The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill facilitates the installation of the official dxpy Python SDK via pip and system-level bioinformatics packages through apt-get and Docker registries (e.g., pulling biocontainers/samtools). These resources are sourced from reputable and well-known providers in the genomics and technology sectors.
[COMMAND_EXECUTION]: Multiple components of the skill, specifically in references/app-development.md and references/configuration.md, demonstrate the use of subprocess.check_call to run external bioinformatics software. This capability is required for the platform's intended analytical workflows.
[REMOTE_CODE_EXECUTION]: The skill provides instructions for packaging local code into applets and deploying them to remote DNAnexus workers for execution. This is a core feature of the platform and is documented neutrally as a standard operational procedure.
[PROMPT_INJECTION]: The skill exhibits an indirect prompt injection surface as it is designed to ingest external genomics data which is then used as input for shell-based bioinformatics tools.
Ingestion points: Data is brought into the environment via dxpy.download_dxfile and file contents are read using the DXFile.open_file method in references/data-operations.md.
Boundary markers: The provided instructions and examples do not include delimiters or specific warnings to the agent regarding potential instructions embedded within the processed data objects.
Capability inventory: The environment allows for significant command execution via subprocess and the launching of cloud-based jobs using the dxpy.DXApplet.run method.
Sanitization: There is no evidence of input validation or sanitization of data contents before they are passed to execution handlers in the provided reference materials.

dnanexus-integration