Mercurial > repos > biowebdb > flash
annotate Flash_wrapper.rb @ 1:e70d522bcaae draft default tip
Include xml
| author | biowebdb |
|---|---|
| date | Thu, 20 Mar 2014 14:58:18 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| 1 | 1 #!/usr/bin/ruby |
| 2 require 'logger' | |
| 3 require "#{ENV['biowebdb']}/bioinformatics/Bioinformatics" | |
| 4 c = Bioinformatics.program 'Flash' | |
| 5 c.logger(Logger.new(STDOUT)) | |
| 6 c.sequence1 = ARGV[0] | |
| 7 c.sequence2 = ARGV[1] | |
| 8 c.readLen = ARGV[2] | |
| 9 c.fragLen = ARGV[3] | |
| 10 c.maxOverlap = ARGV[4] | |
| 11 c.workPath = '/tmp/' | |
| 12 c.execute(c.lineCommand) | |
| 13 | |
| 14 Kernel.system("cp #{c.outExtended} #{ARGV[5]}") | |
| 15 Kernel.system("cp #{c.outNotComb1} #{ARGV[6]}") | |
| 16 Kernel.system("cp #{c.outNotComb2} #{ARGV[7]}") | |
| 17 |