genevalidatorapp 1.5.4 → 2.0.0

data/bin/genevalidatorapp

@@ -1,284 +0,0 @@
-#!/usr/bin/env ruby
-require 'readline'
-require 'English'
-require 'slop'
-
-ENV['RACK_ENV'] ||= 'production'
-
-# display name for tools like `ps`
-$PROGRAM_NAME = 'genevalidatorapp'
-
-begin
-  Slop.parse!(strict: true, help: true) do
-    banner <<BANNER
-SUMMARY:
-  GeneValidator - Identify problems with predicted genes
-
-USAGE:
-  $ genevalidatorapp [options]
-
-Examples:
-  # Launch GeneValidatorApp with the given config file
-  $ genevalidatorapp --config ~/.genevalidatorapp.conf
-
-  # Launch GeneValidatorApp with 8 threads at port 8888
-  $ genevalidatorapp --num_threads 8 --port 8888
-
-  # Create a config file with the other arguments
-  $ genevalidatorapp -s -d ~/database_dir
-
-BANNER
-    # - Add Web_dir ? or simply default to ~/.genevalidatorapp/runs/
-
-    on 'c', 'config_file=',
-       'Use the given configuration file',
-       argument: true
-
-    on 'g', 'gv_public_dir=',
-       'The public directory that is served to the web application.',
-       argument: true
-
-    on 'b', 'bin=',
-       'Load BLAST+ and/or MAFFT binaries from this directory',
-       argument: true,
-       as: Array
-
-    on 'd', 'database_dir=',
-       'Read BLAST database from this directory',
-       argument: true
-
-    on 'f', 'default_database_path=',
-       'The path to the default BLAST database',
-       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 GeneValidatorApp on',
-       argument: true
-
-    on 'p', 'port=',
-       'Port to run GeneValidatorApp on',
-       argument: true
-
-    on 's', 'set',
-       'Set configuration value in default or given config file'
-
-    on 'l', 'list_databases',
-       'List BLAST databases'
-
-    on 'D', 'devel',
-       'Start GeneValidatorApp in development mode'
-
-    on '-v', '--version',
-       'Print version number of GeneValidatorApp 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
-    end
-
-    run do
-      if version?
-        require 'genevalidatorapp/version'
-        puts GeneValidatorApp::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 'genevalidatorapp'
-
-      begin
-        GeneValidatorApp.init clean_opts[to_h]
-
-      # The aim of following error recovery scenarios is to guide user to a
-      # working GeneValidatorApp installation. We expect to land following
-      # error scenarios either when creating a new GeneValidatorApp (first
-      # time or later), or updating config values using -s CLI option.
-
-      rescue GeneValidatorApp::CONFIG_FILE_ERROR => e
-
-        puts e
-        exit!
-
-      rescue GeneValidatorApp::NUM_THREADS_INCORRECT => e
-
-        puts e
-
-        unless num_threads?
-          puts 'You can set the correct value by running:'
-          puts
-          puts '  genevalidatorapp -s -n <value>'
-          puts
-        end
-
-        exit!
-
-      rescue GeneValidatorApp::BIN_DIR_NOT_FOUND => e
-
-        puts e
-
-        unless bin?
-          puts 'You can set the correct value by running:'
-          puts
-          puts '  genevalidatorapp -s -b <value>'
-          puts
-        end
-
-        exit!
-
-      rescue GeneValidatorApp::EXTENSION_FILE_NOT_FOUND => e
-
-        puts e
-
-        unless require?
-          puts 'You can set the correct value by running:'
-          puts
-          puts '  genevalidatorapp -s -r <value>'
-          puts
-        end
-
-        exit!
-
-      rescue GeneValidatorApp::DATABASE_DIR_NOT_FOUND => e
-
-        puts e
-
-        unless database_dir?
-          puts 'You can set the correct value by running:'
-          puts
-          puts '  genevalidatorapp -s -d <value>'
-          puts
-        end
-
-        exit!
-
-      rescue GeneValidatorApp::BLAST_NOT_INSTALLED,
-             GeneValidatorApp::BLAST_NOT_EXECUTABLE,
-             GeneValidatorApp::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.
-        puts
-        puts <<MSG
-GeneValidatorApp can use NCBI BLAST+ that you may have on your system already.
-Please enter the path to NCBI BLAST+.
-
-Press Ctrl+C to quit.
-MSG
-        puts
-        response = Readline.readline('>> ').to_s.strip
-        unless response.empty?
-          unless File.basename(response) == 'bin'
-            response = File.join(response, 'bin')
-          end
-          fetch_option(:bin).value = File.join(response)
-          puts
-          redo
-        end
-
-
-      rescue GeneValidatorApp::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
-GeneValidatorApp needs to know where your BLAST+ databases are.
-Please enter the path to the relevant directory.
-
-Press Ctrl+C to quit.
-MSG
-
-        puts
-        response = Readline.readline('>> ').to_s.strip
-        fetch_option(:database_dir).value = response
-        redo
-
-      rescue GeneValidatorApp::NO_BLAST_DATABASE_FOUND,
-             GeneValidatorApp::NO_PROTEIN_BLAST_DATABASE_FOUND => e
-        unless list_databases?
-          # Print error raised.
-          puts
-          puts e
-          exit!
-        end
-
-      rescue GeneValidatorApp::BLAST_DATABASE_ERROR => e
-
-        puts e
-        exit!
-
-      rescue => e
-        # This will catch any unhandled error and some very special errors.
-        # Ideally we will never hit this block. If we do, there's a bug in
-        # GeneValidatorApp or something really weird going on. If we hit this
-        # error block we show the stacktrace to the user requesting them to
-        # post the same to our Google Group.
-        puts <<MSG
-Something went wonky
-
-Looks like you have encountered a bug in GeneValidatorApp. Please could you
-report this incident here -
-https://github.com/wurmlab/genevalidatorapp/issues
-
-Error:
-#{e.backtrace.unshift(e.message).join("\n")}
-MSG
-        exit!
-      end
-
-      if list_databases?
-        puts GeneValidatorApp::Database.all
-        exit
-      end
-
-      if set?
-        GeneValidatorApp.config.write_config_file
-        exit
-      end
-
-      GeneValidatorApp.config.write_config_file if fetch_option(:set).value
-
-      GeneValidatorApp.run
-    end
-  end
-rescue Slop::Error => e
-  puts e
-  puts "Run '#{$PROGRAM_NAME} -h' for help with command line options."
-  exit
-end

data/docker/Dockerfile

@@ -1,21 +0,0 @@
-# GeneValidator
-#
-# A web wrapper for GeneValidator (identify problems with predicted genes)
-#
-# If you use GeneValidator in your work, please cite us as follows:
-#
-#  Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2016.
-#  GeneValidator: identify problems with protein-coding gene predictions.
-#  Bioinformatics, doi: 10.1093/bioinformatics/btw015.
-#
-# VERSION 1.0.0
-
-FROM ubuntu:16.04
-MAINTAINER Bruno Vieira <mail@bmpvieira.com>
-
-LABEL Description="Identify problems with protein-coding gene predictions http://genevalidator.sbcs.qmul.ac.uk" Version="1.0.0"
-
-RUN apt-get update
-RUN apt-get install -y build-essential ruby ruby-dev ncbi-blast+ mafft zlib1g-dev libgsl0-dev
-RUN gem install genevalidatorapp
-CMD genevalidatorapp -d /db