The Agent Skills Directory

[COMMAND_EXECUTION]: The documentation describes using the Python subprocess module within DNAnexus applications to execute bioinformatics tools like samtools or bwa inside isolated worker VMs. This is a standard practice for the platform's execution environment.
[EXTERNAL_DOWNLOADS]: The skill provides instructions for managing app dependencies, including installing Python packages at runtime via pip and pulling Docker images from public registries. These operations are intended for the configuration of the remote DNAnexus execution environment, not the local agent environment.
[CREDENTIALS_UNSAFE]: The documentation includes templates for authentication using API tokens. However, it explicitly includes security best practices advising users never to hardcode tokens in source code and to use secure environment variables or the dx login CLI instead.

dnanexus-integration