Ruby IO::popen and crossbow

http://www.ruby-doc.org/core/classes/IO.html#M000880

Looking to use this method ( I think)

To run this commandline command, from within ruby:

$CROSSBOW_HOME/cb_emr \
    --name "Crossbow-Ecoli" \ 
    --preprocess \ 
    --input=s3n://bgs.crossbow-01/example/e_coli/small.manifest \ 
    --output=s3n://bgs.crossbow-01/example/e_coli/output_small \ 
    --reference=s3n://

The above is what I enter in to the command line to run directly from console

So I'm pretty sure I've got the IO method correct... but I'm fai开发者_开发知识库rly lost on translating the above code into the input

THis should do the trick:

command =<<END_OF_COMMAND
#{ENV["CROSSBOW_HOME"]}/cb_emr \
    --name "Crossbow-Ecoli" \ 
    --preprocess \ 
    --input=s3n://bgs.crossbow-01/example/e_coli/small.manifest \ 
    --output=s3n://bgs.crossbow-01/example/e_coli/output_small \ 
    --reference=s3n://
END_OF_COMMAND

IO.popen(command) do |handle|
  handle.each_line do |line|
     puts line
  end
end

I am iterating over each line of the output, because I'm guessing you may want to process it somehow.