Skip to content

Instantly share code, notes, and snippets.

@fstrozzi

fstrozzi/gist:1815523

Created February 13, 2012 09:45
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save fstrozzi/1815523 to your computer and use it in GitHub Desktop.
Save fstrozzi/1815523 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
gistfile1.rb
desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification"
Bio::Ngs::Cufflinks::Quantification.new.thor_task(self, :quant) do |wrapper, task, gtf, outputdir, bam|
wrapper.params = task.options
wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF" => gtf }
wrapper.run :arguments=>[bam], :separator => "="
end
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment