lib/bio/db/primer3.rb in bio-polyploid-tools-1.2.0 vs lib/bio/db/primer3.rb in bio-polyploid-tools-1.2.1

@@ -32,16 +32,20 @@
     end
   end
 
   def self.run(opts={})
     puts "Primer3.run running..."
-
+    timeout = 600
     f_in=opts[:in]
     f_out=opts[:out]
+    timeout = opts[:timeout] if opts[:timeout]
     opts.delete(:in)
     opts.delete(:out)
     primer_3_in = File.read(f_in)
-    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr=''
+    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr='' do |cid|
+      sleep timeout
+      Process.kill 9, cid
+    end
     # $stderr.puts cmdline
     if status.exitstatus == 0
       File.open(f_out, 'w') { |f| f.write(stdout) }
     else
       raise Primer3Exception.new(), "Error running primer3. Command line was 'primer3_core'\nPrimer3 STDERR was:\n#{stderr}"