benchos-primer-designer

name	benchos-primer-designer
description	Design LIC, sequencing, and optional Gibson or CPEC-style fragment primers from an NCBI accession or pasted DNA sequence. Use when the user wants naming-ready primer sets generated inside BenchOS.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli`, `benchos-cli`, and the curated `python-basic` capability pack with Primer3 and Biopython support.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS Primer Designer

Use this skill when the user wants to:

• generate LIC cloning primers for a CDS
• generate sequencing primers from an accession or pasted sequence
• optionally propose fragment primers for long constructs
• save a naming-ready TSV or JSON result into the BenchOS workspace

Quick Rules

• Use the shared wrapper instead of rewriting Primer3 calls inline.
• Prefer explicit raw sequence input when the user already has the CDS sequence.
• If the user provides raw sequence input, require a gene name.
• Treat SeqViz plasmid visualization as a later plasmid-map workflow, not part of the current v1 primer-design path.

Browser Tool

BenchOS also exposes this skill in the website Tools page as Primer Designer. The browser tool supports accession or raw sequence input, restriction-site checks, and TSV export. Use the website when the user wants an interactive design session; use this skill when they want agent-driven execution and saved artifacts.

Default Workflow

1. Confirm whether the user has:
   • an accession identifier, or
   • a raw DNA sequence plus gene name
2. Install the capability pack:

{ "args": ["capabilities", "install", "--name", "python-basic"] }

3. Run the shared script:

{
  "args": [
    "exec",
    "--capability",
    "python-basic",
    "--cwd",
    ".",
    "--",
    "/opt/benchos/shared-skills/benchos-primer-designer/scripts/primer_designer_cli.py",
    "--input-type",
    "sequence",
    "--source-text",
    "ATGGCC...",
    "--gene-name",
    "TIM",
    "--index-number",
    "101",
    "--initials",
    "LF",
    "--output-dir",
    "artifacts/primers/tim-run-001",
    "--json"
  ]
}

4. Report the LIC, sequencing, and optional fragment primers clearly.
5. If the user wants the output persisted elsewhere in BenchOS, attach or append the generated TSV or JSON through the normal entry or registry APIs.

Outputs

• primer-designer-results.json: structured result payload
• primer-designer-primers.tsv: naming-ready primer table

Notes

• v1 supports accession or raw sequence driven primer design.
• v1.5 is planned to add plasmid or GenBank-backed SeqViz visualization for primer placement on plasmid maps.