Class: MiGA::Cli::Action::Init

Inherits:
MiGA::Cli::Action show all
Includes:
DaemonHelper, FilesHelper
Defined in:
lib/miga/cli/action/init.rb

Defined Under Namespace

Modules: DaemonHelper, FilesHelper

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods included from FilesHelper

#check_additional_files, #check_configuration_script, #check_mytaxa_database, #check_mytaxa_scores, #check_phyla_lite, #check_rdp_classifier, #close_rc_file, #open_rc_file

Methods included from DaemonHelper

#configure_bash_daemon, #configure_daemon, #configure_qsub_msub_daemon, #configure_slurm_daemon, #configure_ssh_daemon

Methods inherited from MiGA::Cli::Action

#complete, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#empty_action ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 89

def empty_action
end

#list_requirements ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 105

def list_requirements
  if cli.ask_user(
    'Would you like to see all the requirements before starting?',
    'no', %w(yes no)
  ) == 'yes'
    cli.puts ''
    req_path = File.join(MiGA.root_path, 'utils', 'requirements.txt')
    File.open(req_path, 'r') do |fh|
      fh.each_line { |ln| cli.puts ln }
    end
    cli.puts ''
  end
end

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 12

def parse_cli
  cli.interactive = true
  cli.defaults = {
    mytaxa: nil,
    rdp: nil,
    reads: nil,
    optional: nil,
    config: File.join(ENV['MIGA_HOME'], '.miga_modules'),
    ask: false,
    auto: false,
    dtype: :bash
  }
  cli.parse do |opt|
    opt.on(
      '-c', '--config PATH',
      'Path to the Bash configuration file',
      "By default: #{cli[:config]}"
    ) { |v| cli[:config] = v }
    opt.on(
      '--[no-]mytaxa',
      'Should I try setting up MyTaxa and its dependencies?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:mytaxa] = v }
    opt.on(
      '--[no-]rdp',
      'Should I try setting up the RDP classifier?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:rdp] = v }
    opt.on(
      '--[no-]read-processing',
      'Should I try setting up read processing software?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:reads] = v }
    opt.on(
      '--[no-]optional',
      'Should I try setting up the optional software?',
      'Automatically sets answers for mytaxa, rdp, and reads'
    ) { |v| cli[:optional] = v }
    opt.on(
      '--daemon-type STRING',
      'Type of daemon launcher, one of: bash, ssh, qsub, msub, slurm',
      "By default: interactive (#{cli[:dtype]} if --auto)"
    ) { |v| cli[:dtype] = v.to_sym }
    %w[R ruby python].each do |bin|
      opt.on(
        "--path-to-#{bin} STRING",
        "Use this path to #{bin} instead of testing for executables"
      ) { |v| cli[:"path_to_#{bin}"] = v }
    end
    opt.on(
      '--ask-all',
      'Ask for the location of all software',
      'By default, only the locations missing in PATH are requested'
    ) { |v| cli[:ask] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 69

def perform
  cli.puts <<~BANNER
    ===[ Welcome to MiGA, the Microbial Genome Atlas ]===

    I'm the initialization script, and I'll sniff around your computer to
    make sure you have all the requirements for MiGA data processing.

  BANNER
  list_requirements
  rc_fh = open_rc_file
  check_configuration_script(rc_fh)
  paths = check_software_requirements(rc_fh)
  check_additional_files(paths)
  check_libraries(paths)
  configure_daemon
  close_rc_file(rc_fh)
  cli.puts 'Configuration complete. MiGA is ready to work!'
  cli.puts ''
end

#run_cmd(cli, cmd, opts = {}) ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 92

def run_cmd(cli, cmd, opts = {})
  opts = { return: :output, source: cli[:config] }.merge(opts)
  MiGA::MiGA.run_cmd(cmd, opts)
end

#run_r_cmd(cli, paths, cmd, opts = {}) ⇒ Object 



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# File 'lib/miga/cli/action/init.rb', line 97

def run_r_cmd(cli, paths, cmd, opts = {})
  run_cmd(
    cli,
    "echo #{cmd.shellescape} | #{paths['R'].shellescape} --vanilla -q",
    { err2out: true, stdout: '/dev/null' }.merge(opts)
  )
end