# Downloads ## DNAnexus Platform SDK The DNAnexus Platform SDK - also called `dx-toolkit` - includes the `dx` command-line client. It provides 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 [Apache v2.0 license](https://www.apache.org/licenses/LICENSE-2.0.html). This SDK does not collect any user identifiable information. {% hint style="info" %} If you plan to rely on the user interface to interact with the Platform, using the command-line interface only to upload files, you likely don't need to download the full SDK. The [Upload Agent](#upload-agent) may be enough to meet your needs. {% endhint %} ### Installing the Python SDK and Command Line Tools #### Before You Begin Before installing the Python SDK and command line tools, ensure that you are running [Python 3.](https://www.python.org/downloads/) #### Installation The Python SDK components - `dxpy` bindings and command line tools, including `dx` - are distributed through [PyPI](https://pypi.org/project/dxpy/). Use [pip3](https://pip.pypa.io/en/stable/) to download and install the [`dxpy`](https://pypi.org/project/dxpy/) package: ```shell pip3 install dxpy ``` If you see a warning similar to the one below, update your `PATH` environment variable to include the path where pip3 installed the new commands. ``` WARNING: The scripts dx, dx-app-wizard, dx-build-app and dx-build-applet are installed in '/Users/user-amy/Library/Python/3.9/bin' which is not on PATH. Consider adding this directory to PATH ``` #### Enabling Tab Completion If you're using Z shell (`zsh`), which is included in recent versions of macOS, enable tab completion by entering the following command (or add it to your `.zshrc`): ```shell autoload -Uz compinit && compinit autoload bashcompinit && bashcompinit eval "$(register-python-argcomplete dx|sed 's/-o default//')" ``` If you're not using Z shell (`zsh`), enable tab completion by entering the following command (or add it to your `.bashrc`): ```shell eval "$(register-python-argcomplete dx|sed 's/-o default//')" ``` #### Upgrading `dxpy` To upgrade the `dxpy` package after installing it using `pip3`, enter the following command: ```shell pip3 install --upgrade dxpy ``` #### Troubleshooting To avoid character set problems when running the `dx` command, set the `PYTHONIOENCODING` environment variable to UTF-8 as follows: ```shell export PYTHONIOENCODING=UTF-8 ``` If you're using the macOS 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`. On Windows, the DNAnexus SDK requires Windows 10 and later. If you encounter the error `ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108) error` when running `dx` commands, such as `dx head file-xxx`, install `python-certifi-win32` using `pip install python-certifi-win32`. ### Building from Source See the `Readme.md` file in the [`dx-toolkit` GitHub repository](https://github.com/dnanexus/dx-toolkit#installing-the-toolkit-from-source) for information on build-time dependencies, Java, C++ and R bindings and additional installation instructions. ### Using the SDK #### Using a Proxy To direct `dx-toolkit` to a proxy, set the `HTTP_PROXY` or `HTTPS_PROXY` environment variable to an appropriate value: ```shell export HTTP_PROXY=hostname:port ``` #### TLS Settings 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`. 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. [Contact DNAnexus Support](mailto:support@dnanexus.com) if you are using Windows and have trouble connecting through a proxy. #### Learn More * The [Command Line Quickstart](https://documentation.dnanexus.com/getting-started/cli-quickstart) helps you get started on accessing the platform via the command-line interface. * The [Developer](https://documentation.dnanexus.com/developer) section contains comprehensive information on how to use the SDK to interact with, and write your own applications for the Platform. ### Java, R, and C++ SDKs See the [`dx-toolkit` GitHub repository](https://github.com/dnanexus/dx-toolkit#installing-the-toolkit-from-source) for the Java, R, and C++ SDKs. ## Upload Agent 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. {% hint style="info" %} Using the Upload Agent requires an authentication token. [Create an authentication token](https://documentation.dnanexus.com/user/login-and-logout#generating-a-token) before proceeding. {% endhint %} ### Features The Upload Agent uses multiple parallel connections for fast upload speeds. It automatically compresses uncompressed text files, such as FASTA, FASTQ, QSEQ, and other text formats, before upload for greater efficiency. The Upload Agent works without user interaction. This makes it suitable for automating uploads of entire sequencing runs. The agent can automatically resume previously interrupted uploads. You can monitor the progress of individual file uploads along with average and instantaneous transfer rates. ### Installing the Upload Agent The Upload Agent is available pre-built for 64-bit Linux, macOS, and Windows. #### Installation on 64-bit Linux Install the Upload Agent on 64-bit Linux as follows: ```shell 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 ``` #### Installation on macOS Install the Upload Agent on macOS as follows: ```shell curl \ https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.33-osx.zip \ -o ua.zip unzip ua.zip cd dnanexus-upload-agent-*-osx ./ua ``` #### Installation on Windows To install the Upload Agent on Windows: 1. Download [DNAnexus Upload Agent 1.5.33 Installer.exe](https://dnanexus-sdk.s3.amazonaws.com/DNAnexus%20Upload%20Agent%201.5.33%20Installer.exe) or [`dnanexus-upload-agent-1.5.33-windows.zip`](https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.33-windows.zip) 2. Unzip the file using your favorite utility 3. Run `ua.exe` ### Using the Upload Agent [See this page for full details on the features and usage of the Upload Agent](https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/batch/upload-agent). ## Download Agent 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. ### Features and Usage For a detailed description of Download Agent features and usage, review the [README file in the Download Agent GitHub repository](https://github.com/dnanexus/dxda/blob/master/README.md). ### Downloads A list of Download Agent releases is available in [Releases section of the Download Agent GitHub repository](https://github.com/dnanexus/dxda/releases). The [Download Agent Docker repository](https://hub.docker.com/r/dnanexus/dxda/tags/) provides access to experimental builds corresponding to commits to the master branch. ## dxCompiler dxCompiler is a tool for building a DNAnexus workflows from a workflows written in [Workflow Description Language (WDL)](https://github.com/openwdl/wdl/blob/legacy/versions/1.1/SPEC.md). It is distributed as a [JAR file](https://en.wikipedia.org/wiki/JAR_\(file_format\)) that can be executed using Java (version 8 or 11). ### Installing dxCompiler To set up and use dxCompiler, follow these steps: * [Set up](#dnanexus-platform-sdk) the `dx` DNAnexus command-line tool * Run `dx login` to log into DNAnexus * Select a dxCompiler execution method: * Using a JAR file * Download the dxCompiler JAR file from the [releases section](https://github.com/dnanexus/dxCompiler/releases) of the dxCompiler GitHub repository * Install Java SDK 8 or 11 * Run dxCompiler using `java -jar dxCompiler.jar compile workflow_file.wdl` * Using a Docker container * Build a Docker image with dxCompiler and Java version 8 or 11 following the [instructions](https://github.com/dnanexus/dxCompiler/tree/develop/scripts/docker_image#build-docker) in the dxCompiler GitHub repository * Install the Docker CLI * Use [`docker_run.sh`](https://github.com/dnanexus/dxCompiler/blob/develop/scripts/docker_image/docker_run.sh) script to invoke dxCompiler with the built Docker container image More detailed setup instructions and sample WDL workflows can be found in the [dxCompiler GitHub README](https://github.com/dnanexus/dxCompiler/blob/develop/README.md#setup).