qu-cmdwrapper 1.0.0

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Files changed (67) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +17 -0
  3. data/Gemfile +5 -0
  4. data/LICENSE.txt +22 -0
  5. data/README.md +32 -0
  6. data/Rakefile +1 -0
  7. data/lib/qu/cmdwrapper.rb +10 -0
  8. data/lib/qu/cmdwrapper/cmd.rb +109 -0
  9. data/lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit +0 -0
  10. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal +0 -0
  11. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntthal +0 -0
  12. data/lib/qu/cmdwrapper/ext_bin/linux/32/oligotm +0 -0
  13. data/lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core +0 -0
  14. data/lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa +0 -0
  15. data/lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit +0 -0
  16. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal +0 -0
  17. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntthal +0 -0
  18. data/lib/qu/cmdwrapper/ext_bin/linux/64/oligotm +0 -0
  19. data/lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core +0 -0
  20. data/lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa +0 -0
  21. data/lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit +0 -0
  22. data/lib/qu/cmdwrapper/ext_bin/mac/32/ntthal +0 -0
  23. data/lib/qu/cmdwrapper/ext_bin/mac/32/oligotm +0 -0
  24. data/lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core +0 -0
  25. data/lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa +0 -0
  26. data/lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit +0 -0
  27. data/lib/qu/cmdwrapper/ext_bin/mac/64/ntthal +0 -0
  28. data/lib/qu/cmdwrapper/ext_bin/mac/64/oligotm +0 -0
  29. data/lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core +0 -0
  30. data/lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa +0 -0
  31. data/lib/qu/cmdwrapper/primer3_config/dangle.dh +128 -0
  32. data/lib/qu/cmdwrapper/primer3_config/dangle.ds +128 -0
  33. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh +131 -0
  34. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds +131 -0
  35. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh +34 -0
  36. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds +31 -0
  37. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh +257 -0
  38. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds +256 -0
  39. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  40. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  41. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh +79 -0
  42. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds +81 -0
  43. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh +21 -0
  44. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds +18 -0
  45. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh +256 -0
  46. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds +256 -0
  47. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh +256 -0
  48. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds +256 -0
  49. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  50. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  51. data/lib/qu/cmdwrapper/primer3_config/loops.dh +30 -0
  52. data/lib/qu/cmdwrapper/primer3_config/loops.ds +30 -0
  53. data/lib/qu/cmdwrapper/primer3_config/stack.dh +256 -0
  54. data/lib/qu/cmdwrapper/primer3_config/stack.ds +256 -0
  55. data/lib/qu/cmdwrapper/primer3_config/stackmm.dh +256 -0
  56. data/lib/qu/cmdwrapper/primer3_config/stackmm.ds +256 -0
  57. data/lib/qu/cmdwrapper/primer3_config/tetraloop.dh +77 -0
  58. data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds +77 -0
  59. data/lib/qu/cmdwrapper/primer3_config/triloop.dh +16 -0
  60. data/lib/qu/cmdwrapper/primer3_config/triloop.ds +16 -0
  61. data/lib/qu/cmdwrapper/primer3_config/tstack.dh +256 -0
  62. data/lib/qu/cmdwrapper/primer3_config/tstack2.dh +256 -0
  63. data/lib/qu/cmdwrapper/primer3_config/tstack2.ds +256 -0
  64. data/lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds +256 -0
  65. data/lib/qu/cmdwrapper/version.rb +5 -0
  66. data/qu-cmdwrapper.gemspec +24 -0
  67. metadata +137 -0
@@ -0,0 +1,5 @@
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+ module Qu
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+ module Cmdwrapper
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+ VERSION = "1.0.0"
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+ end
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+ end
@@ -0,0 +1,24 @@
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'qu/cmdwrapper/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "qu-cmdwrapper"
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+ spec.version = Qu::Cmdwrapper::VERSION
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+ spec.authors = ["Wubin Qu"]
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+ spec.email = ["quwubin@gmail.com"]
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+ spec.description = %q{A wrapper for command-line tools, mostly are bioinformatics related tools}
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+ spec.summary = %q{A wrapper for command-line tools}
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+ spec.homepage = "https://github.com/quwubin/qu-cmdwrapper"
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files`.split($/)
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_runtime_dependency 'qu-utils', '~> 1.0'
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+
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+ spec.add_development_dependency "bundler", "~> 1.3"
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+ end
metadata ADDED
@@ -0,0 +1,137 @@
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+ --- !ruby/object:Gem::Specification
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+ name: qu-cmdwrapper
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+ version: !ruby/object:Gem::Version
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+ version: 1.0.0
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+ platform: ruby
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+ authors:
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+ - Wubin Qu
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2014-04-15 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: qu-utils
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.0'
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.3'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.3'
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+ description: A wrapper for command-line tools, mostly are bioinformatics related tools
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+ email:
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+ - quwubin@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - ".gitignore"
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.md
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+ - Rakefile
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+ - lib/qu/cmdwrapper.rb
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+ - lib/qu/cmdwrapper/cmd.rb
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+ - lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit
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+ - lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal
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+ - lib/qu/cmdwrapper/ext_bin/linux/32/ntthal
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+ - lib/qu/cmdwrapper/ext_bin/linux/32/oligotm
59
+ - lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core
60
+ - lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa
61
+ - lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit
62
+ - lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal
63
+ - lib/qu/cmdwrapper/ext_bin/linux/64/ntthal
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+ - lib/qu/cmdwrapper/ext_bin/linux/64/oligotm
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+ - lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core
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+ - lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa
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+ - lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit
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+ - lib/qu/cmdwrapper/ext_bin/mac/32/ntthal
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+ - lib/qu/cmdwrapper/ext_bin/mac/32/oligotm
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+ - lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core
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+ - lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa
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+ - lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit
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+ - lib/qu/cmdwrapper/ext_bin/mac/64/ntthal
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+ - lib/qu/cmdwrapper/ext_bin/mac/64/oligotm
75
+ - lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core
76
+ - lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa
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+ - lib/qu/cmdwrapper/primer3_config/dangle.dh
78
+ - lib/qu/cmdwrapper/primer3_config/dangle.ds
79
+ - lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh
80
+ - lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds
81
+ - lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh
82
+ - lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds
83
+ - lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh
92
+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds
95
+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh
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+ - lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds
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+ - lib/qu/cmdwrapper/primer3_config/loops.dh
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+ - lib/qu/cmdwrapper/primer3_config/loops.ds
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+ - lib/qu/cmdwrapper/primer3_config/stack.dh
100
+ - lib/qu/cmdwrapper/primer3_config/stack.ds
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+ - lib/qu/cmdwrapper/primer3_config/stackmm.dh
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+ - lib/qu/cmdwrapper/primer3_config/stackmm.ds
103
+ - lib/qu/cmdwrapper/primer3_config/tetraloop.dh
104
+ - lib/qu/cmdwrapper/primer3_config/tetraloop.ds
105
+ - lib/qu/cmdwrapper/primer3_config/triloop.dh
106
+ - lib/qu/cmdwrapper/primer3_config/triloop.ds
107
+ - lib/qu/cmdwrapper/primer3_config/tstack.dh
108
+ - lib/qu/cmdwrapper/primer3_config/tstack2.dh
109
+ - lib/qu/cmdwrapper/primer3_config/tstack2.ds
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+ - lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds
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+ - lib/qu/cmdwrapper/version.rb
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+ - qu-cmdwrapper.gemspec
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+ homepage: https://github.com/quwubin/qu-cmdwrapper
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
128
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 2.2.0
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+ signing_key:
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+ specification_version: 4
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+ summary: A wrapper for command-line tools
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+ test_files: []