test/data/BS00068396_51.fa", "test/data/BS00068396_51_blast.tab", "test/data/BS00068396_51_contigs.aln", "test/data/BS00068396_51_contigs.dnd", "test/data/BS00068396_51_contigs.fa", "test/data/BS00068396_51_contigs.fa.fai", "test/data/BS00068396_51_contigs.fa.nhr", "test/data/BS00068396_51_contigs.fa.nin", "test/data/BS00068396_51_contigs.fa.nsq", "test/data/BS00068396_51_contigs.nhr", "test/data/BS00068396_51_contigs.nin", "test/data/BS00068396_51_contigs.nsq", "test/data/BS00068396_51_exonerate.tab", "test/data/BS00068396_51_for_polymarker.fa", "test/data/BS00068396_51_genes.txt", "test/data/IWGSC_CSS_1AL_scaff_1455974.fa", "test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa", "test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai", "test/data/LIB1716.bam", "test/data/LIB1716.bam.bai", "test/data/LIB1719.bam", "test/data/LIB1719.bam.bai", "test/data/LIB1721.bam", "test/data/LIB1721.bam.bai", "test/data/LIB1722.bam", "test/data/LIB1722.bam.bai", "test/data/PST130_7067.csv", "test/data/PST130_7067.fa", "test/data/PST130_7067.fa.fai", "test/data/PST130_reverse_primer.csv", "test/data/S22380157.fa", "test/data/S22380157.fa.fai", "test/data/S22380157.vcf", "test/data/S58861868/LIB1716.bam", "test/data/S58861868/LIB1716.sam", "test/data/S58861868/LIB1719.bam", "test/data/S58861868/LIB1719.sam", "test/data/S58861868/LIB1721.bam", "test/data/S58861868/LIB1721.sam", "test/data/S58861868/LIB1722.bam", "test/data/S58861868/LIB1722.sam", "test/data/S58861868/S58861868.fa", "test/data/S58861868/S58861868.fa.fai", "test/data/S58861868/S58861868.vcf", "test/data/S58861868/header.txt", "test/data/S58861868/merged.bam", "test/data/S58861868/merged_reheader.bam", "test/data/S58861868/merged_reheader.bam.bai", "test/data/Test3Aspecific.csv", "test/data/Test3Aspecific_contigs.fa", "test/data/bfr_out_test.csv", "test/data/chr4D_C14473543T/chr4D_C14473543T.csv", "test/data/chr4D_C14473543T/chr4D_C14473543T.fa", "test/data/headerMergeed.txt", "test/data/headerS2238015", "test/data/mergedLibs.bam", "test/data/mergedLibsReheader.bam", "test/data/mergedLibsSorted.bam", "test/data/mergedLibsSorted.bam.bai", "test/data/patological_cases5D.csv", "test/data/primer_3_input_header_test", "test/data/short_primer_design_test.csv", "test/data/test_from_mutant.csv", "test/data/test_iselect.csv", "test/data/test_iselect_reference.fa", "test/data/test_iselect_reference.fa.fai", "test/data/test_primer3_error.csv", "test/data/test_primer3_error_contigs.fa", "test/test_bfr.rb", "test/test_blast.rb", "test/test_exon_container.rb", "test/test_exonearate.rb", "test/test_snp_parsing.rb", "test/test_wrong_selection.sh" ] s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze s.licenses = ["MIT".freeze] s.rubygems_version = "2.7.4".freeze s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze 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.freeze, [">= 1.5.1"]) s.add_runtime_dependency(%q.freeze, [">= 2.6.2"]) s.add_runtime_dependency(%q.freeze, [">= 0"]) s.add_runtime_dependency(%q.freeze, [">= 2.5.2"]) s.add_development_dependency(%q.freeze, [">= 2.10"]) s.add_development_dependency(%q.freeze, [">= 0"]) s.add_development_dependency(%q.freeze, [">= 0"]) else s.add_dependency(%q.freeze, [">= 1.5.1"]) s.add_dependency(%q.freeze, [">= 2.6.2"]) s.add_dependency(%q.freeze, [">= 0"]) s.add_dependency(%q.freeze, [">= 2.5.2"]) s.add_dependency(%q.freeze, [">= 2.10"]) s.add_dependency(%q.freeze, [">= 0"]) s.add_dependency(%q.freeze, [">= 0"]) end else s.add_dependency(%q.freeze, [">= 1.5.1"]) s.add_dependency(%q.freeze, [">= 2.6.2"]) s.add_dependency(%q.freeze, [">= 0"]) s.add_dependency(%q.freeze, [">= 2.5.2"]) s.add_dependency(%q.freeze, [">= 2.10"]) s.add_dependency(%q.freeze, [">= 0"]) s.add_dependency(%q.freeze, [">= 0"]) end end