Installing DNAnexus on Helix

Objective and Audience

DNAnexus provides a web-based graphical user interface for existing apps and workflows developed for their platform. The DNAnexus Apps List webpage has a list of vetted apps and workflows. The content below is for people that want to run DNAnexus from the command-line or develop applets/apps/workflows on the DNAnexus platform. This page provides instructions on installation on Helix – High-Performance Computing at the NIH.

The DNAnexus has excellent installation documentation on their download webpage and provides download links to components software packages (DNAnexus Platform SDK, Upload Agent and Download Agent) for Linux, Macintosh and Window platforms.

Log in to Biowulf and Load Relavent Modules

Installation of DNAnexus with Anaconda environment will require modules and a place to install software components.

module load DNAnexus

Installing DNAnexus Platform SDK

The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, and other utilities for working with DNA data on the platform. Our SDK is released under the Apache v2.0 license.

Select the most current distribution at DNAnexus-Platform-SDK.

wget https://wiki.dnanexus.com/images/files/dx-toolkit-v0.236.2-centos-amd64.tar.gz
tar -xzf dx-toolkit-v0.236.2-centos-amd64.tar.gz
source dx-toolkit/environment
dx upgrade

Installing DNAnexus Upload Agent

The Upload Agent is a command-line tool for uploading files to the DNAnexus Platform. It is a fast and convenient alternative to using the web interface for uploading files.

Select the most current distribution at Upload Agent.

wget https://wiki.dnanexus.com/images/files/dnanexus-upload-agent-1.5.29-linux.tar.gz
tar -xzf dnanexus-upload-agent-1.5.29-linux.tar.gz
alias ua=~/bin/dna_nexus/dnanexus-upload-agent-1.5.29-linux/ua
ua --help

Login

You will need your username and password. Authentication will be active for 30 days (login logout details).
dx login

What is next?