dnanexus-integration
Builds and operates reproducible genomics workloads on DNAnexus
by k-dense-aiFree
Description
dnanexus-integration is an agent skill for building, running and operating genomics workloads on the DNAnexus platform. It covers the dx command-line tool and the dxpy Python library for automation, files, records, folders, projects and metadata. It also covers apps and applets defined by dxapp.json, jobs, workflow analyses, retries, monitoring and cost controls, native workflows, and WDL and CWL workflows through dxCompiler, plus Nextflow imports. The skill's aim is to let you operate the platform correctly rather than guess at its semantics. Use it when you need to run a reproducible sequencing or genomics pipeline on DNAnexus, to package an analysis as an app, or to manage data and cost on the platform. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk. Install it with npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill dnanexus-integration.…
Highlights
- dx CLI and dxpy automation
- Apps and applets from dxapp.json
- Native workflows and dxCompiler
- Nextflow imports
- Job monitoring and cost controls
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dnanexus-integration FAQ
What does the skill cover?
Operating DNAnexus genomics workloads through the dx CLI and dxpy, including apps, workflows, jobs and cost controls.
Which workflow languages?
Native DNAnexus workflows, WDL and CWL through dxCompiler, and Nextflow imports.
How are apps defined?
By a dxapp.json file, as the skill describes.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill dnanexus-integration.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best dnanexus-integration alternatives?
Popular alternatives to dnanexus-integration include gget, biopython and bulk-rnaseq. See all dnanexus-integration alternatives