Mercurial > repos > biowebdb > arpa
comparison wrapper_arpa.rb @ 1:2b93b36547ba draft default tip
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| author | biowebdb |
|---|---|
| date | Wed, 03 Feb 2016 11:23:41 -0500 |
| parents | |
| children |
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| 0:7548aa64d696 | 1:2b93b36547ba |
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| 1 #!/usr/bin/env ruby | |
| 2 ## | |
| 3 ## Wrapper Arpa | |
| 4 ## | |
| 5 ## By: Isis Soledad, 2015 | |
| 6 ## | |
| 7 ## Updates: | |
| 8 ## - Rodrigo Jardim, 206 | |
| 9 ## | |
| 10 | |
| 11 # ARGV[0] - Output File | |
| 12 # ARGV[1] - Input File in Fasta Format | |
| 13 # ARGV[2] - ARPA Complement Parameters | |
| 14 output = ARGV[0] | |
| 15 dirOut = "/tmp/arpa_#{Time.now.strftime("%Y%m%d%H%M%S")}" | |
| 16 file = ARGV[1] | |
| 17 params = ARGV[2] | |
| 18 | |
| 19 # Create Output temporary dir | |
| 20 unless File.directory?(dirOut) | |
| 21 Kernel.system("mkdir #{dirOut}") | |
| 22 end | |
| 23 | |
| 24 # Copy Input file to temporary dir | |
| 25 unless File.exist?("#{dirOut}/#{File.basename(file)}") | |
| 26 Kernel.system("cp #{file} #{dirOut}/#{File.basename(file)}.fasta") | |
| 27 end | |
| 28 | |
| 29 #puts "python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null" | |
| 30 | |
| 31 # Call OS process | |
| 32 Kernel.system("python /usr/local/arpa/arpa.py #{params} -o #{dirOut} #{dirOut}/#{File.basename(file)}.fasta 1>/dev/null") | |
| 33 | |
| 34 # Copact temporary dir | |
| 35 Kernel.system("cd #{dirOut} && zip output.zip *" | |
| 36 | |
| 37 # Copy compact file to output galaxy | |
| 38 Kernel.system("cp #{dirOut}/output.zip #{output}") | |
| 39 | |
| 40 # Remove temporary dir | |
| 41 Kernel.system("rm -rf #{dirout}") |