mpkocher

mpkocher

"""Example of Convert to RST"""

import sys
from collections import namedtuple

from pbcommand.cli import get_default_argparser_with_base_opts
from pbcommand.validators import validate_dir
from pbsmrtpipe.models import Pipeline

__version__ = "0.1.0"

mpkocher

(pbsmrtpipe_test)21326a76b5b1ca7c27f82fc74fe4ea7b $> ipython -i generate_file_types_r_code.py 
Python 2.7.10 (default, Jul 13 2015, 12:05:58) 
Type "copyright", "credits" or "license" for more information.

IPython 5.0.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

mpkocher

from pbcommand.models import FileTypes
# Generate the pbcommandR file type definitions from the python code
# https://github.com/PacificBiosciences/pbcommandR/blob/master/R/common.R


def to_n(ext):
    return ext.replace(".", '').replace("_", "")


def to_r(ft):

mpkocher

object Example {

  trait DataSet {
    def name: String
  }

  case class SubreadSet(name: String) extends DataSet
  case class AlignSet(name: String) extends DataSet

mpkocher

pbcommand >= 0.4.5

mpkocher

mpkocher

Automation of Analysis Job Submission

Analysis Jobs can submitted using pbservice using a JSON file that specifies the pipeline template id and the entry points as UUID.

pbservice run-analysis --host smrtlink-bihourly --port 8081 --block --debug /path/to/analysis-job.json

The analysis-job.json encodes the pipeline template and DataSet entry points that should be used. The DataSets are referenced by UUID and pipeline entry point point id/label are dependent on a specific pipeline id (e.g., pbsmrtpipe.pipelines.resequencing).

The --block option will block the process and poll the job status. In the absence of the --block, the job will only be submitted.

mpkocher

mpkocher

#!/usr/bin/env python

import os
import sys
import logging
from pbcommand.utils import setup_log

try:
    import pbcommand
except ImportError: