BioClaw add-omics-runtime-pack

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.

install

source · Clone the upstream repo

git clone https://github.com/Runchuan-BU/BioClaw

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/Runchuan-BU/BioClaw "$T" && mkdir -p ~/.claude/skills && cp -r "$T/.claude/skills/add-omics-runtime-pack" ~/.claude/skills/runchuan-bu-bioclaw-add-omics-runtime-pack && rm -rf "$T"

manifest: .claude/skills/add-omics-runtime-pack/SKILL.md

source content

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