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On this page
  • Prerequisites
  • Getting Started
  • Getting the Example Workflow
  • Running a Workflow

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DNAnexus

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Last updated 4 months ago

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supports WDL workflows through their dx-toolkit and dxCompiler tools. This guide demonstrates running the 02_download_collection_files.wdl workflow, which typically takes 5-10 minutes to complete.

Prerequisites

Before beginning, ensure you have the following:

  • Java 8 or higher

  • Python 3.5 or higher

  • Optional: cURL,

Getting Started

The following software and workflows are required and will be installed and used as part of this tutorial:

Getting the Example Workflow

Clone with Git:

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository:

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

Installing Required Tools

Download dxCompiler:

Download the latest version of dxCompiler by one of the following methods. This allows direct conversion and uploading of WDL workflows to DNAnexus.

Using cURL

curl -o dxCompiler.jar -L https://github.com/dnanexus/dxCompiler/releases/download/2.4.6/dxCompiler-2.4.6.jar

Or download from the releases page to the current directory and rename the file to dxCompiler.jar.

Install and initialize dx-toolkit

Download and initialize dx-toolkit. You will be prompted to log into your DNAnexus account.

pip3 install dxpy
dxlogin

Running a Workflow

  • Create a project on DNAnexus where the workflow and associated files will be stored.

  • Once your project has been setup, import the WDL workflow 02_download_collection_files.wdl to the DNAnexus platform using dxCompiler.

java -jar ./dxCompiler.jar compile ./examples/wdl/02_download_collection_files.wdl n -project dnastack-client-library-worked-examples n -folder /download_collection_files

To run the newly created workflow on the DNAnexus platform, select the project folder and Workflow item, and click "Run" as Analysis.

  • To view the progress of the workflow at any time, select the "Monitor" tab.

  • Inputs or parameters of the workflow can be modified. For example, to download from a different collection.

  • The output files can be found in and downloaded from the folder specified in the Run dialog. In this case, the root of the DNAnexus project.

Or and Unzip

DNAnexus
A DNAnexus platform account (including free tier)
git
02_download_collection_files.wdl
dx-toolkit
dxCompiler
Download