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DNAnexus Genomics Platform Integration

Guides an agent through building, running and operating DNAnexus genomics apps, data and workflows safely

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
12 files

What it does

Once installed, the agent follows a structured playbook for DNAnexus, a cloud platform used for genomics and biomedical data. It helps with the dx command-line tool and the dxpy Python library, building apps and applets from dxapp.json files, transferring and searching files, launching and monitoring compute jobs, and importing WDL, CWL or Nextflow pipelines. It is told to start read-only, confirm before billable, destructive or permission-changing actions, and never reveal API tokens.

Great for

  • Bioinformatics engineers who build or run pipelines on DNAnexus
  • Platform admins automating project, file and job management with dxpy
  • Teams validating dxapp.json configurations before building apps

Skip it if

  • Anyone without a DNAnexus account, since most steps need platform access and credentials
  • Handling regulated or PHI data outside an approved DNAnexus environment, because the skill can move data and must be governed by your organisation's policies
  • Unattended bulk deletions or launches, since the examples are illustrative and were not run against a live account

Try asking

  • “Validate my dxapp.json for an applet and then build it”
  • “Find all closed BAM files in /results in my project and list their archival state”
  • “Write a dxpy script that launches a workflow with a cost limit and monitors it”
  • “Help me import this Nextflow pipeline into DNAnexus”
Step-by-step guide: how to use DNAnexus Genomics Platform IntegrationInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 12 original files, the MIT licence and an attribution note.

    dnanexus-integration.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip dnanexus-integration.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip dnanexus-integration.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Give the agent explicit project IDs, folders and region up front so it can resolve them and show impact before acting.
  • Run the bundled validate_dxapp.py script with --strict before any dx build to catch configuration problems offline.
  • Use selected-project API tokens and keep secrets in a secret manager rather than in the shell or chat.

What's inside

  • references/app-development.md
  • references/authentication.md
  • references/configuration.md
  • references/data-operations.md
  • references/job-execution.md
  • references/operations-and-troubleshooting.md
  • references/python-sdk.md
  • references/sources.md
  • references/workflow-languages.md
  • scripts/inspect_dxpy.py
  • scripts/validate_dxapp.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.