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Sources and Version Baseline

Verification

Last verified: 2026-07-23

Component	Verified baseline
DNAnexus Platform docs	2026 documentation and release notes through 2026-07-21
dx-toolkit / dxpy	0.410.0, released 2026-07-14
Python requirement	Python 3.8+ on PyPI
App Execution Environment	Ubuntu 24.04 and 20.04, version 0
dxCompiler	2.17.0
Upload Agent	1.5.33
Download Agent	0.6.3
dxFUSE	1.6.1
Nextaur	1.13.0
Nextflow engines exposed by dx-toolkit 0.410.0	25.10 and 24.10
Nextflow 25.10 asset baseline	Nextflow 25.10.4 with nf-amazon 3.4.4

Version-specific examples in this skill are pinned for reproducibility. Before upgrading, inspect release notes, run scripts/inspect_dxpy.py, and rebuild/test apps in a non-production project.

Documentation Index and Releases

• DNAnexus documentation index (llms.txt)
• DNAnexus 2026 release notes
• Downloads
• Index of dx commands
• dx-toolkit GitHub repository
• dx-toolkit changelog
• dxpy on PyPI
• Generated Python API reference

The release notes are date-versioned by platform deployment. The skill baseline incorporates:

• 2026-07-21: dx-toolkit 410.0 malicious-file download warning
• 2026-07-14: strengthened session/password controls
• 2026-06-23: dxCompiler 2.17.0 authenticated WDL imports
• 2026-06-09: file download API securityStatus
• 2026-05-19: dxCompiler resource-retry support
• 2026-03-17: automatic upgrade on insufficient-resource retry
• 2026-02-03: retired instance type validation
• 2026-01-27: dynamic instance type selection

Authentication

• Login and Logout
• Environment Variables
• dx-toolkit environment bootstrap
• API Authentication
• API Protocols and Errors

Key current points:

• Environment variables override saved CLI configuration.
• dx env displays token material.
• Tokens without explicit expiry default to one month.
• Token revocation terminates associated active jobs/transfers.
• New interactive sessions use an 18-hour inactivity timeout.

Apps and Applets

• Introduction to Building Apps
• Developer Quickstart
• App Metadata (dxapp.json)
• I/O and Run Specifications
• App Execution Environment
• App Permissions
• Types of Errors
• Developing Apps and Applets FAQ

Dependencies:

• Dependency management
• Python packages in Ubuntu 24.04 AEE
• Asset Build Process
• Docker Images

Data and Projects

• Uploading and Downloading Files
• dx upload
• dx download
• Upload Agent
• Download Agent
• Download Agent repository
• Download Agent 0.6.3 release
• dxFUSE 1.6.1 release
• Data Object Lifecycle
• Files API
• Data Object Metadata
• Folders and Deletion
• Cloning
• Project Permissions and Sharing
• Project API Methods
• Project Data Access Controls
• Search API
• Service Limits

Execution and Workflows

• Running Apps and Workflows
• Running Apps and Applets
• Running Workflows
• Monitoring Executions
• Job Lifecycle
• Execution Cost and Spending Limits
• Running Analyses API
• Workflows and Analyses API
• Building and Running Workflows
• Importing Workflows

WDL, CWL, and Nextflow

• dxCompiler repository
• dxCompiler 2.17.0 release
• dxCompiler release notes
• Running Nextflow Pipelines

Check these sources together. Platform documentation describes supported integration behavior; compiler/tool release notes describe version-specific language and runtime changes.

Corrected Legacy Patterns

The previous skill version contained examples that should not be copied:

Legacy pattern	Current guidance
license: Unknown	Skill is MIT; dxpy upstream is Apache-2.0
Declaring DX_SECURITY_CONTEXT in skill metadata	Authenticate through CLI/named secret injection; never expose token
dx build --app only	--app remains an alias; current help documents --create-app
dxapi described as required	dxapi is optional
runSpec.systemRequirements	Deprecated in source manifests; use regionalOptions.<region>.systemRequirements
Top-level resources	Deprecated; use region-specific resources
Static instance list	Discover current regional types; retired types are rejected
DXFile.open_file()	Use dxpy.open_dxfile()
name="*.bam" without mode	Add name_mode="glob"
ResourceNotFound imported as dxpy exception	Inspect DXAPIError.name
Treating every wait_on_done() exception as remote failure	In dxpy 0.410.0, DXJobFailureError also covers termination and local wait timeout; re-describe state
Runtime pip install as primary dependency strategy	Prefer pinned venv/assets/saved images
Pulling floating Docker tags	Pin digest and preferably store docker save tarball
dxpy.dxlink(job.get_output_ref(...))	Pass get_output_ref() directly

Refresh Procedure

When updating this skill:

1. Check PyPI for the current dxpy release and Python requirement.
2. Read platform release notes since the verification date.
3. Read dx-toolkit and dxCompiler release notes.
4. Run:

bash uv run --with "dxpy==<new-version>" \ "scripts/inspect_dxpy.py" --strict

1. Compare dx build --help, dx run --help, and search command help.
2. Test dxapp.json validation and a minimal build in a sandbox project.
3. Test representative file, job, analysis, WDL/CWL, and Nextflow workflows.
4. Update the date/version table and skill metadata.version.

Do not update examples from memory alone.