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1 #!/usr/bin/env ruby
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2 ##
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3 ## Wrapper Arpa
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4 ##
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5 ## By: Isis Soledad, 2015
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6 ##
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7 ## Updates:
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8 ## - Rodrigo Jardim, 206
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9 ##
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10
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11 # ARGV[0] - Output File
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12 # ARGV[1] - Input File in Fasta Format
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13 # ARGV[2] - ARPA Complement Parameters
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14 output = ARGV[0]
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15 dirOut = "/tmp/arpa_#{Time.now.strftime("%Y%m%d%H%M%S")}"
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16 file = ARGV[1]
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17 params = ARGV[2]
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18
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19 # Create Output temporary dir
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20 unless File.directory?(dirOut)
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21 Kernel.system("mkdir #{dirOut}")
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22 end
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23
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24 # Copy Input file to temporary dir
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25 unless File.exist?("#{dirOut}/#{File.basename(file)}")
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26 Kernel.system("cp #{file} #{dirOut}/#{File.basename(file)}.fasta")
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27 end
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28
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29 #puts "python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null"
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30
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31 # Call OS process
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32 Kernel.system("python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null")
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33
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34 # Copact temporary dir
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35 Kernel.system("cd #{dirOut} && zip output.zip *"
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36
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37 # Copy compact file to output galaxy
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38 Kernel.system("cp #{dirOut}/output.zip #{output}")
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39
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40 # Remove temporary dir
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41 Kernel.system("rm -rf #{dirout}")
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