Module Expr Str ImportFrom alias Import alias Import alias Import alias ImportFrom alias alias FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str Assign NameStore Call AttributeLoad NameLoad attr keyword Str Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str keyword Str keyword AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Str Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign NameStore BinOpMod Str SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore BinOpMod Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad Str Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad Str Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq NameLoad Num body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad Str Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore ListLoad Str Str AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list
N/A N/A Manage a cluster's life cycle. __future__ print_function N/A argparse N/A os N/A sys bcbiovm.aws bootstrap common setup_cmd N/A N/A awsparser N/A N/A N/A parser_sub_b N/A N/A awsparser add_parser cluster help Run and manage AWS clusters N/A parser_b N/A N/A parser_sub_b add_subparsers title [cluster specific actions] N/A parser N/A N/A parser_b add_parser bootstrap help Update a bcbio AWS system with the latest code and tools formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument -R --no-reboot default False action store_true help Don't upgrade the cluster host OS and reboot N/A N/A N/A parser add_argument -q --quiet dest verbose action store_false default True help Quiet output when running Ansible playbooks N/A N/A N/A parser set_defaults func bootstrap_cluster N/A parser N/A N/A parser_b add_parser command help Run a script on the bcbio frontend node inside a screen session formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument script metavar SCRIPT help Local path of the script to run. The screen session name is the basename of the script. N/A N/A N/A parser set_defaults func run_remote N/A parser N/A N/A parser_b add_parser ssh help SSH to a bcbio cluster formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument -q --quiet dest verbose action store_false default True help Quiet output when running Ansible playbooks N/A N/A N/A parser add_argument args metavar ARG nargs * help Execute the following command on the remote machine instead of opening an interactive shell. N/A N/A N/A parser set_defaults func ssh N/A parser N/A N/A parser_b add_parser start help Start a bcbio cluster formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument -R --no-reboot default False action store_true help Don't upgrade the cluster host OS and reboot N/A N/A N/A parser add_argument -q --quiet dest verbose action store_false default True help Quiet output when running Ansible playbooks N/A N/A N/A parser set_defaults func start N/A parser N/A N/A parser_b add_parser setup help Rerun cluster configuration steps formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument -q --quiet dest verbose action store_false default True help Quiet output when running Ansible playbooks N/A N/A N/A parser set_defaults func setup N/A parser N/A N/A parser_b add_parser stop help Stop a bcbio cluster formatter_class N/A argparse ArgumentDefaultsHelpFormatter N/A parser N/A N/A common add_default_ec_args parser N/A N/A N/A parser add_argument -q --quiet dest verbose action store_false default True help Quiet output when running Ansible playbooks N/A N/A N/A parser set_defaults func stop N/A bootstrap_cluster N/A N/A args N/A N/A N/A Bootstrap bcbio, or upgrade bcbio on an existing cluster. N/A N/A N/A bootstrap bootstrap args N/A run_remote N/A N/A args N/A N/A N/A Run a script on the frontend node inside a screen session. N/A config N/A N/A common ecluster_config N/A args econfig N/A cluster N/A N/A config load_cluster N/A args cluster N/A frontend N/A N/A cluster get_frontend_node N/A client N/A N/A frontend connect known_hosts_file N/A cluster known_hosts_file N/A cmd echo $HOME N/A N/A stdin stdout stderr N/A N/A client exec_command cmd N/A remote_home N/A N/A N/A N/A stdout read strip N/A remote_file N/A N/A N/A os path join remote_home N/A N/A N/A os path basename N/A args script N/A log_file N/A %s.log N/A N/A N/A N/A os path splitext remote_file N/A 0 N/A screen_name N/A N/A N/A N/A os path splitext N/A N/A N/A os path basename remote_file N/A 0 N/A sftp N/A N/A client open_sftp N/A N/A N/A sftp put N/A args script remote_file N/A N/A N/A sftp close N/A cmd N/A chmod a+x %s remote_file N/A N/A N/A client exec_command cmd N/A cmd N/A N/A screen -d -m -S {} bash -c '{} &> {}' format screen_name remote_file log_file N/A N/A stdin stdout stderr N/A N/A client exec_command cmd N/A N/A N/A stdout read N/A N/A N/A client close N/A N/A print N/A N/A Running {} on AWS in screen session {} format remote_file screen_name N/A ssh N/A N/A args N/A N/A N/A SSH to a cluster. N/A ec_args N/A elasticluster ssh N/A args cluster N/A ec_args N/A N/A common bcbio_args_to_ec ec_args args N/A N/A N/A sys exit N/A N/A common wrap_elasticluster ec_args N/A start N/A N/A args N/A N/A N/A Start and bootstrap a cluster. N/A ec_args N/A elasticluster start N/A args cluster N/A ec_args N/A N/A common bcbio_args_to_ec ec_args args N/A status N/A N/A common wrap_elasticluster ec_args N/A N/A status 0 N/A N/A N/A N/A sys exit status N/A N/A bootstrap_cluster args N/A setup N/A N/A args N/A N/A N/A Rerun cluster configuration commands. N/A ec_args N/A elasticluster setup N/A args cluster N/A ec_args N/A N/A common bcbio_args_to_ec ec_args args N/A N/A N/A sys exit N/A N/A common wrap_elasticluster ec_args N/A stop N/A N/A args N/A N/A N/A Stop a cluster. N/A ec_args N/A elasticluster stop N/A args cluster N/A ec_args N/A N/A common bcbio_args_to_ec ec_args args N/A N/A N/A sys exit N/A N/A common wrap_elasticluster ec_args N/A