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Download, install, and get started using the DNAnexus Platform SDK, the DNAnexus upload and download agents, and dxCompiler.
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Download, install, and get started using the DNAnexus Platform SDK, the DNAnexus upload and download agents, and dxCompiler.
Last updated
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The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; and Python, Java, C++ and R bindings for working on the DNAnexus Platform.
The SDK is released under the . This SDK does not collect any user identifiable information.
Before installing the Python SDK and command line tools, ensure that you are running
The SDK's Python components - dxpy bindings and command line tools, including dx- are distributed through . Use to download and install the package:
If you see a warning similar to the one below, please update your PATH environment variable to include the path where pip3 installed the new commands.
If you're using Z shell (zsh), which is included in recent versions of OS X, enable tab completion by entering the following command, or adding it to your .zshrc:
If you're not using Z shell (zsh), enable tab completion by entering the following command, or add it to your .bashrc:
To upgrade the dxpypackage after installing it using pip3, enter the command:
If you're using the OS X Xcode command line tools and running Python 3, the psutil dependency may fail to compile. To prevent this from happening, set export ARCHFLAGS="-arch x86_64" before installing dxpy.
To avoid character set problems when running the dx command, set the PYTHONIOENCODING environment variable to UTF-8 as follows:
To direct dx-toolkit to a proxy, set the HTTP_PROXY or HTTPS_PROXY environment variable to an appropriate value:
By default, dx-toolkit uses certificates installed on your system to create secure connections. If your system requires an additional TLS certificate, and dx-toolkit doesn't appear to be using a certificate installed on your system, you have two options. The first, and most secure, is to set the DX_CA_CERT environment variable to the path of the PEM-encoded TLS certificate file required by your parent organization. The second option is to connect insecurely, avoiding certificate verification altogether, by setting DX_CA_CERT=NOVERIFY.
The DNAnexus Upload Agent is a command-line tool for uploading files to the DNAnexus Platform. Using the Upload Agent is a fast and convenient alternative to uploading files via the Platform UI.
Fast Parallel Uploads - Data is uploaded using multiple parallel connections for faster upload speeds.
Automatic Compression - Text files (such as FASTA, FASTQ, qseq, and other text files) can be automatically compressed before upload, for greater 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 - Users can monitor the progress of individual file uploads, as well as average/instantaneous transfer rates.
The Upload Agent is available pre-built for 64-bit Linux, OS X, and Windows.
Install the Upload Agent on 64-bit Linux as follows:
Install the Upload Agent on OS X as follows:
To install the Upload Agent on Windows:
Unzip the file using your favorite utility
Run ua.exe
The DNAnexus Download Agent is a command-line tool for downloading large numbers of files from the DNAnexus Platform to a local environment. It is designed to ensure the success of downloads that can take a long time to complete.
To set up and use dxCompiler, follow these steps:
Run dx login to log into DNAnexus
Select a dxCompiler execution method:
Using a JAR file
Install Java SDK 8 or 11
Run dxCompiler using java -jar dxCompiler.jar compile workflow_file.wdl
Using a Docker container
Install the Docker CLI
See the Readme.md file in the for information on build-time dependencies, Java, C++ and R bindings and additional installation instructions.
When using Windows, environments can be customized in a wide variety of ways. As a result, issues can arise even when using the TLS settings detailed in the previous paragraph. if you are using Windows and have trouble connecting through a proxy.
The will get you started on accessing the platform via the command-line interface.
The section contains comprehensive information on how to use the SDK to interact with, and write your own applications for the Platform.
Using the Upload Agent requires an authentication token. Please before proceeding.
Download or
.
For a detailed description of Download Agent features and usage, please review the .
A list of Download Agent releases is available in . The provides access to experimental builds corresponding to commits to the master branch.
dxCompiler is a tool for building a DNAnexus workflows from a workflows written in . It is distributed as a that can be executed using Java (version 8 or 11).
the dx DNAnexus command-line tool
Download the dxCompiler JAR file from the of the dxCompiler Github repository
Build a Docker image with dxCompiler and Java version 8 or 11 following the in the dxCompiler Github repository
Use script to invoke dxCompiler with the built Docker container image
More detailed setup instructions and sample WDL workflows can be found in the .