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):

jfeala

import time
import logging

import boto3
import luigi

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

jfeala

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

import boto3
import requests

s3 = boto3.client('s3')

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