pacsomatic

80 / 100 · Low risk

Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.

By anubhavg-icpl/vibe (GitHub) · coding · 13 stars · scanned at commit d51e7ac

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

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 coding skill.

Found in 70 places.

skills/sci-pacsomatic/SKILL.md, line 99python scripts/run_pacsomatic.py \
skills/sci-pacsomatic/SKILL.md, line 114python scripts/run_pacsomatic.py \
skills/sci-pacsomatic/SKILL.md, line 141python -m unittest discover -s tests -v

Show 17 more

skills/sci-pacsomatic/scripts/run_pacsomatic.py, line 76completed = subprocess.run(["java", "-version"], capture_output=True, text=True)
skills/sci-pacsomatic/scripts/run_pacsomatic.py, line 118completed = subprocess.run(cmd)
skills/sci-pacsomatic/scripts/run_pacsomatic.py, line 152completed = subprocess.run(cmd, capture_output=True, text=True)
skills/sci-pacsomatic/scripts/run_pacsomatic.py, line 178completed = subprocess.run(cmd)
skills/sci-pacsomatic/scripts/run_pacsomatic.py, line 578completed = subprocess.run(cmd, shell=True, text=True, capture_output=True)
.claude/settings.json, line 9"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-bash'",
.claude/settings.json, line 19"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-edit'",
.claude/settings.json, line 31"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-edit'",
.claude/settings.json, line 41"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-bash'",
.claude/settings.json, line 52"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" route'",
.claude/settings.json, line 63"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-restore'",
.claude/settings.json, line 68"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" import'",
.claude/settings.json, line 79"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 90"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" sync'",
.claude/settings.json, line 102"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-manual'"
.claude/settings.json, line 106"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 116"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-auto'"

and 50 more places

Downloads and installs other software

The author does not mention this. It runs automatically when the plugin is installed.

Found in 10 places.

.claude/settings.json, line 166"Bash(npx @claude-flow*)",
.claude/settings.json, line 167"Bash(npx claude-flow*)",
.mcp.json, line 4"command": "npx",

Show 7 more

hooks/cmods/README.md, line 96npx eslint --fix "$FILE" 2>/dev/null
hooks/cmods/post-edit-format.sh, line 29npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 32npx biome format --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 80npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 86npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/pre-commit-lint.sh, line 38echo "$files" | xargs npx eslint --max-warnings 0 2>/dev/null
hooks/hooks.json, line 106"command": "#!/bin/bash\n# Run TypeScript check after editing TS files\ninput=$(cat)\nfile_path=$(echo \"$input\" | jq -r '.tool_input.file_path // \"\"')\n\nif

Install

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

if [ -e ~/.agents/skills/'pacsomatic' ] || [ -L ~/.agents/skills/'pacsomatic' ]; then echo 'A skill folder named pacsomatic already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/anubhavg-icpl/vibe' "$d" && git -C "$d" checkout --quiet 'd51e7ac9a34111cd2e63daed83c2198f91570050' -- 'skills/sci-pacsomatic' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sci-pacsomatic' ~/.agents/skills/'pacsomatic' && 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/'pacsomatic' ~/.claude/skills/'pacsomatic' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-08	`d51e7ac`	80