Pipeline Description

Genomics data → ADAM/Spark → Parquet → Aggregation-DF/Spark → Cassandra → Scala Service → Curl/Notebook-client

• [Instructions][instructions]
  • [Git][git]
• [Docker image][docker-image]
  • [Run image][run-image]
• [Setup][setup]
• [Use][use]
  • [Cassandra][cassandra]
  • [Spark Notebook][spark-notebook]
  • [Run the full pipeline][run-the-full-pipeline]

Instructions

Git

Make sure my local clone is up to date

git pull

Docker image

Get the docker image from the docker hub:

docker pull xtordoir/pipeline

Run image

Running the image and optionally mounting the cloned notebooks directory in the docker image:

docker run -it -m 8g -p 30080:80 -p 34040:4040 -p 34041:4041 -p 39160:9160 -p 39042:9042 -p 39200:9200 -p 37077:7077 -p 36060:6060 -p 36061:6061 -p 32181:2181 -p 38090:8090 -p 38099:8099 -p 30000:10000 -p 30070:50070 -p 30090:50090 -p 39092:9092 -p 36066:6066 -p 39000:9000 -p 39999:19999 -p 36081:6081 -p 35601:5601 -p 37979:7979 -p 38989:8989 xtordoir/pipeline bash

If you want to save the notebooks, you can ask docker to mount the local folder from the git clone.

docker run -it -m 8g -v `pwd`/notebooks:/root/pipeline/notebooks -p 30080:80 -p 34040:4040 -p 34041:4041 -p 39160:9160 -p 39042:9042 -p 39200:9200 -p 37077:7077 -p 36060:6060 -p 36061:6061 -p 32181:2181 -p 38090:8090 -p 38099:8099 -p 30000:10000 -p 30070:50070 -p 30090:50090 -p 39092:9092 -p 36066:6066 -p 39000:9000 -p 39999:19999 -p 36081:6081 -p 35601:5601 -p 37979:7979 -p 38989:8989 xtordoir/pipeline bash

Setup

From now on we are inside the docker instance.

We setup the services

cd pipeline

The following script will init the services and will create schemas among other things.

source devoxx-setup.sh

Use

After a little time, all services should be up, e.g. cassandra

source config/bash/.profile

Cassandra

Try starting the cassandra shell for instance:

cqlsh $IP_eth0

Spark Notebook

The spark Notebook is available in the browser

http://<localhost or docker ip>:39000

Run the full pipeline

FIRST: Be sure you've entered the pipeline folder and executed source config/bash/.profile !!!

The order of operations are the following: Open the spark notebook on [http://:39000](http://:39000).

Enter the pipeline folder.

1. Click on AdamToDataframe. Read the comments and run each cell through the end. This example pre-process some genomics data
2. On the Main page of the spark notebook, click on the Running Tab and shutdown the running notebook (to save your resources)
3. Click open the AggregateAndSaveToCassandra, again run it all. This is computing stats and saving them in Cassandra.
4. Again, shutdown the notebook in the Running tab on the main page.
5. In the terminal, cd rest-api && sed -i s/\$\{IP_eth0\}/${IP_eth0}/ src/main/resources/application.conf && sbt run. This is starting the REST service in Akka HTTP reading data from Cassandra and serving them in JSON.
6. Open the Rest Call notebook and execute it. This one uses Akka HTTP (client now) to access the REST service and plot some data.
7. Open the Rest Call (using HTML form) notebook. It's essentially the same as above but present the REST calls in an HTML form instead of query parameter in a String.