jfeala

"""
AWS Batch wrapper for Luigi

From the AWS website:

    AWS Batch enables you to run batch computing workloads on the AWS Cloud. 

    Batch computing is a common way for developers, scientists, and engineers 
    to access large amounts of compute resources, and AWS Batch removes the 
    undifferentiated heavy lifting of configuring and managing the required 

jfeala

import os
from subprocess import check_output
from tempfile import mkstemp
import sys

import boto3
import requests

s3 = boto3.client('s3')

jfeala

import time
import logging

import boto3
import luigi

POLL_TIME = 2
client = boto3.client('ecs')
logger = logging.getLogger('luigi-interface')

jfeala

import requests
import json
from os.path import join

CGHUB_API_ENDPOINT = 'https://cghub.ucsc.edu/cghub/metadata'
SAMPLE_MAPPING = {'tumor': ['0' + str(i) for i in range(1,10)],
                  'normal': ['1' + str(i) for i in range(5)]}
LIBRARY_MAPPING = {'dna': 'DNA-Seq', 'rna': 'RNA-Seq', 'mirna': 'miRNA-Seq'}

def cgquery(full_details=False, **query_dict):