Agent Skills for the David H. O'Connor (DHO) Lab

Each skill is a self-contained reference guide — a SKILL.md with YAML frontmatter (name, description) in the portable Agent Skills format. An AI coding agent loads a skill on demand when its trigger conditions match, so lab-specific institutional knowledge doesn't have to be re-derived every time.

Skills

Skill	Use it when
chtc-oconnor-jobs	Running OConnor-group HTCondor batch campaigns on CHTC — staging large data, transferring execute-node inputs, packaging runtimes, starting with a canary, bounding concurrency, and retaining only verified outputs.
dholk	Working with LabKey or the DHO Lab's DHOLK instance — exploring containers and schemas, writing queries or client scripts, and configuring MCP tools without committing API keys. The MCP tools are read-only, but generated scripts may not be.
duckdb-dholk	Analyzing DHOLK tables locally with DuckDB through duck-lk. This thin bridge depends on the dholk skill in this repository and the upstream duck-lk skill.
nf-ospool	Setting up or debugging a Nextflow workflow on CHTC / OSPool with the nf-ospool executor plugin — instant-crash jobs, multi-day condor_q-empty hangs, HasCHTCStaging matchmaking, containers, and why sharedFilesystem = false.
nf-ospool-test	Verifying a CHTC / OSPool setup actually works before a long run — a live smoke test that submits one tiny probe job and confirms the staging path is healthy. Companion to nf-ospool.

Installing

Use the skills installer and choose which skills and coding agents you want to configure. Installation is local to the current project by default; pass --global to install for your user account.

With npm:

npx skills@latest add dholab/skills

With pnpm:

pnpm dlx skills@latest add dholab/skills

With Bun:

bunx skills@latest add dholab/skills

To inspect the available skills without installing them:

npx skills@latest add dholab/skills --list

Manual installation

Clone the repository, then link or copy each desired skill directory into the folder your agent scans for skills:

• Claude Code: ~/.claude/skills/
• Codex: ~/.codex/skills/
• GitHub Copilot CLI: ~/.copilot/skills/
• Gemini CLI: ~/.gemini/skills/
• OpenCode: ~/.config/opencode/skills/

git clone https://github.com/dholab/skills.git dholab-skills
cd dholab-skills

# Symlinks stay in sync when you pull repository updates. Set this path to the
# directory for your agent from the list above.
SKILLS_DIR=~/.claude/skills
mkdir -p "$SKILLS_DIR"
ln -s "$PWD/skills/chtc-oconnor-jobs" "$SKILLS_DIR/chtc-oconnor-jobs"
ln -s "$PWD/skills/dholk"          "$SKILLS_DIR/dholk"
ln -s "$PWD/skills/duckdb-dholk"   "$SKILLS_DIR/duckdb-dholk"
ln -s "$PWD/skills/nf-ospool"      "$SKILLS_DIR/nf-ospool"
ln -s "$PWD/skills/nf-ospool-test" "$SKILLS_DIR/nf-ospool-test"

To install independent copies instead, replace each ln -s command with cp -R.

The agent then exposes them by name (in Claude Code, as /chtc-oconnor-jobs, /dholk, /duckdb-dholk, /nf-ospool, and /nf-ospool-test).

Contributing

Add a new skill as skills/<name>/SKILL.md with YAML frontmatter (name, description). Keep the description focused on when to use the skill (start with "Use when…"). See the existing skills for the house style.