Clara AGX Metagenomics Assembly

This container is deprecated. It was released as part of the Clara Holoscan SDK v0.1 and will no longer be compatible with Clara Holoscan SDK v0.2.

What is Clara AGX Metagenomics Assembly?

The Clara AGX Metagenomics Assembly container provides tools for genome assembly compiled with support for ARM and AGX hardware.

The current latest software versions include:

Package	Version
Shasta	0.7.0

How to Run

Packages are compiled and stored in the /opt/ directory.

Using Shasta

The Shasta binaries are located in /opt/shasta/bin.

To run the Shasta container with data located on your host, you will need to use bind mounts with the -v flag like the following:

docker run -v((HOST_DIRECTORY)):/mnt/data -t nvcr.io/ea-clara-agx/agx-metagenomics-assembly	
 shasta --input /mnt/data/((INPUT_PATH)) --threads 8 --assemblyDirectory /mnt/data/((OUTPUT_PATH))

The recommended configuration for shasta is using 8 threads with the --threads 8 option.

Please refer to the Shasta manual for further instructions:

• Shasta Quickstart Guide
• Shasta Documentation

Requirements

Either a Jetson Xavier AGX device, or the Clara AGX Developer Kit running Jetpack 4.5 or later.

License

Licenses are available and can be viewed in the container. By pulling and using the container, you accept the terms and conditions of these licenses.

Suggested Reading

For documentation, SDK, and how to get a Clara Developer Kit: https://developer.nvidia.com/clara-holoscan-sdk

Use the NVIDIA Devtalk forum for questions regarding this Release: https://forums.developer.nvidia.com/c/healthcare/clara-holoscan-sdk/