robnewman

$ tree simple-igv-test 
simple-igv-test
├── igv-options-interact.json
├── igv-options.json
└── quilt_summarize.json

0 directories, 3 files

robnewman

{
  "reference": {
    "id": "hg19",
    "name": "Human (CRCh37/hg19)",
    "fastaURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",
    "indexURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai",
    "cytobandURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
  },
  "locus": "chr2:65,222,853-65,826,902",
  "tracks": [

robnewman

quilt3 push examples/simple-igv \
  --registry $YOUR_S3_BUCKET \
  --dir simple-igv-test \
  --message 'Add simple IGV examples'

robnewman

{
  "reference": {
    "id": "hg19",
    "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta",
    "cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/b37/b37_cytoband.txt"
  },
  "locus": "8:128,750,948-128,751,025",
  "tracks": [
    {
      "name": "Genes",

robnewman

[
  {
    "path": "igv-options-interact.json",
    "title": "Three track interactive genome sequence in BEDPE and bigWig formats example",
    "description": "A simple, interactive, publicly available Human genome sequence (three tracks) in BEDPE and bigWig formats from the Broad Institute: Human (CRCh37/hg19)",
    "types": ["igv"],
    "expand": true
  },
  {
    "path": "igv-options.json",

robnewman

# Helpers
import os
from datetime import datetime, timedelta

# Apache Airflow
from airflow.operators.python_operator import PythonOperator

# Quilt
import t4

robnewman

# Helpers
import json

# Apache Airflow
from airflow.operators.python_operator import PythonOperator

def write_to_json(**context):
    data_directory = context['directory']
    file_name = context['filename']
    keywords = context['task_instance'].xcom_pull(task_ids='scrape_articles')

robnewman

from datetime import datetime, timedelta
from airflow import DAG

default_args = {
    'owner': 'robnewman',
    'depends_on_past': False,
    'start_date': datetime(2019, 1, 1),
    'email': ['support@example.com'],
    'email_on_failure': False,
    'email_on_retry': False,

robnewman

# Helpers
from time import time

# Apache Airflow
from airflow.operators.python_operator import PythonOperator

# Newspaper3k
import newspaper
from newspaper import Article

robnewman

# Helpers
import os
import json
from time import time
from datetime import datetime, timedelta

# Apache Airflow
from airflow import DAG
from airflow.operators.python_operator import PythonOperator