# File lib/bio/shell/setup.rb, line 15
15:   def initialize
16:     check_ruby_version
17: 
18:     # command line options
19:     getoptlong
20: 
21:     # setup working directory
22:     savedir = setup_savedir
23: 
24:     # load configuration and plugins
25:     Bio::Shell.configure(savedir)
26: 
27:     # set default to irb mode
28:     Bio::Shell.cache[:mode] = @mode || :irb
29: 
30:     case Bio::Shell.cache[:mode]
31:     when :web
32:       # setup rails server
33:       Bio::Shell::Web.new
34:     when :irb
35:       # setup irb server
36:       Bio::Shell::Irb.new
37:     when :script
38:       # run bioruby shell script
39:       Bio::Shell::Script.new(@script)
40:     end
41:   end

    # File lib/bio/shell/setup.rb, line 43
43:   def check_ruby_version
44:     if RUBY_VERSION < "1.8.2"
45:       raise "BioRuby shell runs on Ruby version >= 1.8.2"
46:     end
47:   end

    # File lib/bio/shell/setup.rb, line 50
50:   def getoptlong
51:     opts = GetoptLong.new
52:     opts.set_options(
53:       [ '--rails',   '-r',  GetoptLong::NO_ARGUMENT ],
54:       [ '--web',     '-w',  GetoptLong::NO_ARGUMENT ],
55:       [ '--console', '-c',  GetoptLong::NO_ARGUMENT ],
56:       [ '--irb',     '-i',  GetoptLong::NO_ARGUMENT ]
57:     )
58:     opts.each_option do |opt, arg|
59:       case opt
60:       when /--rails/, /--web/
61:         @mode = :web
62:       when /--console/, /--irb/
63:         @mode = :irb
64:       end
65:     end
66:   end

     # File lib/bio/shell/setup.rb, line 105
105:   def install_savedir(savedir)
106:     FileUtils.makedirs(savedir)
107:   end

     # File lib/bio/shell/setup.rb, line 68
 68:   def setup_savedir
 69:     arg = ARGV.shift
 70: 
 71:     # Options after the '--' argument are not parsed by GetoptLong and
 72:     # are passed to irb or rails.  This hack preserve the first option
 73:     # when working directory of the project is not given.
 74:     if arg and arg[/^-/]
 75:       ARGV.unshift arg
 76:       arg = nil
 77:     end
 78: 
 79:     if arg.nil?
 80:       # run in the current directory
 81:       if File.exist?(Bio::Shell::Core::HISTORY)
 82:         savedir = Dir.pwd
 83:       else
 84:         savedir = File.join(ENV['HOME'].to_s, ".bioruby")
 85:         install_savedir(savedir)
 86:       end
 87:     elsif File.file?(arg)
 88:       # run file as a bioruby shell script
 89:       savedir = File.join(File.dirname(arg), "..")
 90:       @script = arg
 91:       @mode = :script
 92:     else
 93:       # run in new or existing directory
 94:       if arg[/^#{File::SEPARATOR}/]
 95:         savedir = arg
 96:       else
 97:         savedir = File.join(Dir.pwd, arg)
 98:       end
 99:       install_savedir(savedir)
100:     end
101: 
102:     return savedir
103:   end