text: """Fabric deployment file to install genomic data on remote instances.
  
  Designed to automatically download and manage biologically associated
  data on cloud instances like Amazon EC2.
  
  Fabric (http://docs.fabfile.org) manages automation of remote servers.
  
  Usage:
      fab -i key_file -H servername -f data_fabfile.py install_data
  """
  import os
  import sys
  
  from fabric.main import load_settings
  from fabric.api import *
  from fabric.contrib.files import *
  from fabric.context_managers import path
  try:
      import boto
  except ImportError:
      boto = None
  
  # preferentially use local cloudbio directory
  for to_remove in [p for p in sys.path if p.find("cloudbiolinux-") > 0]:
      sys.path.remove(to_remove)
  sys.path.append(os.path.dirname(__file__))
  
  from cloudbio.utils import _setup_logging, _configure_fabric_environment
  from cloudbio.biodata import genomes
  
  # -- Host specific setup
  
  env.remove_old_genomes = False
  
  def setup_environment():
      """Setup environment with required data file locations.
      """
      _setup_logging(env)
      _add_defaults()
      _configure_fabric_environment(env, ignore_distcheck=True)
  
  def _add_defaults():
      """Defaults from fabricrc.txt file; loaded if not specified at commandline.
      """
      env.config_dir = os.path.join(os.path.dirname(__file__), "config")
      conf_file = "tool_data_table_conf.xml"
      env.tool_data_table_conf_file = os.path.join(os.path.dirname(__file__),
                                                   "installed_files", conf_file)
      if not env.has_key("distribution"):
          config_file = os.path.join(env.config_dir, "fabricrc.txt")
          if os.path.exists(config_file):
              env.update(load_settings(config_file))
  
  CONFIG_FILE = os.path.join(os.path.dirname(__file__), "config", "biodata.yaml")
  
  def install_data(config_source=CONFIG_FILE):
      """Main entry point for installing useful biological data.
      """
      setup_environment()
      genomes.install_data(config_source)
  
  def install_data_raw(config_source=CONFIG_FILE):
      """Installing useful biological data building from scratch. Useful for debugging.
      """
      setup_environment()
      genomes.install_data(config_source, approaches=["raw"])
  
  def install_data_s3(config_source=CONFIG_FILE, do_setup_environment=True):
      """Install data using pre-existing genomes present on Amazon s3.
      """
      setup_environment()
      genomes.install_data_s3(config_source)
  
  def install_data_rsync(config_source=CONFIG_FILE):
      """Install data using Galaxy rsync data servers.
      """
      setup_environment()
      genomes.install_data_rsync(config_source)
  
  def install_data_ggd(recipe, organism):
      """Install data using Get Genomics Data (GGD) recipes.
      """
      setup_environment()
      from cloudbio.biodata import ggd, genomes
      genome_dir = os.path.join(genomes._make_genome_dir(), organism)
      recipe_file = os.path.join(os.path.dirname(__file__), "ggd-recipes", organism, "%s.yaml" % recipe)
      ggd.install_recipe(genome_dir, env, recipe_file, organism)
  
  def upload_s3(config_source=CONFIG_FILE):
      """Upload prepared genome files by identifier to Amazon s3 buckets.
      """
      setup_environment()
      genomes.upload_s3(config_source)
  