gistfile1.txt

$./cb_emr \
    --name "Crossbow-HG18" \
    --preprocess \
    --input=s3n://bg-crossbow-01/example/human_g18/small.manifest \
    --output=s3n://bg-crossbow-01/example/human_g18/output_full \
    --reference=s3n://bg-crossbow-01/crossbow-refs/hg18.jar \
    --instances 1





command =<<END_OF_COMMAND
#{ENV["CROSSBOW_HOME"]}/cb_emr \
    --name "Crossbow-HG18" \
    --preprocess \
    --input=s3n://bg-crossbow-01/example/human_g18/small.manifest \
    --output=s3n://bg-crossbow-01/example/human_g18/output_full \
    --reference=s3n://bg-crossbow-01/crossbow-refs/hg18.jar \
    --instances 1
END_OF_COMMAND

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