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.
If you plan to do most of your interaction with the platform via the website, 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.
You can download the SDK built for your platform:
- Unpack the SDK:
tar -xzf dx-toolkit*.tar.gz
Note: Python 2.7 is required. Command-line tools in the SDK will not work with Python 2.6 or Python 3.
- Initialize your environment as follows:
Congratulations! You are now ready to use the Platform SDK.
- The Command-Line Quickstart will get you started on accessing the platform from the command-line.
- The Developer Portal contains comprehensive information on how to use the SDK to interact with and write your own applications for the DNAnexus Platform.
Building from source
Download either of the following source packages:
Readme.md file in the archive for build-time dependencies and further installation instructions (or view on Github).
The Python components of the SDK (
dxpy bindings and most of the command-line tools) are distributed through PyPI. Use pip to download and install the
Note: OS X 10.9 users with Python < 2.7.6 from python.org or pythonbrew may encounter Python issue 18458
when using the Python interpreter interactively. Upgrade to Python 2.7.6 or greater to resolve the issue.
Ubuntu APT repository
If you are running Ubuntu 16.04 or 14.04, see Ubuntu Repository for instructions on
how to obtain the DNAnexus SDK via APT.
Upgrading the DNAnexus SDK
dx upgrade command is a useful tool to ensure that the users of the DNAnexus platform have the latest command-line tools and can customize their toolkit to suit the requirements of their project. This command will upgrade your DNAnexus SDK to the latest version recommended. The
dx upgrade command can also revert your dx-toolkit to a previous version.
dx upgrade without any arguments will upgrade your DNAnexus SDK to the most recent version. Alternatively, you can provide
dx upgrade with 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 v0.228.0
Downloading dx-toolkit-v0.263.0-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 v0.228.0 into place...
upgrade.sh: Updated to version v0.228.0. 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
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
- 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
- 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
Unpack and run the downloaded file. You should then see a help message.
- 64-bit Linux:
$ tar -xzf dnanexus-upload-agent-*-linux.tar.gz
$ cd dnanexus-upload-agent-*-linux
- Mac OS X
$ unzip dnanexus-upload-agent-*-osx.zip
$ cd dnanexus-upload-agent-*-osx
- Unzip the file using your favorite utility
- Run "ua.exe"
Note for Windows 7/2008 users:
If you receive an error message saying: 'schannel: failed to setup extended errors', please install this hotfix
This program requires that you have an API key. Please create an
API key before proceeding.
See the Upload Agent Guide for more info about how
to use the tool.
- Install any missing software dependencies. You will need R, as well as the packages
RJSONIO. You can install these packages from within R with the following commands.
- You should now be able to install the
dxR package. You can use the R graphical interface to select and install the downloaded file. Or, you can run the following command using the path to the file you downloaded.
Alternatively, you can also run the following command from the command-line (outside of R) to install the package.
You can use the
> install.packages("dxR_*", repos=NULL)
-l flag to specify a local directory in which to
install the package if you do not have system permissions to install
it for all users. If taking such an approach, you should set your
R_LIBS environment variable appropriately if you have not already.
R CMD INSTALL dxR_* -l $R_LIBS
This section discusses common issues we have encountered when installing dx-toolkit on a variety of platforms.
Exception thrown when logging in
On October 15th, 2017 DNAnexus disabled support for TLS 1.0 and 1.1, and this is a common cause of login issues. Addressing these issues is typically system-specific. To see if your Python release supports TLS 1.2, you can run:
python2.7 -c "import ssl ; print(ssl.OPENSSL_VERSION)"
If that command prints an OpenSSL version that is less than 1.0.1, then you will need to take additional steps to obtain a Python release with TLS 1.2 support.
For Linux, the correct solution will depend on what distribution you are using. This article by Stripe provides a nice summary of how to install the required packages.
macOS / OS X
If you have the option of installing macOS High Sierra (10.13) on the machine, we recommend you perform this upgrade since Apple has added TLS 1.2 support to the SSL library used by the Python release that ships with the OS.
If you do not have the option of upgrading macOS, you can use homebrew to obtain a TLS 1.2-capable Python. Please go to https://brew.sh and follow their instructions to install homebrew.
Next, install Python:
Inspect your path by running this command:
to see if the dir
/usr/local/opt/python/libexec/bin is present.
If it's not, you may need to add this line to your
~/.bash_profile file to insert homebrew's python
bin directory at the head of your
You can double-check the value that should be used in that export command by running
brew info python and examining the export command that is printed in the "Caveats" section.