Download, install, and get started using the DNAnexus Platform SDK, the DNAnexus upload and download agents, and dxCompiler.
The DNAnexus Platform SDK (a.k.a.
dx-toolkit) includes the
dxcommand-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform.
Note: If you plan to do most of your interaction with the platform through the web UI, and will use the command-line only to upload files, you probably do not need to download the SDK. The Upload Agent (discussed below) is our specialized tool for uploading to the platform and may be all that you need from this page.
Versions of Mac OS X 10.8 and higher come with Python 2.7 preinstalled. However, DNAnexus is deprecating usage of Python 2.7 and it is recommended that you check your version of Python to ensure you are using Python 3 (links to Windows and Linux downloads as well) instead before moving onto the next steps.
pip3 install dxpy
To enable tab completion after installing with pip3, run the following command or add it to your
eval "$(register-python-argcomplete dx|sed 's/-o default//')"
If you use later version of MacOS with Z shell (zsh), enable tab completion by running the following command or adding it to your
autoload -Uz compinit && compinit
autoload bashcompinit && bashcompinit
eval "$(register-python-argcomplete dx|sed 's/-o default//')"
Congratulations! You are now ready to use the
dxcommand-line tool and the
dx-toolkitto a proxy, please set the
HTTP_PROXYenvironment variable to something like
HTTPS_PROXYis also supported.
dx-toolkituses certificates installed on the system to create secure connections. If your system requires an additional TLS certificate and the
dx-toolkitdoesn't appear to be using a certificate installed on your system, there are two options in order of preference. First, set the
DX_CA_CERTenvironment variable to the path of the PEM-encoded TLS certificate file required by your parent organization. You can also connect insecurely by avoiding certificate verification all together by setting
For Windows users, the way environments are customized can vary enough to where the settings above may still cause issues. Please contact [email protected] if you are having trouble connecting through a proxy.
You can download the SDK for Java, R, C++, and Python2.7 built for your platform:
Linux and Mac
- 1.Unpack the SDK:$ tar -xzf dx-toolkit*.tar.gzNote: The tarballs include Python 2.7 version of
dxcommand, which will be supported until March 1, 2021.
- 2.If you are using
zshon MacOS, please update your
~/.zshrcfile as followsecho "autoload -Uz compinit && compinit" >> ~/.zshrc && source ~/.zshrc
- 3.Initialize your environment as follows:$ cd dx-toolkit && source environment
Windows (Windows 10 and later versions are supported)
dx-toolkit*.exeto start the installation. Systems with Windows Defender enabled may present a warning before launching the dx-toolkit installer. If you see this warning window, click "More Info", and choose "Run Anyway". The sources for the Windows installer are here.
- 2.After the installation is completed, find and click on the DNAnexus CLI shortcut on the Windows Start Menu.
If your organization does not allow installation on Windows systems without the installer package's signature, please get in contact with the support team at [email protected] for possible alternative installation method.
Congratulations! You are now ready to use the Platform SDK.
dx upgradewithout any arguments will upgrade your DNAnexus SDK to the most recent version. Alternatively, you can provide
dx upgradewith a version of the DNAnexus SDK that you would prefer to have installed on your local system.
Upgrading to the latest version:
$ dx upgrade
Upgrading to v0.325.1
Downloading dx-toolkit-v0.325.1-osx.tar.gz (using curl -O -L)...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 9874k 100 9874k 0 0 3279k 0 0:00:03 0:00:03 --:--:-- 3279k
Backing up version v0.227.1...
Moving version v0.306.0 into place...
upgrade.sh: Updated to version v0.306.0. Previous version saved in /Users/user-amy/dnanexus/dx-toolkit/build/v0.227.1.
Please close this terminal, open a new terminal, and source the environment file in the dx-toolkit folder
Upgrading to a previous version:
$ dx upgrade v0.225.0
Download either of the following source packages:
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.
- Fast Parallel Uploads: Data is uploaded using multiple parallel connections for faster upload speeds.
- Automatic Compression: Text files (such as FASTA, FASTQ, qseq, and others) can be automatically compressed before upload, for better efficiency.
- Automated Uploads: No user interaction is required; the client can be used to automate uploads of entire sequencing runs.
- Resumable Uploads: Previously interrupted uploads can be automatically resumed.
- Progress Reporting: You can monitor individual file upload progress and also average/instantaneous transfer rates.
The Upload Agent is available pre-built for the three main flavors of operating systems:
- 64-bit Linux:wget \https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.33-linux.tar.gz -O - |\tar -xzf -cd dnanexus-upload-agent-*-linux./ua
- Mac OS Xcurl \https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.33-osx.zip \-o ua.zipunzip ua.zipcd dnanexus-upload-agent-*-osx./ua
The Download Agent is a command-line tool for downloading large quantities of files from DNAnexus to a local environment. It is designed to resiliently manage downloads over potentially long periods of time.
dxCompiler is used to generate a DNAnexus workflow from a workflow written in Workflow Description Language (WDL). dxCompiler is a JAR file that can be run with Java 8 or later, and can be downloaded from the releases section of the DNAnexus dxCompiler Github repository. dxCompiler is also released as a public docker container that includes the Java dependency. dxCompiler README documents the setup instructions and sample workflows.
Before using dxCompiler, ensure you have the following dependencies installed:
dxcommand-line tool is installed and initialized with