Module Expr Str Import alias Import alias Import alias Import alias Import alias identifier Import alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias identifier FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If CompareEq SubscriptLoad NameLoad Index Str Str body Assign TupleStore NameStore NameStore NameStore Call NameLoad SubscriptLoad NameLoad Index Str NameLoad NameLoad SubscriptLoad NameLoad Index Str Return TupleLoad NameLoad NameLoad Call NameLoad NameLoad NameLoad NameLoad NameLoad orelse If CompareEq SubscriptLoad NameLoad Index Str Str body Assign TupleStore NameStore NameStore Call NameLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotIn Str NameLoad body Assign SubscriptStore NameLoad Index Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Return TupleLoad NameLoad NameLoad Call AttributeLoad NameLoad attr NameLoad orelse Raise Call NameLoad BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body If CompareIn Str NameLoad body Return TupleLoad SubscriptLoad NameLoad Index Str NameLoad orelse If CompareEq SubscriptLoad NameLoad Index Str Str body Return Call NameLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str NameLoad orelse Raise Call NameLoad BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Str If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad body With Call NameLoad NameLoad Str NameStore body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Dict Str Call AttributeLoad NameLoad attr ListLoad Str Str NameLoad Dict Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareEq SubscriptLoad NameLoad Index Str Str body Assign NameStore BinOpMod Str TupleLoad Call AttributeLoad NameLoad attr ListLoad Str Str NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call NameLoad NameLoad NameLoad Call AttributeLoad NameLoad attr ListLoad Str Str NameLoad Return NameLoad orelse Raise Call NameLoad BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad With Call NameLoad NameLoad NameStore body Expr Call AttributeLoad NameLoad attr ListLoad Str Str Str NameLoad Str NameLoad Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If Call AttributeLoad NameLoad attr NameLoad body If CompareIn SubscriptLoad NameLoad Index Num ListLoad Str Str Str body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str orelse Assign NameStore NameLoad For NameStore Call AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str Str Expr Call NameLoad NameLoad NameLoad NameLoad Return Call AttributeLoad NameLoad attr NameLoad NameLoad orelse Return NameLoad decorator_list Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad Dict NameLoad NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call NameLoad ListLoad Str Assign NameStore Dict NameLoad NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If BoolOpAnd UnaryOpNot Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr NameLoad CompareNotIn SubscriptLoad NameLoad Index Num NameLoad body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Call NameLoad Call NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad decorator_list Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Dict Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str If UnaryOpNot NameLoad body Return TupleLoad NameLoad Dict NameLoad orelse Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad BinOpMod Str Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad NameLoad Return TupleLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Str If UnaryOpNot NameLoad body Return NameLoad For NameStore NameLoad body If CompareEq SubscriptLoad NameLoad Slice Call NameLoad NameLoad NameLoad body Return NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body If Call NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad For NameStore ListLoad Str Str Str Str Str body If Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd NameLoad NameLoad body If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad NameLoad BinOpAdd NameLoad NameLoad orelse Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad NameLoad orelse If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Return NameLoad decorator_list Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str FunctionDef arguments args NameParam defaults body If NameLoad body Assign NameStore DictComp NameLoad NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Assign NameStore IfExp NameLoad Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad NameLoad NameLoad If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Return NameLoad orelse Return NameLoad decorator_list Return NameLoad decorator_list
N/A N/A Reconstitute an analysis in a temporary directory on the current machine.

Handles copying or linking files into a work directory, running an analysis,
then handing off outputs to ship back to subsequent processing steps.
 N/A os N/A uuid N/A shutil N/A subprocess N/A toolz tz N/A yaml bcbio utils bcbio.distributed.transaction file_transaction bcbio.log logger bcbio.pipeline config_utils bcbiovm.docker remap bcbiovm.ship pack ship_n_pack prep_workdir N/A N/A pack parallel args N/A N/A N/A Unpack necessary files and directories into a temporary structure for processing
     N/A N/A N/A pack N/A type shared N/A N/A N/A workdir remap_dict new_args N/A _create_workdir_shared N/A pack N/A workdir args parallel N/A pack N/A tmpdir N/A N/A workdir new_args N/A _shared_finalizer new_args workdir remap_dict parallel N/A N/A N/A N/A pack N/A type S3 N/A N/A N/A workdir new_args N/A _unpack_s3 N/A N/A pack N/A buckets N/A run args N/A N/A datai data N/A N/A config_utils get_dataarg new_args N/A N/A dirs data N/A N/A N/A data N/A dirs N/A N/A N/A N/A data N/A dirs N/A work workdir N/A N/A new_args N/A datai data N/A N/A workdir new_args N/A N/A ship_n_pack send_run_integrated pack N/A N/A N/A ValueError N/A Cannot handle work directory preparation type: %s pack N/A prep_datadir N/A N/A pack args N/A N/A N/A N/A datadir pack N/A N/A N/A N/A pack N/A datadir args N/A N/A N/A N/A pack N/A type S3 N/A N/A N/A _unpack_s3 N/A N/A pack N/A buckets N/A biodata args N/A N/A N/A ValueError N/A Cannot handle biodata directory preparation type: %s pack N/A prep_systemconfig N/A N/A datadir args N/A N/A N/A Prepare system configuration files on bare systems if not present.
     N/A default_system N/A N/A N/A os path join datadir galaxy bcbio_system.yaml N/A N/A N/A N/A utils file_exists default_system N/A N/A N/A open default_system w out_handle N/A N/A N/A _ data N/A N/A config_utils get_dataarg args N/A out N/A resources N/A N/A tz get_in N/A config resources data N/A N/A N/A N/A yaml safe_dump out out_handle default_flow_style False allow_unicode False N/A get_output N/A N/A target_file pconfig N/A N/A N/A Retrieve an output file from pack configuration.
     N/A N/A N/A pconfig N/A type S3 N/A N/A keyname N/A %s/%s N/A N/A N/A tz get_in N/A folders output pconfig N/A N/A N/A os path basename target_file N/A N/A _transfer_s3 target_file keyname N/A N/A tz get_in N/A buckets run pconfig N/A target_file N/A N/A N/A NotImplementedError N/A Unexpected pack information for fetchign output: %s pconfig N/A _transfer_s3 N/A N/A out_fname keyname bucket N/A N/A N/A N/A N/A N/A N/A os path exists out_fname N/A N/A N/A N/A utils safe_makedir N/A N/A N/A os path dirname out_fname N/A N/A file_transaction out_fname tx_out_fname N/A N/A N/A N/A subprocess check_call N/A gof3r get -p tx_out_fname -k keyname -b bucket N/A _unpack_s3 N/A N/A bucket args N/A N/A N/A Create local directory in current directory with pulldowns from S3.
     N/A local_dir N/A N/A utils safe_makedir N/A N/A N/A os path join N/A N/A os getcwd bucket N/A remote_key N/A s3://%s bucket _get_s3 N/A N/A orig_fname context remap_dict N/A N/A N/A Pull down s3 published data locally for processing.
         N/A N/A N/A orig_fname startswith remote_key N/A N/A N/A N/A context N/A 0 N/A reference genome_resources sam_ref N/A N/A cur_dir N/A N/A N/A os path join local_dir genomes N/A N/A cur_dir local_dir N/A fname N/A N/A utils file_plus_index orig_fname N/A N/A out_fname N/A N/A fname replace remote_key cur_dir N/A keyname N/A N/A fname replace N/A remote_key / N/A N/A _transfer_s3 out_fname keyname bucket N/A N/A N/A orig_fname replace remote_key cur_dir N/A N/A orig_fname N/A N/A new_args N/A N/A remap walk_files args _get_s3 N/A remote_key local_dir N/A N/A local_dir new_args N/A _remap_dict_shared N/A N/A workdir new_workdir args N/A N/A N/A Prepare a remap dictionary with directories we should potential copy files from.
     N/A ignore_keys N/A set N/A algorithm N/A out N/A workdir new_workdir _update_remap N/A N/A fname context remap_dict N/A N/A N/A Updated list of directories we should potentially be remapping in.
         N/A N/A N/A N/A N/A fname startswith N/A tuple N/A N/A out keys context N/A N/A context N/A 0 ignore_keys N/A N/A dirname N/A N/A N/A os path normpath N/A N/A N/A os path dirname fname N/A local_dir N/A N/A utils safe_makedir N/A N/A N/A os path join new_workdir external N/A str N/A len out N/A N/A out N/A dirname local_dir N/A N/A N/A N/A remap walk_files args _update_remap N/A N/A out N/A _create_workdir_shared N/A N/A workdir args parallel tmpdir N/A None N/A N/A Create a work directory given inputs from the shared filesystem.

    If tmpdir is not None, we create a local working directory within the
    temporary space so IO and processing occurs there, remapping the input
    argument paths at needed.
     N/A N/A tmpdir N/A N/A N/A workdir N/A args N/A N/A new_workdir N/A N/A utils safe_makedir N/A N/A N/A os path join tmpdir N/A bcbio-work-%s N/A N/A uuid uuid1 N/A remap_dict N/A _remap_dict_shared workdir new_workdir args N/A new_args N/A N/A remap walk_files args N/A _remap_copy_file parallel remap_dict N/A N/A new_workdir remap_dict new_args N/A is_required_resource N/A N/A context parallel N/A N/A N/A fresources N/A N/A parallel get fresources N/A N/A fresources N/A N/A True N/A fresource fresources N/A N/A N/A N/A context N/A N/A len fresource fresource N/A N/A True N/A False N/A _remap_copy_file N/A N/A parallel N/A N/A N/A Remap file names and copy into temporary directory as needed.

    Handles simultaneous transfer of associated indexes.
     _do N/A N/A fname context orig_to_temp N/A N/A N/A new_fname N/A N/A remap remap_fname fname context orig_to_temp N/A N/A N/A N/A os path isfile fname N/A N/A N/A is_required_resource context parallel N/A N/A N/A N/A logger info N/A YES: %s: %s N/A context fname N/A N/A N/A utils safe_makedir N/A N/A N/A os path dirname new_fname N/A ext N/A .idx .gbi .tbi .bai N/A N/A N/A N/A N/A os path exists N/A fname ext N/A N/A N/A N/A N/A N/A os path exists N/A new_fname ext N/A N/A N/A N/A shutil copyfile N/A fname ext N/A new_fname ext N/A N/A N/A N/A logger info N/A NO: %s: %s N/A context fname N/A N/A N/A N/A N/A os path isdir fname N/A N/A N/A N/A utils safe_makedir new_fname N/A new_fname N/A N/A _do N/A _shared_finalizer N/A N/A args workdir remap_dict parallel N/A N/A N/A Cleanup temporary working directory, copying missing files back to the shared workdir.
     _do N/A N/A out N/A N/A N/A remap_dict N/A N/A new_remap_dict N/A v k N/A N/A k v N/A N/A remap_dict items N/A new_out N/A out N/A N/A remap walk_files out N/A _remap_copy_file parallel new_remap_dict None N/A N/A N/A N/A os path exists workdir N/A N/A N/A N/A shutil rmtree workdir N/A new_out N/A N/A out N/A N/A _do N/A