old_contents: #!/usr/bin/python3
  
  HG19_LOCATION = '~/hg19/'
  
  from subprocess import call
  comands = [
      'sudo apt-get install r-bioc-biomart -y',
      'sudo apt-get install r-bioc-bsgenome -y',
      'sudo apt-get install python3-pip',
      'sudo apt-get install bowtie -y',
  ]
  
  for c in comands:
      call(c.split(' '))
  
  #PIP INSTALL (IN THE RUNNING ENV)
  import pip
  py_libs = [
      'rpy2',
      'cutadapt',
  ]
  
  for p in py_libs:
      if pip.main(['install', p]):
          print("{} SUCCESFULY INSTALLED".format(p))
      else:
          return
  
  r_commands = [
      'source("https://bioconductor.org/biocLite.R")',
      'library(BiocInstaller)',
      'biocLite("wavClusteR")',
      'install.packages("doParallel")',
      'biocLite("BSgenome.Hsapiens.UCSC.hg19")',
      'biocLite("XML")',
  ]
  
  import rpy2.robjects as robjects
  
  for r in r_commands:
      robjects.r(r)
  
  
  #hg19 for bowtie
  
  cmd = [
      'cd {}'.format(HG19_LOCATION),
      'wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip',
      'unzip hg19.ebwt.zip',
      'sh make_hg19.sh',
  ]
  
  #for c in cmd:
  #    call(c.split(' '))
  
new_contents: #!/usr/bin/python3
  
  HG19_LOCATION = '~/hg19/'
  
  from subprocess import call
  comands = [
      'sudo apt-get install r-bioc-biomart -y',
      'sudo apt-get install r-bioc-bsgenome -y',
      'sudo apt-get install python3-pip -y',
      'sudo apt-get install bowtie -y',
  ]
  
  for c in comands:
      call(c.split(' '))
  
  #PIP INSTALL (IN THE RUNNING ENV)
  import pip
  py_libs = [
      'rpy2',
      'cutadapt',
  ]
  
  for p in py_libs:
      if pip.main(['install', p]):
          print("{} SUCCESFULY INSTALLED".format(p))
  
  r_commands = [
      'source("https://bioconductor.org/biocLite.R")',
      'library(BiocInstaller)',
      'biocLite("wavClusteR")',
      'install.packages("doParallel")',
      'biocLite("BSgenome.Hsapiens.UCSC.hg19")',
      'biocLite("XML")',
  ]
  
  import rpy2.robjects as robjects
  
  for r in r_commands:
      robjects.r(r)
  
  
  #hg19 for bowtie
  
  download = False
  
  if download:
      cmd = [
          'cd {}'.format(HG19_LOCATION),
          'wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip',
          'unzip hg19.ebwt.zip',
          'sh make_hg19.sh',
      ]
  
  else:
      cmd = [
          'mv ../hg19.ebwt.zip {}/hg19.ebwt.zip'.format(),
          'cd {}'.format(HG19_LOCATION),
          'unzip hg19.ebwt.zip',
          'sh make_hg19.sh',
          ]
  
  for c in cmd:
      call(c.split(' '))
  
subject: install update