The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill downloads and installs the official deepTools package (version 3.5.6) from PyPI, which is the standard repository for Python software.
[EXTERNAL_DOWNLOADS]: The instructions and scripts reference the official uv documentation at docs.astral.sh, which is a well-known service for Python package management.
[COMMAND_EXECUTION]: The skill includes helper scripts (scripts/validate_files.py and scripts/workflow_generator.py) that generate and execute shell commands for processing genomic data. These scripts include robust path sanitization and argument validation to prevent shell injection and are focused entirely on the skill's primary purpose.
[COMMAND_EXECUTION]: The skill instructs the user to make generated workflow scripts executable (chmod +x). This is standard practice for bioinformatics pipelines and is done within the user's local workspace.
[DATA_EXPOSURE_&_EXFILTRATION]: The skill involves processing local BAM, bigWig, and BED files. There are no network operations that exfiltrate this data; all processing and visualization (e.g., generating heatmaps/PNGs) occur locally within the user's environment.

deeptools