bio-polyploid-tools.gemspec in bio-polyploid-tools-0.7.3 vs bio-polyploid-tools.gemspec in bio-polyploid-tools-0.8.0
- old
+ new
@@ -1,46 +1,54 @@
-# Generated by jeweler
+# Generated by juwelier
# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
# -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.7.3 ruby lib
+# stub: bio-polyploid-tools 0.8.0 ruby lib
Gem::Specification.new do |s|
- s.name = "bio-polyploid-tools"
- s.version = "0.7.3"
+ s.name = "bio-polyploid-tools".freeze
+ s.version = "0.8.0"
- s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
- s.require_paths = ["lib"]
- s.authors = ["Ricardo H. Ramirez-Gonzalez"]
- s.date = "2015-08-10"
- s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
- s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
- s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "filter_exonerate_by_identity.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]
+ 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 = "2018-01-18"
+ 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, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "vcfLineToTable.rb".freeze]
s.extra_rdoc_files = [
"README",
"README.md"
]
s.files = [
+ ".travis.yml",
"Gemfile",
- "Gemfile.lock",
"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/polymarker.rb",
+ "bin/polymarker_capillary.rb",
"bin/snp_position_to_polymarker.rb",
"bin/snps_between_bams.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",
@@ -78,25 +86,33 @@
"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/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.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",
@@ -107,53 +123,79 @@
"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/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"
- s.licenses = ["MIT"]
- s.rubygems_version = "2.4.7"
- s.summary = "Tool to work with polyploids, NGS and molecular biology"
+ 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<bio>, [">= 1.4.3"])
- s.add_runtime_dependency(%q<bio-samtools>, [">= 2.0.4"])
- s.add_runtime_dependency(%q<rake>, [">= 0"])
- s.add_runtime_dependency(%q<jeweler>, [">= 0"])
- s.add_runtime_dependency(%q<systemu>, [">= 2.5.2"])
+ s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
+ s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+ s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
+ s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
+ s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
+ s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
else
- s.add_dependency(%q<bio>, [">= 1.4.3"])
- s.add_dependency(%q<bio-samtools>, [">= 2.0.4"])
- s.add_dependency(%q<rake>, [">= 0"])
- s.add_dependency(%q<jeweler>, [">= 0"])
- s.add_dependency(%q<systemu>, [">= 2.5.2"])
+ s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
+ s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+ s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
+ s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
+ s.add_dependency(%q<test-unit>.freeze, [">= 0"])
+ s.add_dependency(%q<juwelier>.freeze, [">= 0"])
end
else
- s.add_dependency(%q<bio>, [">= 1.4.3"])
- s.add_dependency(%q<bio-samtools>, [">= 2.0.4"])
- s.add_dependency(%q<rake>, [">= 0"])
- s.add_dependency(%q<jeweler>, [">= 0"])
- s.add_dependency(%q<systemu>, [">= 2.5.2"])
+ s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
+ s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+ s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
+ s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
+ s.add_dependency(%q<test-unit>.freeze, [">= 0"])
+ s.add_dependency(%q<juwelier>.freeze, [">= 0"])
end
end