--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Flash_wrapper.rb	Thu Mar 20 14:58:18 2014 -0400
@@ -0,0 +1,17 @@
+#!/usr/bin/ruby
+require 'logger'
+require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics"
+c = Bioinformatics.program 'Flash'
+c.logger(Logger.new(STDOUT))
+c.sequence1 = ARGV[0]
+c.sequence2 = ARGV[1]
+c.readLen = ARGV[2]
+c.fragLen = ARGV[3]
+c.maxOverlap = ARGV[4]
+c.workPath = '/tmp/'
+c.execute(c.lineCommand)
+
+Kernel.system("cp #{c.outExtended} #{ARGV[5]}")
+Kernel.system("cp #{c.outNotComb1} #{ARGV[6]}")
+Kernel.system("cp #{c.outNotComb2} #{ARGV[7]}")
+