Add add-omics-runtime-pack skill

[zongtingwei]

Summary

Adds a new contributed skill at .claude/skills/add-omics-runtime-pack/.

This skill teaches Claude Code how to install eight strong omics runtime skills into a BioClaw installation without modifying source code:

• 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/

The bundled runtime pack is flattened for BioClaw's non-recursive skill sync, so each installed runtime skill contains only:

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

Notes

• No source files were modified
• No Docker or container-runner changes were made
• No runtime skills are preinstalled by this PR
• The contribution is delivered entirely as a skill, per CONTRIBUTING.md

Testing

Validated that the contributed skill package contains only the new .claude/skills/add-omics-runtime-pack/ directory.

Validated that the bundled runtime pack has no external absolute-path residue and no nested runtime references directories.

Simulated installation into container/skills/ and verified:

• all 8 runtime skill directories are created
• each runtime skill contains exactly 3 root-level files
• no nested references directories are present after installation
• no BioClaw source files are modified

[Runchuan-BU]

Thanks for the contribution! The skill content looks good, but the files are in the wrong location.

Currently everything is under .claude/skills/add-omics-runtime-pack/references/runtime-pack/ — that's the Claude Code skill directory for developers. These runtime skills need to be in container/skills/ so they get synced into the agent container at build time.

What needs to change:

Move each skill folder from:

.claude/skills/add-omics-runtime-pack/references/runtime-pack/<skill-name>/

To:

container/skills/<skill-name>/

The .claude/skills/add-omics-runtime-pack/SKILL.md (the installer skill itself) can stay where it is — it's the eight runtime skill folders that need to move.

Expected structure:

container/skills/
├── scrna-preprocessing-clustering/
│   ├── SKILL.md
│   ├── commands_and_thresholds.md
│   └── technical_reference.md
├── cell-annotation/
├── chip-seq/
├── atac-seq/
├── differential-expression/
├── proteomics/
├── metagenomics/
└── structural-biology/

Could you update the PR with this change? Let me know if you have any questions.

[zongtingwei]

Thanks for the clarification! I updated the PR so the eight runtime skills now live under container/skills// with the expected flat layout (SKILL.md, technical_reference.md, and commands_and_thresholds.md), while keeping .claude/skills/add-omics-runtime-pack/SKILL.md as the installer skill.

At this point the content and file placement match your requested structure, but the PR is still blocked by CI for two repo-level reasons that are not specific to the skill content itself. First, the current Skill PR Check treats any changes under container/ as source changes, so moving the runtime skills into container/skills/ now causes the workflow to fail with “PRs that add skills should not modify source files.” Second, the test workflow is still failing on the existing db/WhatsApp baseline issue that is being addressed separately in PR #21. So from my side the layout change is done, but this PR will still need either an adjustment to the skill-only check or maintainer guidance on the intended contribution path for runtime skills under container/skills/.

[erik-mingyang]

我看了下，#21 已经 merge 了，而且就是在修你前面提到的 db/WhatsApp baseline test。
所以现在先不用继续改 skill 结构了。你先把这个 PR 同步到最新 main，再 rerun 一次 CI 吧。这样我们就能更清楚地看出来，现在剩下的红灯到底是不是这个 PR 自己的问题。

[zongtingwei]

I rebased this PR onto the latest main and reran CI. The result is now much clearer: the test workflow passes, which means the previous db / WhatsApp baseline issue was resolved after PR #21 was merged. The only remaining failure is Skill PR Check. So at this point the red CI signal is no longer caused by the old test baseline, but by a conflict between the current skill-only workflow rules and the requested file layout. Per the review feedback, the eight runtime skills have already been moved into container/skills/, but the current workflow treats files under container/skills/* as both “new skill files” and “source changes,” which makes this check fail automatically. In other words, the remaining issue is not the skill content itself and not the test baseline anymore; it is the CI rule for how runtime skills under container/skills/ are classified.