<s> """<STR_LIT>""" <EOL> from __future__ import print_function <EOL> import argparse <EOL> import os <EOL> import sys <EOL> from bcbiovm . aws import bootstrap , common <EOL> def setup_cmd ( awsparser ) : <EOL> parser_sub_b = awsparser . add_parser ( "<STR_LIT>" , help = "<STR_LIT>" ) <EOL> parser_b = parser_sub_b . add_subparsers ( title = "<STR_LIT>" ) <EOL> parser = parser_b . add_parser ( "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , <EOL> default = False , action = "<STR_LIT:store_true>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , default = True , <EOL> help = "<STR_LIT>" ) <EOL> parser . set_defaults ( func = bootstrap_cluster ) <EOL> parser = parser_b . add_parser ( "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , metavar = "<STR_LIT>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . set_defaults ( func = run_remote ) <EOL> parser = parser_b . add_parser ( "<STR_LIT>" , help = "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , default = True , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT:args>" , metavar = "<STR_LIT>" , nargs = "<STR_LIT:*>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . set_defaults ( func = ssh ) <EOL> parser = parser_b . add_parser ( "<STR_LIT:start>" , help = "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , <EOL> default = False , action = "<STR_LIT:store_true>" , <EOL> help = "<STR_LIT>" ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , default = True , <EOL> help = "<STR_LIT>" ) <EOL> parser . set_defaults ( func = start ) <EOL> parser = parser_b . add_parser ( "<STR_LIT>" , help = "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , default = True , <EOL> help = "<STR_LIT>" ) <EOL> parser . set_defaults ( func = setup ) <EOL> parser = parser_b . add_parser ( "<STR_LIT>" , help = "<STR_LIT>" , <EOL> formatter_class = argparse . ArgumentDefaultsHelpFormatter ) <EOL> parser = common . add_default_ec_args ( parser ) <EOL> parser . add_argument ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT>" , default = True , <EOL> help = "<STR_LIT>" ) <EOL> parser . set_defaults ( func = stop ) <EOL> def bootstrap_cluster ( args ) : <EOL> """<STR_LIT>""" <EOL> bootstrap . bootstrap ( args ) <EOL> def run_remote ( args ) : <EOL> """<STR_LIT>""" <EOL> config = common . ecluster_config ( args . econfig ) <EOL> cluster = config . load_cluster ( args . cluster ) <EOL> frontend = cluster . get_frontend_node ( ) <EOL> client = frontend . connect ( known_hosts_file = cluster . known_hosts_file ) <EOL> cmd = "<STR_LIT>" <EOL> stdin , stdout , stderr = client . exec_command ( cmd ) <EOL> remote_home = stdout . read ( ) . strip ( ) <EOL> remote_file = os . path . join ( remote_home , os . path . basename ( args . script ) ) <EOL> log_file = "<STR_LIT>" % os . path . splitext ( remote_file ) [ <NUM_LIT:0> ] <EOL> screen_name = os . path . splitext ( os . path . basename ( remote_file ) ) [ <NUM_LIT:0> ] <EOL> sftp = client . open_sftp ( ) <EOL> sftp . put ( args . script , remote_file ) <EOL> sftp . close ( ) <EOL> cmd = "<STR_LIT>" % remote_file <EOL> client . exec_command ( cmd ) <EOL> cmd = "<STR_LIT>" . format ( <EOL> screen_name , remote_file , log_file ) <EOL> stdin , stdout , stderr = client . exec_command ( cmd ) <EOL> stdout . read ( ) <EOL> client . close ( ) <EOL> print ( "<STR_LIT>" . format ( <EOL> remote_file , screen_name ) ) <EOL> def ssh ( args ) : <EOL> """<STR_LIT>""" <EOL> ec_args = [ "<STR_LIT>" , "<STR_LIT>" , args . cluster ] <EOL> ec_args = common . bcbio_args_to_ec ( ec_args , args ) <EOL> sys . exit ( common . wrap_elasticluster ( ec_args ) ) <EOL> def start ( args ) : <EOL> """<STR_LIT>""" <EOL> ec_args = [ "<STR_LIT>" , "<STR_LIT:start>" , args . cluster ] <EOL> ec_args = common . bcbio_args_to_ec ( ec_args , args ) <EOL> status = common . wrap_elasticluster ( ec_args ) <EOL> if status != <NUM_LIT:0> : <EOL> sys . exit ( status ) <EOL> bootstrap_cluster ( args ) <EOL> def setup ( args ) : <EOL> """<STR_LIT>""" <EOL> ec_args = [ "<STR_LIT>" , "<STR_LIT>" , args . cluster ] <EOL> ec_args = common . bcbio_args_to_ec ( ec_args , args ) <EOL> sys . exit ( common . wrap_elasticluster ( ec_args ) ) <EOL> def stop ( args ) : <EOL> """<STR_LIT>""" <EOL> ec_args = [ "<STR_LIT>" , "<STR_LIT>" , args . cluster ] <EOL> ec_args = common . bcbio_args_to_ec ( ec_args , args ) <EOL> sys . exit ( common . wrap_elasticluster ( ec_args ) ) </s>
