The Agent Skills Directory

EXTERNAL_DOWNLOADS (LOW): The script scripts/run_blat_local.py automatically downloads genomic reference files (.2bit) from UCSC servers (hgdownload.cse.ucsc.edu and hgdownload.soe.ucsc.edu) if they are missing from the local system. Although UCSC is a standard and reputable repository for bioinformatics data, it is not included in the strictly defined list of trusted organizations. The download logic uses curl with hardcoded URLs.\n- COMMAND_EXECUTION (INFO): The skill executes external binaries (blat and curl) via subprocess.run using argument lists. This correctly mitigates shell injection risks by avoiding the use of shell=True and string concatenation for command building.\n- PROMPT_INJECTION (INFO): The skill handles user-supplied DNA sequences and FASTA files, which constitutes an indirect prompt injection surface (Category 8). \n
Ingestion points: Raw sequence strings passed via CLI or sequence data read from FASTA files in scripts/run_blat_local.py.\n
Boundary markers: No explicit boundary markers are used in the prompt interpolation, but the data is handled as a file-based input to a binary.\n
Capability inventory: The skill can execute system commands (blat, curl) and write to temporary files.\n
Sanitization: The skill validates that FASTA files contain single sequences and enforces ASCII encoding for query sequences. The risk is categorized as INFO/LOW because the input is processed by a specialized local tool (BLAT) and does not influence the agent's core decision-making logic or security boundaries.

bio-blat