Agent SkillMCP planned

AutoBSgenome for Agents

AutoBSgenome can be used by coding agents and research assistants to check existing BSgenome packages, trigger builds, poll status, and return R installation commands.

Skill workflow

The current integration path for Codex, Claude, and similar agent environments.

Trigger phrases

Use when a user needs a BSgenome package, mentions TSSr, motifmatchr, ChIPseeker, Gviz, or has a missing genome error.

Skill file

skill.md

MCP status

Useful later, but not required for the current web/API product.

A future MCP server can expose tools like package lookup, metadata fetch, build submission, status polling, and publish.

For now, the HTTP API already provides the stable backend surface that an MCP server would wrap.

API Commands

Trigger a build

curl -s -X POST https://api.autobsgenome.org/api/build \
  -H "Content-Type: application/json" \
  -d '{
    "package_name": "BSgenome.Aluchuensis.NCBI.AkawachiiIFO4308",
    "organism": "Aspergillus luchuensis",
    "accession": "GCF_016861625.1",
    "data_source": "ncbi",
    "version": "1.0.0",
    "circ_seqs": "character(0)"
  }'

Poll build status

curl -s https://api.autobsgenome.org/api/status/JOB_ID

Install from the repository

install.packages("PACKAGE_NAME",
  repos = "https://johnnychen1113.github.io/autoBSgenome")