benchos-plasmid-creator

name	benchos-plasmid-creator
description	Insert raw or accession-resolved DNA sequences into BenchOS demo plasmid backbones and export the final plasmid FASTA. Use when the user wants a BenchOS CLI or agent-driven version of the Plasmid Creator tool.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli`, `benchos-cli`, and the curated `python-basic` capability pack.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS Plasmid Creator

Use this skill when the user wants to:

• insert a DNA sequence into a BenchOS demo plasmid backbone
• resolve an accession to nucleotide FASTA before insertion
• export the final plasmid sequence into the BenchOS workspace

Browser Tool

BenchOS also exposes this workflow in the website Tools page as Plasmid Creator. Use the browser tool for quick inspection and FASTA export; use this skill for agent-driven runs and saved artifacts.

Quick Rules

• Use the shared wrapper script rather than re-implementing the BenchOS demo backbone assembly inline.
• Accept either raw DNA sequence or accession input.
• Keep outputs under artifacts/plasmids/<run-name>/ when possible.

Default Workflow

1. Confirm the backbone and whether the user is giving raw DNA or an accession.
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-plasmid-creator/scripts/plasmid_creator_cli.py",
    "--input-type",
    "sequence",
    "--source-text",
    "ATGGCC...",
    "--backbone",
    "438-A",
    "--output-dir",
    "artifacts/plasmids/run-001",
    "--json"
  ]
}

4. Read plasmid-creator.json and report the final plasmid length and source summary.
5. If the user wants the FASTA persisted elsewhere in BenchOS, attach or append it through the normal entry or registry APIs.

Outputs

• plasmid-creator.json: structured result payload
• plasmid-creator.fasta: final plasmid sequence

Notes

• The BenchOS demo backbone fragments are bundled with the shared skill so CLI behavior stays deterministic.
• Accession resolution uses NCBI nucleotide FASTA fetch before insertion.