add-omics-runtime-pack

name	add-omics-runtime-pack
description	Audit or refresh a curated pack of eight high-signal omics runtime skills in a BioClaw installation. Use when the user wants stronger built-in guidance for common omics analyses inside agent containers without changing BioClaw source code. Ensures the eight runtime skill folders exist under `container/skills/` with the expected flat file layout.
disable-model-invocation	true

Add Omics Runtime Pack

This skill verifies that eight strong runtime skills are present under container/skills/ for common BioClaw analysis tasks.

What This Adds

• container/skills/scrna-preprocessing-clustering/
• container/skills/cell-annotation/
• container/skills/chip-seq/
• container/skills/atac-seq/
• container/skills/differential-expression/
• container/skills/proteomics/
• container/skills/metagenomics/
• container/skills/structural-biology/

Each runtime skill must contain only root-level files:

• SKILL.md
• technical_reference.md
• commands_and_thresholds.md

What This Must Not Change

• Do not modify src/, container/agent-runner/, Dockerfile, or any application code.
• Do not modify src/container-runner.ts.
• Do not add Python packages, R packages, or other dependencies.
• Do not add nested references/ directories under container/skills/<skill>/.

The contribution is delivered as runtime skill content plus this installer skill, without any source-code changes.

Why The Runtime Skills Must Stay Flat

BioClaw syncs container/skills/<skill>/ into /home/node/.claude/skills/<skill>/ inside the container, but the sync only copies the first directory level.

That means:

• container/skills/<skill>/SKILL.md will sync
• container/skills/<skill>/technical_reference.md will sync
• container/skills/<skill>/commands_and_thresholds.md will sync
• container/skills/<skill>/references/... will not sync

So every installed runtime skill must be flat.

Runtime Skill Source Of Truth

The runtime-ready versions now live directly in:

container/skills/

Treat those directories as the source of truth. Do not recreate alternate copies under .claude/skills/.

Implementation Steps

Run all steps directly. Only pause if one of the target runtime skill directories already exists and appears user-modified.

1. Verify Current State

Check:

pwd
ls -la container/skills
for skill in \
  scrna-preprocessing-clustering \
  cell-annotation \
  chip-seq \
  atac-seq \
  differential-expression \
  proteomics \
  metagenomics \
  structural-biology
do
  test -e "container/skills/$skill" && echo "$skill already exists" || echo "$skill missing"
done

If any target directory already exists, inspect it before changing anything.

2. Create Or Update The Eight Runtime Skill Directories

For each skill listed below, ensure container/skills/<skill>/ exists and contains exactly the three required root-level files.

Runtime skill	Required files
scrna-preprocessing-clustering	SKILL.md, technical_reference.md, commands_and_thresholds.md
cell-annotation	SKILL.md, technical_reference.md, commands_and_thresholds.md
chip-seq	SKILL.md, technical_reference.md, commands_and_thresholds.md
atac-seq	SKILL.md, technical_reference.md, commands_and_thresholds.md
differential-expression	SKILL.md, technical_reference.md, commands_and_thresholds.md
proteomics	SKILL.md, technical_reference.md, commands_and_thresholds.md
metagenomics	SKILL.md, technical_reference.md, commands_and_thresholds.md
structural-biology	SKILL.md, technical_reference.md, commands_and_thresholds.md

Do not invent alternate content unless the committed runtime files clearly conflict with the current repository state.

3. Preserve The Runtime-Ready Shape

For every installed runtime skill:

• keep only the three root-level files above
• do not create README.md
• do not create nested references/
• keep the relative links in SKILL.md pointing to technical_reference.md and commands_and_thresholds.md

4. Validate The Installed Pack

Run these checks:

find container/skills -maxdepth 2 -type f | sort
find container/skills -maxdepth 3 -type d -name references

The second command should produce no output for the eight installed skills.

Also confirm that no duplicate copy of the runtime pack remains under .claude/skills/add-omics-runtime-pack/.

Also confirm no external-path residue remains:

grep -RniE "/Users/|omics-skills-repo-template|bioSkills-main|OpenClaw-Medical-Skills-main|claude-scientific-skills-main" \
  container/skills/scrna-preprocessing-clustering \
  container/skills/cell-annotation \
  container/skills/chip-seq \
  container/skills/atac-seq \
  container/skills/differential-expression \
  container/skills/proteomics \
  container/skills/metagenomics \
  container/skills/structural-biology

That search should return no matches.

5. Report The Result

Summarize:

• which runtime skill directories were created
• whether all eight contain exactly the three required files
• whether any pre-existing directories needed conflict resolution
• that no source files were modified