aneeshpanoli

# pull the official image
FROM tensorflow/tensorflow:latest-gpu-jupyter

# make a dir inside the container to copy files
WORKDIR /tfjupyter

# install additional packages
COPY requirements.txt .
COPY entrypoint.sh .
RUN ["chmod", "+x", "entrypoint.sh"]

aneeshpanoli

version: "3"

services:
  tensorflow:
    container_name: TfJupyter
    build:
      context: .
      dockerfile: Dockerfile
    volumes:
      - .:/tf

aneeshpanoli

def set_conf():
    conf = SparkConf().setAppName("App")
    conf = (conf.setMaster('local[*]')
      .set('spark.executor.memory', '4G')
      .set('spark.driver.memory', '16G')
      .set('spark.driver.maxResultSize', '8G'))
    return conf

aneeshpanoli

import os

#download SRA tool kit
def setup_sra_tool(url):
  !wget $url
  !gunzip sratoolkit.2.9.6-1-ubuntu64.tar.gz
  !tar -xf sratoolkit.2.9.6-1-ubuntu64.tar
  
  
#download SRA file and extract fastq

aneeshpanoli

from subprocess import STDOUT, check_call, check_output

def install_java_scala():
          try:
          java_ver = check_output(['java', '-version'], stderr=STDOUT)
        except:
          java_ver = b''
        try:
          scala_ver = check_output(['scala', '-version'], stderr=STDOUT)
        except:

aneeshpanoli

aneeshpanoli

def startup():
  global matrix
  matrix = load_large_matrix()
  

# then you would
from yourapp import matrix