Class: Bio::Ngs::Utils

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ngs/utils.rb

Defined Under Namespace

Classes: BinaryNotFound

Constant Summary collapse

@@skip_check_binaries = 
false

Class Method Summary collapse

Class Method Details

.binary(name) ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 36

def binary(name)
  unless skip_check_binaries?
    begin
      if !(plugin_binaries_found = find_binary_files(name)).empty?
        return plugin_binaries_found.first
      elsif (os_binary = Bio::Command.query_command ["which", name]) != ""
        return os_binary.tr("\n","")
      else
        raise BinaryNotFound.new(:skip_task=>true), "No binary found with this name: #{name}"
      end
    rescue BinaryNotFound => e
      warn e.message
    end
  end
end

.compile_source(tool_name, tool_record, path_external, path_binary) ⇒ Object

uncompress



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# File 'lib/bio/ngs/utils.rb', line 148

def compile_source(tool_name, tool_record, path_external, path_binary)
  puts "Uncompressing #{tool_name}..."
  tool_dir_name = uncompress_any(tool_name, tool_record)
  puts "Compiling #{tool_name}..."
  cd(tool_dir_name) do
    #system "#{tool_record["lib"]}='#{path_external}/bin/common/lib'" if tool_record["lib"]
    #system "#{tool_record["flags"]}='-O2'" if tool_record["flags"]
    system "PKG_CONFIG_PATH='#{path_external}/bin/common/lib/pkgconfig' ./configure --prefix=#{path_binary} --bindir=#{path_binary}"
    system "make"
    system "make install"
  end #cd
end

.download_and_uncompress(url, fileout) ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 117

def download_and_uncompress(url,fileout)
  self.download_with_progress(:url => url,:mode => "b",:filename => fileout)
  self.uncompress_gz_file(fileout)
end

.download_with_progress(opts = {:url => nil, :mode => "", :filename => nil}) ⇒ Object

extend_system_path



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# File 'lib/bio/ngs/utils.rb', line 82

def download_with_progress(opts = {:url => nil, :mode => "", :filename => nil})
require "open-uri"
require "progressbar"
puts "Downloading from #{opts[:url]}"
filename = (opts[:filename]) ? opts[:filename] : opts[:url].split('/')[-1]
mode = (opts[:mode]) ? opts[:mode] : ""
pbar = nil
open(opts[:url],"r"+mode,
  :content_length_proc => lambda {|t|
    if t && 0 < t
      pbar = ProgressBar.new('', t)
      pbar.file_transfer_mode
    end
  },
  :progress_proc => lambda {|s|
    pbar.set s if pbar
  }) do |remote|
    open(filename,"w"+mode) {|file| file.write remote.read(16384) until remote.eof?}
  end
  puts "\nDone"
end

.extend_system_path ⇒ Object

tag_filename



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# File 'lib/bio/ngs/utils.rb', line 70

def extend_system_path
  path = File.expand_path(File.dirname(__FILE__))
  common_dir= File.join(path,"ext","bin","common")
  os_dir = File.join(path,"ext","bin",self.os_type)
  sub_dirs = Dir[os_dir+"/*"].select do |file|
    File.directory?(file)
  end.map do |dir|
    ":"+dir
  end.join
  ENV["PATH"]+=":"+common_dir+":"+os_dir + sub_dirs
end

.find_binary_files(binary_name) ⇒ Object

search in the current gem’s directory for installed binaries which the name binary_name it’s a recursive search in common and os specific directories return an array: empty if the binary can not be found otherwise full path to the binaries it is up to the user choose which binary to use, it’s suggested to use the first in the array to have a behavirou similar to the search PATH



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# File 'lib/bio/ngs/utils.rb', line 189

def find_binary_files(binary_name)
  path = File.expand_path(File.dirname(__FILE__))
  Find.find(File.join(path,"ext","bin","common"),File.join(path,"ext","bin",self.os_type)).select do |f|
    File.file?(f) && File.basename(f) == binary_name
  end
end

.install_binary(tool_name, tool_record, path_external, path_binary) ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 171

def install_binary(tool_name, tool_record, path_external, path_binary)
  require 'fileutils'
  include FileUtils::Verbose
  puts "Uncompressing #{tool_name}"
  uncompressed_tool_dir_name = uncompress_any(tool_name, tool_record)
  puts "Installing #{tool_name}"
  path_binary_tool = File.join(path_binary,tool_name)
  FileUtils.remove_dir(path_binary_tool) if Dir.exists?(path_binary_tool)
  FileUtils.mkdir(path_binary_tool)
  FileUtils.cp_r "#{uncompressed_tool_dir_name}/.", path_binary_tool, :preserve=>true
end

.just_make(tool_name, tool_record, path_external, path_binary) ⇒ Object

uncompress_compile



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# File 'lib/bio/ngs/utils.rb', line 161

def just_make(tool_name, tool_record, path_external, path_binary)
  puts "Uncompressing #{tool_name}..."
  tool_dir_name = uncompress_any(tool_name, tool_record)
  puts "Compiling #{tool_name}..."
  cd(tool_dir_name) do
    system "make"
    FileUtils.cp tool_name,path_binary
  end #cd
end

.os_type ⇒ Object

binary



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# File 'lib/bio/ngs/utils.rb', line 52

def os_type
  require 'rbconfig'
  case RbConfig::CONFIG['host_os']
  when /darwin/ then return "osx"
  when /linux/ then return "linux"
  when /mswin|mingw/ then raise NotImplementedError, "This plugin does not run on Windows"
  end
end

.skip_check_binaries ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 28

def skip_check_binaries
  @@skip_check_binaries=true
end

.skip_check_binaries? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/ngs/utils.rb', line 32

def skip_check_binaries?
  @@skip_check_binaries
end

.tag_filename(filename, tag, extension) ⇒ Object

Remove from filename the dot and the extension, adds the tag and the new extension



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# File 'lib/bio/ngs/utils.rb', line 62

def tag_filename(filename, tag, extension)
  if filename=~/\..*/
    filename.gsub(/\..*/, "_#{tag}.#{extension}")
  else
    "#{filename}_#{tag}.#{extension}"
  end
end

.uncompress_any(tool_name, tool_record) ⇒ Object

uncompress_command



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# File 'lib/bio/ngs/utils.rb', line 132

def uncompress_any(tool_name, tool_record)
  tool_file_name = "#{tool_record["basename"]}.#{tool_record["suffix"]}"
  tool_dir_name = tool_record["basename"]
  uncompress = uncompress_command(tool_record["suffix"])
  STDERR.puts "#{uncompress} #{tool_file_name}"
  system "#{uncompress} #{tool_file_name}"
  STDERR.puts "completed."
  if Dir.exists?(tool_dir_name)
    tool_dir_name
  elsif Dir.exists?("#{tool_name}-#{tool_record['version']}")
    "#{tool_name}-#{tool_record['version']}"
  else
    raise "BioNGS can not identify the uncompressed destination folder"
  end
end

.uncompress_command(suffix) ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 122

def uncompress_command(suffix)
  case suffix
  when "tar.bz2" then "tar xvfj"
  when "tar.gz" then "tar xvfz"
  when "zip" then "unzip"
  else
    raise "Unkonw suffix."
  end
end

.uncompress_gz_file(file_in) ⇒ Object 



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# File 'lib/bio/ngs/utils.rb', line 104

def uncompress_gz_file(file_in)
  require 'zlib'
  puts "Uncompressing file #{file_in}"
  file_out = file_in.gsub(/.gz/,"")
  Zlib::GzipReader.open(file_in) {|gz|
    open(file_out,"w") do |file|
      file.write gz.read
    end
  }
  puts "Done\n"
end