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Library and Tools for interfacing to PacBio pbsmrtpipe workflow engine.

Project description

pbcommand High Level Overview




PacBio Officially Supported Library. Note the APIs are still in flux and not yet 1.0.0.

[Full Docs](

[![Circle CI](](

PacBio library for common utils, models, and tools to interface with pbsmrtpipe workflow engine.

To integrate with the pbsmrtpipe workflow engine you must to be able to generate a **Tool Contract** and to be able to run from a **Resolved Tool Contract**.

A **Tool Contract** contains the metadata of the exe, such as the file types of inputs, outputs and options.

Example [Tool Contract Json]( (and [Avro Schema](

Example [Resolved Tool Contract Json]( (and [Avro Schema](

There are two principle use cases, first wrapping/calling python functions that have been defined in external python packages, or scripts. Second, creating a CLI tool that supports emitting tool contracts, running resolved tool contracts and complete argparse style CLI.

Example from **pbcommand.cli.examples**


import sys
import logging

from pbcommand.models import FileTypes
from pbcommand.cli import registry_builder, registry_runner

log = logging.getLogger(__name__)

registry = registry_builder("pbcommand", "python -m pbcommand.cli.examples.dev_quick_hello_world ")

def _example_main(input_files, output_files, **kwargs):
# Simple Function that should imported from your library code
# write mock output files for testing purposes, otherwise the End-to-End test will fail
xs = output_files if isinstance(output_files, (list, tuple)) else [output_files]
for x in xs:
with open(x, 'w') as writer:
writer.write("Mock data\n")
return 0

@registry("dev_qhello_world", "0.2.1", FileTypes.FASTA, FileTypes.FASTA, nproc=1, options=dict(alpha=1234))
def run_rtc(rtc):
return _example_main(rtc.task.input_files[0], rtc.task.output_files[0], nproc=rtc.task.nproc)

@registry("dev_fastq2fasta", "0.1.0", FileTypes.FASTQ, FileTypes.FASTA)
def run_rtc(rtc):
return _example_main(rtc.task.input_files[0], rtc.task.output_files[0])

if __name__ == '__main__':
sys.exit(registry_runner(registry, sys.argv[1:]))


A driver is the commandline interface that the workflow engine will call.

The driver will be called with "${exe} /path/to/resolved_tool_contract.json"

The tool contracts can be emitted to a directory and used in [pbsmrtpipe](

$> python -m pbcommand.cli.examples.dev_quick_hello_world -o /path/to/my-tool-contracts

Creating a Full Commandline Tool with TC/RTC and argparse support

Three Steps
- define Parser
- add running from argparse and running from Resolved ToolContract funcs to call your main
- add call to driver

Import or define your main function.

def run_my_main(fasta_in, fasta_out, min_length):
# do stuff. Main should return an int exit code
return 0

Define a function that will add inputs, outputs and options to your parser.

from pbcommand.models import FileTypes

def add_args_and_options(p):
# FileType, label, name, description
p.add_input_file_type(FileTypes.FASTA, "fasta_in", "Fasta File", "PacBio Spec'ed fasta file")
# File Type, label, name, description, default file name
p.add_output_file_type(FileTypes.FASTA, "fasta_out", "Filtered Fasta file", "Filtered Fasta file", "filter.fasta")
# Option id, label, default value, name, description
# for the argparse, the read-length will be translated to --read-length and (accessible via args.read_length)
p.add_int("pbcommand.task_options.dev_read_length", "read-length", 25, "Length filter", "Min Sequence Length filter")
return p

Define Parser

from pbcommand.models import TaskTypes, SymbolTypes, get_pbparser

def get_contract_parser():
tool_id = "example_namespace.tasks.my_id"
version = "0.1.0" # or reuse __version__
display_name = "My Example Tool"
# Number of processors to use, can also be SymbolTypes.MAX_NPROC
nproc = 1
# Log file, tmp dir, tmp file. See ResourceTypes in models, ResourceTypes.TMP_DIR
resource_types = ()
# Commandline exe to call "{exe}" /path/to/resolved-tool-contract.json
driver_exe = "python -m pbcommand.cli.example.dev_app --resolved-tool-contract "
desc = "Dev app for Testing that supports emitting tool contracts"
is_distributed = False
# set to True if you want your task to be submitted to the cluster manager (e.g., SGE) if
# one is provided to the workflow engine.
p = get_pbparser(tool_id, version, display_name, desc, driver_exe, is_distributed=is_distributed, nproc=nproc, resource_types=resource_types)
return p

Define a Wrapping layer to call your main from both the tool contract and raw argparse IO layer

def _args_runner(args):
# this is the args from parser.parse_args()
# the properties of args are defined as "labels" in the add_args_and_options func.
return run_my_main(args.fasta_in, args.fasta_out, args.read_length)

def _resolved_tool_contract_runner(resolved_tool_contract):
:type resolved_tool_contract: pbcommand.models.ResolvedToolContract"""
rtc = resolved_tool_contract
# all options are referenced by globally namespaced id. This allows tools to use other tools options
# e.g., pbalign to use blasr defined options.
return run_my_main(rtc.task.input_files[0], rtc.task.outputs[0], rtc.task.options["pbcommand.task_options.dev_read_length"])

Add running layer

import sys
import logging
from pbcommand.utils import setup_log
from pbcommand.cli import pbparser_runner

log = logging.getLogger(__name__)

def main(argv=sys.argv):
# New interface that supports running resolved tool contracts"Starting {f} version {v} pbcommand example dev app".format(f=__file__, v="0.1.0"))
return pbparser_runner(argv[1:],
_args_runner, # argparse runner func
_resolved_tool_contract_runner, # tool contract runner func
log, # log instance
setup_log # setup log func
if __name__ == '__main__':

Now you can run your tool via the argparse standard interface as well as emitting a **Tool Contract** to stdout from the commandline interface.

> python -m 'pbcommand.cli.examples.dev_app' --emit-tool-contract

And you can run the tool from a **Resolved Tool Contract**

> python -m pbcommand.cli.example.dev_app --resolved-tool-contract /path/to/resolved_contract.json

See the dev apps in ["pbcommand.cli.examples"]( for a complete application (They require pbcore to be installed).

In addition to TC/RTC support, there's a complete argparse support for the task options. An example of **help** is shown below.

(pbcommand_test)pbcommand $> python -m 'pbcommand.cli.examples.dev_app' --help
usage: [-h] [-v] [--versions] [--emit-tool-contract]
[--resolved-tool-contract RESOLVED_TOOL_CONTRACT]
[--log-level LOG_LEVEL] [--debug]
[--read-length READ_LENGTH]
fasta_in fasta_out

Dev app for Testing that supports emitting tool contracts

positional arguments:
fasta_in PacBio Spec'ed fasta file
fasta_out Filtered Fasta file

optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--versions Show versions of individual components (default: None)
--emit-tool-contract Emit Tool Contract to stdout (default: False)
--resolved-tool-contract RESOLVED_TOOL_CONTRACT
Run Tool directly from a PacBio Resolved tool contract
(default: None)
--log-level LOG_LEVEL
Set log level (default: 10)
--debug Debug to stdout (default: False)
--read-length READ_LENGTH
Min Sequence Length filter (default: 25)

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