muscle_bio 0.2.0 → 0.3.0
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/README.md +6 -17
- data/lib/muscle_bio.rb +9 -1
- data/lib/muscle_bio/version.rb +1 -1
- data/muscle_bio.gemspec +1 -1
- metadata +3 -2
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: aa933fcac87a7b3662ee990c35d61d1df51a26ba
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data.tar.gz: 3b87a66959ff6d3dd2811290507fb40f022555f4
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SHA512:
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metadata.gz:
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metadata.gz: e75e2958cb504d8d394af1817471c814c5cf24daa215dea5de4a82100d456add5b47efe073c9bc5eca2a17748c39dc20101cf91190917bfc2e537a5a903ab20e
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data.tar.gz: b9c12e81029f8d2b707712bf364232ada0315466974758c5ad195574b688ee8580ed6832acbdf3ccd6580f3f3b111ce53dd9c3197944f0c07e14ac34d932d757
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data/Gemfile.lock
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data/README.md
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# MuscleBio
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TODO: Delete this and the text above, and describe your gem
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Supported on Mac, Linux, and Windows.
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## Installation
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@@ -22,22 +20,13 @@ Or install it yourself as:
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## Usage
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## Development
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After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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## Contributing
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require 'muscle_bio'
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MuscleBio.run('muscle -in ../sample/sequence.fasta -out ../sample/sequence.afa')
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#pass string in as your current Muscle command
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The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
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MuscleBio.init(fileIn, fileOut, maxIters)
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#maxIters is optional
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data/lib/muscle_bio.rb
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file = File.join( File.dirname(__FILE__), 'runnable/'+file)
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cmd = cmd.sub 'sudo ', ''
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cmd = cmd.sub 'muscle', file
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cmd = 'sudo ' + cmd
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cmd = 'sudo ' + cmd + " -quiet"
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`#{cmd}`
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end
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def self.init(fileIn, fileOut, maxIters = nil)
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cmd = "muscle -in " + fileIn + " -out " + fileOut
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if maxIters != nil
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cmd += " -maxiters " + maxIters
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end
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self.run(cmd)
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end
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end
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data/lib/muscle_bio/version.rb
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data/muscle_bio.gemspec
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@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
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spec.email = ["clarkmu@gmail.com"]
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spec.summary = %q{Run Muscle from Ruby gem}
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spec.description = %q{Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/}
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spec.description = %q{Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/. For instructions on how to use, see https://github.com/clarkmu/muscle_bio}
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spec.homepage = "http://swanstrom.web.unc.edu/"
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spec.license = "MIT"
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metadata
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--- !ruby/object:Gem::Specification
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name: muscle_bio
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.3.0
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platform: ruby
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authors:
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- Michael Clark
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.0'
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description: Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle
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description: Multiple Sequence Alignment for Ruby scripts. Muscle found at https://www.ebi.ac.uk/Tools/msa/muscle/. For
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instructions on how to use, see https://github.com/clarkmu/muscle_bio
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email:
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- clarkmu@gmail.com
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executables: []
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