msa-search-nim

77 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a devops skill usually runs commands, installs tools and uses cloud credentials.

By stanfish06/skillquarium (GitHub) · devops · 12 stars · scanned at commit ced6c96

Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain dock…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this. Expected for a devops skill.

Found in 9 places.

skills/msa-search-nim/SKILL.md, line 58set -a
skills/msa-search-nim/SKILL.md, line 100until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done
skills/msa-search-nim/SKILL.md, line 115: "${LOCAL_NIM_CACHE:?Set LOCAL_NIM_CACHE}"

Show 6 more

skills/msa-search-nim/SKILL.md, line 137docker run --rm --entrypoint list-model-profiles nvcr.io/nim/colabfold/msa-search:2
skills/msa-search-nim/SKILL.md, line 143docker run --rm --name msa-search \
skills/msa-search-nim/SKILL.md, line 164curl -s localhost:8000/v1/metadata | jq
skills/msa-search-nim/SKILL.md, line 184ngc registry model download-version nim/colabfold/msa-search:uniref30_2302-m18v1
skills/msa-search-nim/SKILL.md, line 219curl -s -H "Authorization: Bearer $NGC_API_KEY" \
skills/msa-search-nim/SKILL.md, line 252for V in uniref30_2302-m18v1 colabfold_envdb_202108-m18v1 pdb70_220313-m18v1 \

Downloads and installs other software

The author does not mention this. Expected for a devops skill.

Found in 1 place.

skills/msa-search-nim/SKILL.md, line 71command -v aria2c >/dev/null || { echo "aria2c required; install it (e.g. apt-get install -y aria2) and re-run"; exit 1; }

Connects to the internet

This is disclosed by the author in the skill's SKILL.md or README. Expected for a devops skill.

Found in 6 places.

skills/msa-search-nim/SKILL.md, line 75curl -fsS -H "Authorization: Bearer $NGC_API_KEY" \
skills/msa-search-nim/SKILL.md, line 100until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done
skills/msa-search-nim/SKILL.md, line 164curl -s localhost:8000/v1/metadata | jq

Show 3 more

skills/msa-search-nim/SKILL.md, line 219curl -s -H "Authorization: Bearer $NGC_API_KEY" \
skills/msa-search-nim/SKILL.md, line 254curl -s -H "Authorization: Bearer $NGC_API_KEY" \
skills/msa-search-nim/SKILL.md, line 302response = requests.post(url, headers=headers, json=payload, timeout=300)

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'msa-search-nim' ] || [ -L ~/.agents/skills/'msa-search-nim' ]; then echo 'A skill folder named msa-search-nim already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/stanfish06/skillquarium' "$d" && git -C "$d" checkout --quiet 'ced6c96bd67acccbf0280a5071e59a523c118c66' -- 'skills/msa-search-nim' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/msa-search-nim' ~/.agents/skills/'msa-search-nim' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'msa-search-nim' ~/.claude/skills/'msa-search-nim' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

Badge for your README

The badge for stanfish06/skillquarium shows the score of its lowest-scoring skill.

SkillTrust badge for stanfish06/skillquarium

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/stanfish06/skillquarium.svg)](https://zalavijaysinh.github.io/skilltrust/repos/stanfish06/skillquarium/)

Score history

Date	Version	Score
2026-11-13	`ced6c96`	77
2026-11-08	`f748ea9`	77