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

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

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

Dependencies:

Data and Projects

Execution and Workflows

WDL, CWL, and Nextflow

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:

Check PyPI for the current dxpy release and Python requirement.
Read platform release notes since the verification date.
Read dx-toolkit and dxCompiler release notes.

Run:

bash

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

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

Do not update examples from memory alone.