Module: ViralSeq::R

Defined in:
lib/viral_seq/R.rb

Class Method Summary collapse

Class Method Details

.check_R ⇒ Object

check if R is installed. if R is installed, return the version number of R.



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# File 'lib/viral_seq/R.rb', line 6

def self.check_R
  begin
    r_version = `R --version`.split("\n")[0]
  rescue Errno::ENOENT
    abort '"R" is not installed. Install R at https://www.r-project.org/' +
          "\n`tcs_sdrm` pipeline aborted."
  end
end

.check_R_packages ⇒ Object

check if required R packages is installed.



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# File 'lib/viral_seq/R.rb', line 16

def self.check_R_packages
  file = File.join(ViralSeq.root, "viral_seq", "util", "check_env.r")
  safe_file = Shellwords.escape(file)
  if system "Rscript #{safe_file}"
    return 0
  else
    raise "Non-zero exit code. Error happens when checking required R packages."
  end
end

.get_sdrm_rscript ⇒ Object

read sdrm rscript as a string.



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# File 'lib/viral_seq/R.rb', line 28

def self.get_sdrm_rscript
  File.read(File.join(ViralSeq.root, "viral_seq", "util", "sdrm_r.r"))
end