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DNAnexus Integration

A skill for building, running and monitoring reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets and workflow importers.

Dev & CodingAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Walks through dx CLI and dxpy basics: login, project selection, uploads/downloads, metadata and safe preflight checks.
  • Covers app/applet development with dxapp.json, offline validation via scripts/validate_dxapp.py, and dx build.
  • Handles execution: launching jobs/analyses, dx watch monitoring, --cost-limit guards, and job chaining via output references.
  • Explains importing WDL/CWL through dxCompiler and Nextflow through dx build --nextflow.
  • Enforces an operating contract: never expose tokens, confirm billable or destructive actions, respect PHI/TRE and org policies.

Who it's for

  • Bioinformaticians and engineers running genomics pipelines on the DNAnexus platform.
  • Developers packaging and publishing internal DNAnexus apps or automating them in CI.
  • Teams handling regulated data who want guardrails against accidental deletion, runaway cost, or credential leakage.

Examples

  1. "Find every BAM in /results" → generates correct find_data_objects(..., name_mode="glob", state="closed") code instead of a silently empty exact-name search.
  2. "Run this applet with a $25 cap and stream logs" → dx run ... --cost-limit 25 followed by dx watch job-xxxx --get-streams.
  3. "Review my dxapp.json" → runs the bundled validator and flags deprecated top-level resources or runSpec.systemRequirements.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/dnanexus-integration/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/dnanexus-integration folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/dnanexus-integration/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/dnanexus-integration ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy the skill: cp -r scientific-agent-skills/skills/dnanexus-integration ~/.claude/skills/
  4. Verify the references/ and scripts/ folders came along.
  5. Install the platform tooling: uv tool install "dxpy==0.410.0", then check with dx --version.
  6. Authenticate with dx login, then confirm with dx whoami and dx pwd.
  7. Restart Claude Code and try a prompt such as "help me upload these FASTQs to my DNAnexus project".
View source on GitHub ↗License: MIT