DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
Install
Use withClaudeCursorCodex
The file stays in the publisher's repository. PlugMCP does not host or rewrite it.
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
name: dnanexus-integration
description: "DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution."
DNAnexus Integration
Overview
DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
When to Use This Skill
This skill should be used when:
Creating, building, or modifying DNAnexus apps/applets
Uploading, downloading, searching, or organizing files and records
When working with DNAnexus, follow this decision tree:
Need to create a new executable?
Yes → Use App Development (references/app-development.md)
No → Continue to step 2
Need to manage files or data?
Yes → Use Data Operations (references/data-operations.md)
No → Continue to step 3
Need to run an analysis or workflow?
Yes → Use Job Execution (references/job-execution.md)
No → Continue to step 4
Writing Python scripts for automation?
Yes → Use Python SDK (references/python-sdk.md)
No → Continue to step 5
Configuring app settings or dependencies?
Yes → Use Configuration (references/configuration.md)
Often you'll need multiple capabilities together (e.g., app development + configuration, or data operations + job execution).
Installation and Authentication
Install dxpy
uv pip install dxpy
Login to DNAnexus
dx login
This authenticates your session and sets up access to projects and data.
Verify Installation
dx --version
dx whoami
Common Patterns
Pattern 1: Batch Processing
Process multiple files with the same analysis:
# Find all FASTQ files
files = dxpy.find_data_objects(
classname="file",
name="*.fastq",
project="project-xxxx"
)
# Launch parallel jobs
jobs = []
for file_result in files:
job = dxpy.DXApplet("applet-xxxx").run({
"input": dxpy.dxlink(file_result["id"])
})
jobs.append(job)
# Wait for all completions
for job in jobs:
job.wait_on_done()
Download bundled/skills/dnanexus-integration/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does dnanexus-integration live?
The publisher keeps it at https://github.com/foryourhealth111-pixel/Vibe-Skills.
Which agents can use dnanexus-integration?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.