Bringing Your App or Workflow to the Research Analysis Platform
In many cases the Platform allows you to use apps and workflows you’ve developed in another environment. This page provides a rundown on how to import apps or workflows of a wide variety of types.
Before You Begin
If you haven’t already, download and install the dx-toolkit, and familiarize yourself with basic dx commands. When working from the CLI, you’ll use the dx-toolkit to perform various tasks in the course of importing, configuring, and running apps and workflows.
Your apps and workflows must have access to any files they need as inputs. If any input file is not already in the project in which you intend to use a particular app or workflow, upload that file to the project in question.
If your app can run on 64-bit Ubuntu Linux, you can package it to run on the Platform. Follow these instructions from the DNAnexus Platform documentation, to import, configure, test, and run your app. You’ll use the dx-app-wizard to set up the proper directory structure to run your app on the platform.
The “Apps” section of the DNAnexus Platform documentation provides further guidance on how to configure your app, and how to upload and ensure it has access to dependencies and input files.
The Stata app itself does not run on the Platform. If you have a Stata license, you can use stata_kernel to access Stata commands and functionality within a Jupyter notebook running on the Platform. See these instructions on how to do this.
There are third-party tools available that can compile a C++ app to run on 64-bit Ubuntu Linux. Once you’ve done so, you can then wrap the newly created Linux app as a Platform app or applet, following the instructions above.
Bringing Your Workflow to the Platform
WDL and Nextflow
To facilitate reproducibility in working with data, the DNAnexus Platform supports the use of WDL and Nextflow workflows.
Converting scripts to WDL workflows ensures reproducibility and allows your workflows to be easily published and shared. Use dxCompiler to compile WDL workflows so that they can be run on the Platform.
Nextflow workflows can be run from the command line in a Cloud Workstation session, or in a Jupyter notebook.
Using a Docker image, you can configure and package your Bash script, along with its dependencies and inputs, then run it on the Platform.