def configure_instance(options, actions):
if "setup_image" in actions:
_configure_package_holds(options)
configure_MI(env)
configure_smtp(options)
configure_sudoers(options)
if "install_biolinux" in actions:
install_biolinux(options)
if "purge_tools" in actions:
purge_tools()
if "setup_tools" in actions:
install_tools(options["tools"])
if "purge_genomes" in actions:
purge_genomes()
if "setup_genomes" in actions:
setup_genomes(options)
if "purge_galaxy" in actions:
purge_galaxy()
if "setup_galaxy" in actions:
seed = _seed_at_configure_time(options)
setup_galaxy(options, seed=seed)
if seed:
seed_workflows(options)
if "setup_ssh_key" in actions:
configure_ssh_key(options)
def configure_instance(options, actions):
if "setup_image" in actions:
_configure_package_holds(options)
configure_MI(env)
configure_smtp(options)
configure_sudoers(options)
if "install_biolinux" in actions:
install_biolinux(options)
if "purge_tools" in actions:
purge_tools()
if "setup_tools" in actions:
install_tools(options["tools"])
if "purge_genomes" in actions:
purge_genomes()
if "setup_genomes" in actions:
setup_genomes(options)
if "purge_galaxy" in actions:
purge_galaxy()
if "setup_galaxy" in actions:
seed = _seed_at_configure_time(options)
setup_galaxy(options, seed=seed)
if seed:
seed_workflows(options)
if "setup_ssh_key" in actions:
configure_ssh_key(options)
def _setup_vm(options, vm_launcher, actions):
destroy_on_complete = get_boolean_option(options, 'destroy_on_complete',
False)
use_galaxy = get_boolean_option(options, 'use_galaxy', False)
try:
ip = vm_launcher.get_ip()
_setup_fabric(vm_launcher, ip, options)
with settings(host_string=ip):
_setup_cloudbiolinux(options)
if 'attach_volumes' in actions:
attach_volumes(vm_launcher, options)
if 'max_lifetime' in options:
seconds = options['max_lifetime']
# Unclear why the sleep is needed, but seems to be otherwise
# this doesn't work.
run("bash -c 'nohup sudo shutdown -h %d &'; sleep 2" % seconds)
configure_instance(options, actions)
do_refresh_galaxy = get_boolean_option(options, 'refresh_galaxy',
False)
do_upload_genomes = get_boolean_option(options, 'upload_genomes',
False)
if do_refresh_galaxy:
refresh_galaxy(env.galaxy_repository)
if use_galaxy:
copy_runtime_properties(ip, options)
if 'transfer' in actions:
transfer_files(options)
if do_upload_genomes:
upload_genomes(options)
if not _seed_at_configure_time(options) and use_galaxy:
seed_database()
seed_workflows(options)
if 'transfer' in actions and use_galaxy:
wait_for_galaxy()
create_data_library_for_uploads(options)
if 'ssh' in actions:
_interactive_ssh(vm_launcher)
if 'attach_ip' in actions:
vm_launcher.attach_public_ip()
if 'snapshot_volumes' in actions:
make_snapshots(vm_launcher, options)
if 'detach_volumes' in actions:
detach_volumes(vm_launcher, options)
if 'package' in actions:
name_template = vm_launcher.package_image_name()
name = eval_template(env, name_template)
vm_launcher.package(name=name)
if not destroy_on_complete:
print 'Your Galaxy instance (%s) is waiting at http://%s' % (
vm_launcher.uuid, ip)
finally:
if destroy_on_complete:
vm_launcher.destroy()
def _setup_vm(options, vm_launcher, actions):
destroy_on_complete = get_boolean_option(options, 'destroy_on_complete', False)
use_galaxy = get_boolean_option(options, 'use_galaxy', False)
try:
ip = vm_launcher.get_ip()
_setup_fabric(vm_launcher, ip, options)
with settings(host_string=ip):
_setup_cloudbiolinux(options)
if 'attach_volumes' in actions:
attach_volumes(vm_launcher, options)
if 'max_lifetime' in options:
seconds = options['max_lifetime']
# Unclear why the sleep is needed, but seems to be otherwise
# this doesn't work.
run("bash -c 'nohup sudo shutdown -h %d &'; sleep 2" % seconds)
configure_instance(options, actions)
do_refresh_galaxy = get_boolean_option(options, 'refresh_galaxy', False)
do_upload_genomes = get_boolean_option(options, 'upload_genomes', False)
if do_refresh_galaxy:
refresh_galaxy(env.galaxy_repository)
if use_galaxy:
copy_runtime_properties(ip, options)
if 'transfer' in actions:
transfer_files(options)
if do_upload_genomes:
upload_genomes(options)
if not _seed_at_configure_time(options) and use_galaxy:
seed_database()
seed_workflows(options)
if 'transfer' in actions and use_galaxy:
wait_for_galaxy()
create_data_library_for_uploads(options)
if 'ssh' in actions:
_interactive_ssh(vm_launcher)
if 'attach_ip' in actions:
vm_launcher.attach_public_ip()
if 'snapshot_volumes' in actions:
make_snapshots(vm_launcher, options)
if 'detach_volumes' in actions:
detach_volumes(vm_launcher, options)
if 'package' in actions:
name_template = vm_launcher.package_image_name()
name = eval_template(env, name_template)
vm_launcher.package(name=name)
if not destroy_on_complete:
print 'Your Galaxy instance (%s) is waiting at http://%s' % (vm_launcher.uuid, ip)
finally:
if destroy_on_complete:
vm_launcher.destroy()
