`dnanexus-integration`

Category: lab-automation · License: MIT · Version: 2.1 · Includes scripts Tags: genomics, cloud computing, bioinformatics pipelines, workflows, DNAnexus

When to use it

Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

Example requests

Ask your agent in plain language, for example:

“How do I download a whole folder from my DNAnexus project to my laptop?”
“I’m getting DXExecDependencyError when my applet starts on Ubuntu 24.04. My dxapp.json has execDepends with pip packages: pysam, pandas, and an old numpy pin. Built with dx build -f. Can you help me fix it and tidy up the config?”
“I have a WGS pipeline written in WDL for 40 samples and I want it to run on our cloud genomics platform where my data already lives under a project called cohort-2026. I need it to be launched in bulk, with the cost capped and a way to see which runs failed. Where do I start?”

Install

# skills.sh (Claude Code, Codex, Cursor, Gemini CLI, Copilot and more)
npx skills add KalarisLabs/research-agent-skills --skill dnanexus-integration

# GitHub CLI
gh skill install KalarisLabs/research-agent-skills dnanexus-integration

In Claude Code you can also add the marketplace with /plugin marketplace add KalarisLabs/research-agent-skills and install the whole lab-automation category with /plugin install lab-automation@research-agent-skills.

Full playbook

Read SKILL.md for the complete workflow, references and any scripts. The agent installer copies the full skill folder.

Get started

Research workflows

Skills by discipline

All skills

Reference

dnanexus-integration — AI agent skill for lab automation

`dnanexus-integration`

When to use it

Example requests

Install

Full playbook

dnanexus-integration

When to use it

Example requests

Install

Related

Full playbook

`dnanexus-integration`