GitHub - googlegenomics/dockerflow: Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API (original) (raw)

Disclaimer

This is not an official Google product.

Update

As of 11 Nov 2017, Dockerflow is no longer actively maintained and will not be enhanced with new features.

For multi-step batch workflows consisting of Docker tasks, we now recommend running in the cloud using:

To run multi-step workflows with dsub, you can create a bash or python script with multiple dsub calls. Execution graphs can be constructed using dsub'sjob control functionality.

For any Dockerflow functionality that is not satisfied by dsub, pleasefile an issue in the dsub repository.

Dockerflow

Dockerflow makes it easy to run a multi-step workflow of Docker tasks usingGoogle Cloud Dataflow for orchestration. Docker steps are run using the Pipelines API.

You can run Dockerflow from a shell on your laptop, and the job will run in Google Cloud Platform using Dataflow's fully managed service and web UI.

Dockerflow workflows can be defined in YAML files, or by writing Java code. Examples of workflows defined in YAML can be found in

Examples of workflows defined in Java can be found in

You can run a batch of workflows at once by providing a CSV file with one row per workflow to define the parameters.

Why Dockerflow?

This project was created as a proof-of-concept that Dataflow can be used for monitoring and management of directed acyclic graphs of command-line tools.

Dataflow and Docker complement each other nicely:

While Dockerflow supports a simple YAML workflow definition, a similar approach could be taken to implement a runner for one of the open standards like [Common Workflow Language] (https://github.com/common-workflow-language/common-workflow-language) orWorkflow Definition Language.

Table of contents

Prerequisites

  1. Sign up for a Google Cloud Platform account and [create a project] (https://console.cloud.google.com/project?).
  2. [Enable the APIs] (https://console.cloud.google.com/flows/enableapi?apiid=genomics,dataflow,storage_component,compute_component&redirect=https://console.cloud.google.com) for Cloud Dataflow, Google Genomics, Compute Engine and Cloud Storage.\
  3. Install the Google Cloud SDK and run
gcloud init  
gcloud auth login  
gcloud auth application-default login

Getting started

Run the following steps on your laptop or local workstation:

  1. git clone this repository.
git clone https://github.com/googlegenomics/dockerflow
  1. Build it with Maven.
cd dockerflow  
mvn package -DskipTests
  1. Set up the DOCKERFLOW_HOME environment.
 export DOCKERFLOW_HOME="$(pwd)"  
 export PATH="${PATH}":"${DOCKERFLOW_HOME}/bin"  
 chmod +x bin/*
  1. Run a sample workflow:
dockerflow --project=MY-PROJECT \  
    --workflow-file=src/test/resources/linear-graph.yaml \  
    --workspace=gs://MY-BUCKET/MY-PATH \  
    --input BASE_DIR=gs://MY-BUCKET/MY-PATH/MY-INPUT-FILE.txt  
    --runner=DirectPipelineRunner

Set MY-PROJECT to your cloud project name, and set MY-BUCKET and MY-PATHto your cloud bucket and folder. You'll need to have a text file in Cloud Storage as well, here called MY-INPUT-FILE.txt. You can copy one fromsrc/test/resources/input-one.txt:

    gsutil cp src/test/resources/input-one.txt gs://MY-BUCKET/MY-PATH/input-one.txt

The example will run Dataflow locally with the DirectPipelineRunner, for orchestration. It will spin up VMs remotely in Google Cloud to run the individual tasks in Docker. Execution of the local Dataflow runner will block until the workflow completes. The DirectPipelineRunner is useful for debugging, because you'll see all of the log messages output to your shell.

To run in your cloud project, and see the pretty Dataflow UI in Google Cloud Console, you can remove the --runner option to use the default Dataflow runner.

Docker and Dataflow vs custom scripts

How is Dataflow better than a shell script?

Dataflow provides:

Docker provides:

Creating your own workflows

The Dockerflow command-line expects a static workflow graph definition in YAML, or the Java class name of a Java definition.

If you'd rather define workflows in code, you'll use the Java SDK. See

Everything that can be done with YAML can also be done (and more compactly) in Java code. Java provides greater flexibility too.

The documentation below provides details for defining workflows in YAML. To create a workflow, you define the tasks and execution graph. You can define the tasks and execution graph in a single file, or your graph can reference tasks that are defined in separate YAML files.

A workflow is a recursive format, meaning that a workflow can contain multiple steps, and each of the steps can be a workflow.

Hello, world

Dockerflow has lots of features for creating complex, real-world workflows. The best way to get started with your own workflows is to look at theexamples.

The hello, world example shows the most basic workflow in both YAML and Java.

All of the advanced features can be seen in the more complexGATK example. Again, it offers both YAML and Java versions. You'll see pretty much the full range of functionality.

Testing

Workflows can be tricky to test and debug. Dataflow has a local runner that makes it easy to fix the obvious bugs before running in your Google Cloud Platform project.

To test locally, set --runner=DirectPipelineRunner. Now Dataflow will run on your local computer rather than in the cloud. You'll be able to see all of the log messages.

Two other flags are really useful for testing: --test=true and--resume=true.

When you set test to true, you'll get a dry run of the pipeline. No calls to the Pipelines API will be made. Instead, the code will print a log message and continue. That lets you do a first sanity check before submitting and running on the cloud. You can catch many errors, mismatched parameters, etc.

When you use the resume flag, Dockerflow will try to resume a failed pipeline run. For example, suppose you're trying to get your 10-step pipeline to work. It fails on step 6. You go into your YAML definition file, or edit your Java code. Now you want to re-run the pipeline. However, it takes 1 hour to run steps 1-5. That's a long time to wait. With --resume=true, Dockerflow will look to see if the outputs of each step exist already, and if they do, it will print a log message and proceed to the next step. That means it takes only seconds to skip ahead to the failed step and try to rerun it.

What next?

FAQ and Troubleshooting

What if I want to run large batch jobs?

Google Cloud Platform has various quotas that affect how many VMs and IP addresses, and how much disk space you can get. Some tips: