Skip to content

Latest commit

 

History

History
77 lines (55 loc) · 3.86 KB

installation.md

File metadata and controls

77 lines (55 loc) · 3.86 KB

INSTALLATION

To run the pipeline you need to install following software. Running the pipeline on Google Cloud or DNAnexus requires additional setup detailed below.

Java 8

Java is required to run execution engine Cromwell and WDL-to-DNAnexus compiler dxWDL. To check which Java version you already have, run:

  $ java -version

You are looking for 1.8 or higher. If the requirement is not fulfilled follow installation instructions for mac or linux or use your favorite installation method.

Docker

Pipeline code is packaged and distributed in Docker containers, and thus Docker installation is needed. Follow instructions for mac or linux.

Singularity

If for some reason you cannot run Docker, install singularity and have a look at HOWTO for an example of how to run pipeline with singularity. Pipeline requires singularity version >=2.5.2, the link takes you to version 2.6.0.

Google Cloud

If you are intending to run the pipeline on Google Cloud platform, the following setup is needed:

  1. Sign up for a Google account.

  2. Go to Google Project page and click "SIGN UP FOR FREE TRIAL" on the top left and agree to terms.

  3. Set up a payment method and click "START MY FREE TRIAL".

  4. Create a Google Project [YOUR_PROJECT_NAME] and choose it on the top of the page.

  5. Create a Google Cloud Storage bucket gs://[YOUR_BUCKET_NAME] by clicking on a button "CREATE BUCKET" and create it to store pipeline outputs.

  6. Find and enable following APIs in your API Manager. Click a back button on your web brower after enabling each.

    • Compute Engine API
    • Google Cloud Storage
    • Google Cloud Storage JSON API
    • Genomics API

  7. Install Google Cloud Platform SDK and authenticate through it. You will be asked to enter verification keys. Get keys from the URLs they provide.

      $ gcloud auth login --no-launch-browser
  $ gcloud auth application-default login --no-launch-browser

  8. If you see permission errors at runtime, then unset environment variable GOOGLE_APPLICATION_CREDENTIALS or add it to your BASH startup scripts ($HOME/.bashrc or $HOME/.bash_profile).

      unset GOOGLE_APPLICATION_CREDENTIALS

  9. Set your default Google Cloud Project. Pipeline will provision instances on this project.

      $ gcloud config set project [YOUR_PROJECT_NAME]
  • For an example on how to run the pipeline on Google Cloud, see HOWTO.

DNAnexus

If you are intending to build and run the pipeline on DNAnexus, the following setup is needed:

  1. Sign up for a DNAnexus account.

  2. Create a new DX project with name [YOUR_PROJECT_NAME] by clicking on "+New Project" on the top left.

  3. Install DNAnexus SDK. Run dx login to log in to the platform using your credentials.

  4. Download dxWDL:

      $ wget https://github.com/dnanexus/dxWDL/releases/download/0.77/dxWDL-0.77.jar

  5. Make dxWDL executable:

      $ chmod 755 dxWDL-0.77.jar
  • For an example on how to run the pipeline on DNAnexus, see HOWTO