changeset 1:2b93b36547ba draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wrapper_arpa.rb	Wed Feb 03 11:23:41 2016 -0500
@@ -0,0 +1,41 @@
+#!/usr/bin/env ruby
+##
+## Wrapper Arpa 
+##
+## By: Isis Soledad, 2015
+##
+## Updates: 
+##      - Rodrigo Jardim, 206
+##
+
+# ARGV[0] - Output File
+# ARGV[1] - Input File in Fasta Format
+# ARGV[2] - ARPA Complement Parameters 
+output = ARGV[0]
+dirOut = "/tmp/arpa_#{Time.now.strftime("%Y%m%d%H%M%S")}"
+file = ARGV[1]
+params = ARGV[2]
+
+# Create Output temporary dir
+unless File.directory?(dirOut)
+    Kernel.system("mkdir #{dirOut}")
+end
+
+# Copy Input file to temporary dir
+unless File.exist?("#{dirOut}/#{File.basename(file)}")
+    Kernel.system("cp #{file} #{dirOut}/#{File.basename(file)}.fasta")
+end
+
+#puts "python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null"
+
+# Call OS process
+Kernel.system("python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null")
+
+# Copact temporary dir
+Kernel.system("cd #{dirOut} && zip output.zip *"
+
+# Copy compact file to output galaxy
+Kernel.system("cp #{dirOut}/output.zip #{output}")
+
+# Remove temporary dir
+Kernel.system("rm -rf #{dirout}")