sequenceserver

#!/usr/bin/env ruby
require 'readline'
require 'English'
require 'slop'

ENV['RACK_ENV'] ||= 'production'

# display name for tools like `ps`
$PROGRAM_NAME = 'sequenceserver'

begin
  Slop.parse!(:strict => true, :help => true) do
    banner <<BANNER
SUMMARY

custom, local, BLAST server

USAGE

sequenceserver [options]

Example:

  # launch SequenceServer with the given config file
  $ sequenceserver -c ~/.sequenceserver.ants.conf

  # use the bundled database formatter utility to prepare databases for use
  # with SequenceServer
  $ sequenceserver -m

DESCRIPTION

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
interface for use locally or over the web.

If BLAST+ is not installed on your system, SequenceServer will offer to install
BLAST+ for you.

You should only ever have to point it to a directory of FASTA files.

In a given directory, SequenceServer is able to tell FASTA files that are yet
to be formatted for use with BLAST+ and format them, and FASTA files that are
already formatted for use with BLAST+, heuristically skipping all other files
in the directory. Directories are scanned recursively. Type of sequences in a
FASTA file is detected automagically. `parse_seqids` option of `makeblastdb` is
used to create BLAST+ databases.
BANNER

    on 'c', 'config_file=',
       'Use the given configuration file',
       :argument => true
    on 'config=',
       'Same as --config_file (deprecated)',
       :argument => true

    on 'b', 'bin=',
       'Load BLAST+ binaries from this directory',
       :argument => true

    on 'd', 'database_dir=',
       'Read FASTA and BLAST database from this directory',
       :argument => true

    on 'n', 'num_threads=',
       'Number of threads to use to run a BLAST search',
       :argument => true

    on 'r', 'require=',
       'Load extension from this file',
       :argument => true

    on 'h', 'host=',
       'Host to run SequenceServer on',
       :argument => true

    on 'p', 'port=',
       'Port to run SequenceServer on',
       :argument => true

    on 's', 'set',
       'Set configuration value in default or given config file'

    on 'm', 'make-blast-databases',
       'Create BLAST databases'

    on 'l', 'list_databases',
       'List BLAST databases'

    on 'u', 'list-unformatted-fastas',
       'List unformatted FASTA files'

    on 'i', 'interactive',
       'Run SequenceServer in interactive mode'

    on 'D', 'devel',
       'Start SequenceServer in development mode'

    on '-v', '--version',
       'Print version number of SequenceServer that will be loaded'

    on '-h', '--help',
       'Display this help message'

    clean_opts = lambda do |hash|
      hash.delete_if { |k, v| k == :set || v.nil? }
      hash[:config_file] ||= hash.delete(:config)
      hash
    end

    run do
      if version?
        gemspec_file = File.join(File.dirname(__FILE__), '..',
                                 'sequenceserver.gemspec')
        gemspec = eval File.read gemspec_file
        puts gemspec.version
        exit
      end

      ENV['RACK_ENV'] = 'development' if devel?

      # Exit gracefully on SIGINT.
      stty = `stty -g`.chomp
      trap('INT') do
        puts ''
        puts 'Aborted.'
        system('stty', stty)
        exit
      end

      require 'sequenceserver'

      begin
        SequenceServer.init clean_opts[to_h]

      # The aim of following error recovery scenarios is to guide user to a
      # working SequenceServer installation. We expect to land following
      # error scenarios either when creating a new SequenceServer (first
      # time or later), or updating config values using -s CLI option.

      rescue SequenceServer::CONFIG_FILE_ERROR => e

        puts e
        exit!

      rescue SequenceServer::BIN_DIR_NOT_FOUND => e

        puts e

        unless bin?
          puts 'You can set the correct value by running:'
          puts
          puts '  sequenceserver -s -b <value>'
          puts
        end

        exit!

      rescue SequenceServer::DATABASE_DIR_NOT_FOUND => e

        puts e

        unless database_dir?
          puts 'You can set the correct value by running:'
          puts
          puts '  sequenceserver -s -d <value>'
          puts
        end

        exit!

      rescue SequenceServer::NUM_THREADS_INCORRECT => e

        puts e

        unless num_threads?
          puts 'You can set the correct value by running:'
          puts
          puts '  sequenceserver -s -n <value>'
          puts
        end

        exit!

      rescue SequenceServer::EXTENSION_FILE_NOT_FOUND => e

        puts e

        unless require?
          puts 'You can set the correct value by running:'
          puts
          puts '  sequenceserver -s -r <value>'
          puts
        end

        exit!

      rescue SequenceServer::BLAST_NOT_INSTALLED,
             SequenceServer::BLAST_NOT_COMPATIBLE => e

        # Show original error message first.
        puts
        puts e

        # Set a flag so that if we recovered from error resulting config can be
        # saved. Config will be saved unless invoked with -b option.
        fetch_option(:set).value = !bin?

        # Ask user if she already has BLAST+ downloaded or offer to download
        # BLAST+ for her.
        puts
        puts <<MSG
SequenceServer can use NCBI BLAST+ that you may have on your system already, or
download the correct package for itself. Please enter the path to NCBI BLAST+
or press Enter to download.

Press Ctrl+C to quit.
MSG
        puts
        response = Readline.readline('>> ').to_s.strip
        if response.empty?
          puts
          puts 'Installing NCBI BLAST+.'
          puts "RUBY_PLATFORM #{RUBY_PLATFORM}"

          version = SequenceServer::MINIMUM_BLAST_VERSION
          url = case RUBY_PLATFORM
                when /i686-linux/   # 32 bit Linux
                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
                  "#{version.chop}/ncbi-blast-#{version}-ia32-linux.tar.gz"
                when /x86_64-linux/ # 64 bit Linux
                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
                  "#{version.chop}/ncbi-blast-#{version}-x64-linux.tar.gz"
                when /darwin/       # Mac
                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
                  "#{version.chop}/" \
                  "ncbi-blast-#{version}-universal-macosx.tar.gz"
                else
                  puts <<ERR
------------------------------------------------------------------------
FAILED!! to install NCBI BLAST+.

We currently support Linux and Mac only (both 32 and 64 bit). If you
believe you are running a supported platform, please open a support
ticket titled "#{RUBY_PLATFORM}" at:

https://github.com/yannickwurm/sequenceserver/issues
------------------------------------------------------------------------

ERR
                end

          archive = File.join('/tmp', File.basename(url))
          # -ip4 is required  to avoid this curl bug http://sourceforge.net/p/curl/bugs/1424/?limit=25
          # see also https://github.com/yannickwurm/sequenceserver/issues/139
          system "curl -ip4 -C - #{url} -o #{archive} && mkdir -p ~/.sequenceserver" \
            "&& tar xvf #{archive} -C ~/.sequenceserver"
          unless $CHILD_STATUS.success?
            puts 'Failed to install BLAST+.'
            puts '  You may need to download BLAST+ from - '
            puts '   http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download'
            puts "  Please ensure that you download BLAST+ version
            #{SequenceServer::MINIMUM_BLAST_VERSION} or higher."
            exit!
          end
          fetch_option(:bin).value =
            "~/.sequenceserver/ncbi-blast-#{version}/bin/"
          redo
        else
          unless File.basename(response) == 'bin'
            response = File.join(response, 'bin')
          end
          fetch_option(:bin).value = File.join(response)
          puts
          redo
        end
      rescue SequenceServer::DATABASE_DIR_NOT_SET => e

        # Show original error message.
        puts
        puts e

        # Set a flag so that if we recovered from error resulting config can be
        # saved. Config will be saved unless invoked with -d option.
        fetch_option(:set).value = !database_dir?

        # Ask user for the directory containing sequences or BLAST+
        # databases.
        puts
        puts <<MSG
SequenceServer needs to know where your FASTA files or BLAST+ databases are.
Please enter the path to the relevant directory (default: current directory).

Press Ctrl+C to quit.
MSG

        puts
        response = Readline.readline('>> ').to_s.strip
        fetch_option(:database_dir).value = response
        redo

      rescue SequenceServer::NO_BLAST_DATABASE_FOUND => e
        unless list_databases? || list_unformatted_fastas? ||
               make_blast_databases?

          # Print error raised.
          puts
          puts e

          # Offer user to format the FASTA files.
          database_dir = SequenceServer.config[:database_dir]
          puts
          puts <<MSG
Search for FASTA files (.fa, .fasta, .fna) in '#{database_dir}' and try
creating BLAST+ databases? [y/n] (Default: y).
MSG
          puts
          print '>> '
          response = STDIN.gets.to_s.strip
          unless response.match(/^[n]$/i)
            puts
            puts 'Searching ...'
            if SequenceServer::Database.unformatted_fastas.empty?
              puts "Couldn't find any FASTA files."
              exit!
            else
              formatted = SequenceServer::Database.make_blast_databases
              exit! if formatted.empty? && !set?
              redo unless set?
            end
          else
            exit! unless set?
          end
        end
      end

      if interactive?
        SequenceServer.irb
        exit
      end

      if list_databases?
        puts SequenceServer::Database.all
        exit
      end

      if list_unformatted_fastas? || make_blast_databases?
        unformatted_fastas = SequenceServer::Database.unformatted_fastas
        if unformatted_fastas.empty?
          puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
               'are formatted.'
          exit
        end
      end

      if list_unformatted_fastas?
        puts unformatted_fastas
        exit
      end

      if make_blast_databases?
        SequenceServer::Database.make_blast_databases
        exit
      end

      if set?
        SequenceServer.config.write_config_file
        exit
      end

      SequenceServer.config.write_config_file if fetch_option(:set).value

      SequenceServer.run
    end
  end
rescue Slop::Error => e
  puts e
  puts "Run '#{$PROGRAM_NAME} -h' for help with command line options."
  exit
end