The Agent Skills Directory

[COMMAND_EXECUTION]: The skill utilizes subprocess.check_call and shell commands to manage Python dependencies via pip, execute bioinformatics software (e.g., samtools, bwa), and interact with the DNAnexus CLI (dx tools).
[EXTERNAL_DOWNLOADS]: The skill facilitates the installation of the dxpy Python SDK and provides instructions for pulling Docker containers from registries such as Biocontainers. It also describes the use of execDepends within the dxapp.json configuration to install system-level Ubuntu packages.
[DATA_EXFILTRATION]: By design, the skill manages the movement of genomics data between local storage and the DNAnexus cloud platform using dedicated SDK functions like dxpy.upload_local_file() and dxpy.download_dxfile(). It also includes guidance on configuring network access for platform-based execution environments.
[SAFE]: The skill processes genomics data formats (FASTQ, BAM, VCF) and platform configuration files (dxapp.json). These are specialized data formats with no evidence of malicious instruction embedding or prompt injection vulnerabilities.

dnanexus-integration