damlab-skills

Curated Cursor Agent Skills for command-line bioinformatics tools used in the Dampier lab. Each skill is an AgentSkills-compatible folder with a SKILL.md (YAML name and description plus usage notes) so coding agents learn how to invoke the tool, common patterns, and where to look up full --help text.

New here? Read INSTALL.md (setup), PHILOSOPHY.md (why this layout), and FAQ.md (troubleshooting). Contributing: CONTRIBUTING.md.

Quickstart

git clone https://github.com/DamLabResources/damlab-skills ~/repos/damlab-skills
cd ~/repos/damlab-skills
bash install.sh

• Default: links skills into ~/.cursor/skills/. Use bash install.sh --openclaw for ~/.openclaw/skills/, or bash install.sh --dest /path/to/skills. See INSTALL.md.
• Restart Cursor (or start a new OpenClaw session) after install.
• Versioning: repo-level history and SemVer policy are in CHANGELOG.md.

Skills

Skill	Tool	Description
samtools	samtools	SAM/BAM/CRAM alignment file manipulation
seqkit	seqkit	FASTA/FASTQ sequence manipulation
csvtk	csvtk	CSV/TSV tabular data manipulation
pod5	pod5	POD5 nanopore raw signal file inspection, merging, filtering, subsetting, and conversion
crispresso	CRISPResso2	CRISPR genome editing outcome analysis from amplicon sequencing (indels, HDR, base editing, prime editing)
rclone	rclone	Sync and transfer files with cloud storage and remote backends (S3, GCS, Drive, SFTP, etc.)
docx	python-docx + pandoc	Read, write, and track-change Microsoft Word .docx files
ncbi-edirect	NCBI EDirect	Search NCBI databases and download papers, sequences, and records (esearch, efetch, elink, xtract)
plotting	Altair + vl-convert	Declarative charts (Vega-Lite): PNG/SVG and interactive HTML from Python or JSON specs
eda	Python (numpy, pandas, matplotlib, seaborn, pingouin, statsmodels, scikit-learn, Jupyter kernel tooling)	Notebook-first collaborative exploratory data analysis workflow for tabular biological data
jupyter-notebook	Jupytext + nbformat + nbconvert	Convert, execute, diff, sync, and read outputs from .ipynb notebooks
create-skill	—	Meta-skill: conventions for adding new skills to this repo
bioinfo-best-practices	—	Meta-skill: workflow conventions for reproducible bioinformatics analysis and debugging
bioinformatics-methods-results-writer	—	Meta-skill: draft Methods and Results manuscript sections from code, notebooks, logs, figures, and tables
deep-research-query	—	Meta-skill: plan and execute rigorous literature searches, evidence syntheses, and review-style summaries for biomedical and computational biology topics

Documentation map

Doc	Purpose
INSTALL.md	Prerequisites, install.sh options (Cursor / OpenClaw / custom), verification, allowlist, update, uninstall
PHILOSOPHY.md	Design goals: conda vs MCP, allowlist-first paths, security
FAQ.md	Common failures (conda missing, allowlist, macOS readlink, OpenClaw discovery)
CONTRIBUTING.md	How to propose changes and add skills
CHANGELOG.md	Repo-level release notes and SemVer
WISHLIST.md	Roadmap ideas

Other agents (OpenClaw, project-local, Claude Code)

• OpenClaw: Uses AgentSkills-compatible directories; install with bash install.sh --openclaw or see OpenClaw skills. You can also copy or point skills.load.extraDirs at this repo’s skills/ tree if your config supports it.
• Project-local sharing: Symlink into .cursor/skills/ in a repo root, or use OpenClaw’s workspace /skills / .agents/skills per their docs.
• Claude Code: No universal skills folder like Cursor; use this repo as the reference tree and point the agent at skills/<name>/SKILL.md. See INSTALL.md and PHILOSOPHY.md.

Why conda environments instead of MCP servers?

Briefly: these skills run real CLI binaries via conda prefix envs under venvs/<tool>/, not a long-lived MCP server—fewer moving parts for file-oriented tools. Full rationale: PHILOSOPHY.md.

Repo structure

damlab-skills/
  CHANGELOG.md
  CONTRIBUTING.md
  FAQ.md
  INSTALL.md
  LICENSE
  PHILOSOPHY.md
  README.md
  WISHLIST.md
  install.sh
  venvs/                    # prefix conda envs (gitignored): venvs/<tool>/
  skills/<tool>/
    SKILL.md                 # frontmatter + subcommands + patterns
    reference.md             # captured --help output
    patterns.md
    environment.yaml         # conda spec; name: is docs-only for prefix installs
    CHANGELOG.md
    bin/                     # symlink -> ../../venvs/<tool>/bin (created by install.sh)

License

MIT. See LICENSE.