Dnanexus Integration

Current dxapp.json Configuration

Quick Navigation

• Manifest purpose

• Applets versus apps

• Input and output specifications

• runSpec

• Regional resources

• Retry and timeout policy

• Dependencies

• Access requirements

• Validation checklist

What dxapp.json Controls

dxapp.json is the source manifest consumed by dx build and dx build --create-app. It describes:

• App metadata and version

• Input and output contracts

• Entry-point interpreter and source file

• Application Execution Environment (AEE)

• Dependencies

• Timeout and restart policies

• Requested project, network, and developer permissions

• Region-specific resources

Do not confuse the source manifest with the canonical API payload produced by the build tool. For field constraints, the API methods /applet/new, /app/new, and the I/O and Run Specifications are authoritative.

Applets Versus Apps

An applet without both input and output specifications cannot be added as a workflow stage.

Minimal Applet

This is valid JSON; comments are intentionally omitted.

{
  "name": "qc-fastq",
  "inputSpec": [
    {
      "name": "reads",
      "class": "file",
      "patterns": ["*.fastq", "*.fastq.gz"],
      "help": "Input FASTQ file"
    }
  ],
  "outputSpec": [
    {
      "name": "report",
      "class": "file",
      "patterns": ["*.html"]
    }
  ],
  "runSpec": {
    "interpreter": "python3",
    "file": "src/qc_fastq.py",
    "distribution": "Ubuntu",
    "release": "24.04",
    "version": "0"
  }
}

The dxapi field is optional; it is not a required manifest field. App names cannot start with app-. App versions are nonempty strings using letters, digits, ., _, +, and -; semantic versioning is recommended, but the API also accepts versions such as release_2026.

Production App Skeleton

Replace the region and instance type with values available to the target project. Do not copy a static instance list from old documentation.

{
  "name": "qc-fastq",
  "title": "FASTQ quality control",
  "summary": "Creates a quality-control report for one FASTQ file",
  "version": "1.0.0",
  "inputSpec": [
    {
      "name": "reads",
      "label": "Reads",
      "class": "file",
      "patterns": ["*.fastq.gz"],
      "help": "A gzip-compressed FASTQ file"
    }
  ],
  "outputSpec": [
    {
      "name": "report",
      "label": "QC report",
      "class": "file",
      "patterns": ["*.html"]
    }
  ],
  "runSpec": {
    "interpreter": "python3",
    "file": "src/qc_fastq.py",
    "distribution": "Ubuntu",
    "release": "24.04",
    "version": "0",
    "timeoutPolicy": {
      "main": {"hours": 4}
    },
    "executionPolicy": {
      "restartOn": {
        "ExecutionError": 1,
        "UnresponsiveWorker": 2,
        "SpotInstanceInterruption": 2
      },
      "maxRestarts": 3
    }
  },
  "access": {
    "network": []
  },
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "main": {
          "instanceType": "mem2_ssd1_v2_x4"
        }
      }
    }
  }
}

Run the bundled offline check from this skill's root before building:

uv run python "scripts/validate_dxapp.py" \
  "path/to/dxapp.json" --kind app --strict

Input and Output Specifications

Common classes:

• Primitives: string, int, float, boolean, hash

• Data objects: file, record, applet

• Arrays: array:int, array:float, array:string, array:boolean, array:file, array:record, and array:applet. array:hash is not supported.

Every parameter needs a unique name and a class. Required array inputs are nonempty; mark an array input optional if an empty value is valid. Useful optional fields include:

• label

• help

• optional

• default

• choices

• patterns

• suggestions

• group

Use patterns as a user-interface hint, not as a security or content validation boundary. Validate actual content in app code.

Defaults must match the declared class. File and record defaults use DNAnexus links, not raw local paths. default, choices, and suggestions apply only to inputs, not outputs.

runSpec

For the source manifest, set:

{
  "runSpec": {
    "interpreter": "python3",
    "file": "src/main.py",
    "distribution": "Ubuntu",
    "release": "24.04",
    "version": "0"
  }
}

Supported combinations at the current baseline:

• Ubuntu 24.04, environment version 0, python3 or bash

• Ubuntu 20.04, environment version 0, python3 or bash

Prefer Ubuntu 24.04 for new development. Use 20.04 only for a tested compatibility requirement and plan migration.

Regional Resources

Current placement

For new manifests, place resource requirements under:

regionalOptions.<region>.systemRequirements.<entry-point>

The older locations below are deprecated:

• runSpec.systemRequirements

• top-level resources

They remain accepted for some single-region compatibility cases but should not be used in new apps.

If one region declares systemRequirements, declare it for every region listed in regionalOptions and omit it from runSpec. Region-bound asset and resource IDs must also be available in the corresponding region.

Fixed instance type

{
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "main": {"instanceType": "mem2_ssd1_v2_x4"},
        "process": {"instanceType": "mem3_ssd1_v2_x8"}
      }
    }
  }
}

Available instance types differ by cloud and region. Retired types are rejected when an app or applet is created or updated.

Dynamic instance selection

Where licensed, provide an ordered fallback list:

{
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "main": {
          "instanceTypeSelector": {
            "allowedInstanceTypes": [
              "mem1_ssd1_v2_x4",
              "mem1_ssd1_v2_x8",
              "mem2_ssd1_v2_x4"
            ]
          }
        }
      }
    }
  }
}

instanceTypeSelector is mutually exclusive with instanceType and clusterSpec for the same entry point. The platform initially gives each allowed type 10 minutes in list order. If none provisions, it repeats the list with doubled windows (20 minutes, then 40, and so on); normal-priority jobs apply the same sequence to on-demand fallback after Spot wait expires. The job description records attempts in instanceTypeTransitions.

Clusters

Cluster requests use clusterSpec in an entry point's system requirements. They may also specify a fixed instanceType; only instanceTypeSelector conflicts with either of those fields. Current cluster types are dxspark, apachespark, and generic. Spark versions and instance availability change; consult the live I/O and Run Specifications instead of hardcoding an old value.

Retry and Timeout Policy

Example:

{
  "runSpec": {
    "executionPolicy": {
      "restartOn": {
        "AppInsufficientResourceError": 2,
        "ExecutionError": 1,
        "JMInternalError": 1,
        "UnresponsiveWorker": 2,
        "SpotInstanceInterruption": 3,
        "*": 0
      },
      "maxRestarts": 4
    },
    "timeoutPolicy": {
      "main": {"hours": 12},
      "process": {"hours": 2}
    },
    "restartableEntryPoints": "all"
  }
}

Use retries only for failures that can plausibly recover. Retrying deterministic AppError or invalid input wastes money.

maxRestarts is the total restart ceiling across failure reasons. It must be a non-negative integer below 10 and defaults to 9; set a smaller explicit bound for cost control.

Automatic upgrade after AppInsufficientResourceError requires:

1. An applicable restartOn count.

2. The organization policy that permits instance upgrade on restart.

3. A larger instance in the same family.

If dynamic selection was used initially, an insufficient-resource retry uses the platform's upgrade decision rather than the original selector list.

Jobs normally have a 30-day maximum runtime. Set a shorter workload-specific timeout whenever possible.

Dependencies

Choose the most reproducible workable option:

1. Bundled source/resources for small, version-controlled files.

2. Asset bundles for reusable system and Python environments.

3. Saved Docker image tarballs stored as project data or assets.

4. execDepends for simple APT dependencies when drift is acceptable.

5. Runtime downloads only when unavoidable and integrity-checked.

Bundled resources

Files under resources/ are packaged by dx build and unpacked into the AEE. Do not bundle secrets, private keys, or mutable credentials.

execDepends

Runtime package repositories can change between executions. Pin versions where the package manager supports it and do not rely on floating packages for regulated or production workloads.

On Ubuntu 24.04 AEE, PIP_BREAK_SYSTEM_PACKAGES=1 is set for compatibility, but PyPI packages can still conflict with APT-managed Python packages and cause DXExecDependencyError.

Prefer a virtual environment:

python3 -m venv "/home/dnanexus/venv"
source "/home/dnanexus/venv/bin/activate"
python3 -m pip install --requirement "requirements.txt"

Pin the requirements and build them into an asset for repeated production use. For a Python command-line application, pipx can isolate the tool.

Asset bundles

Asset source layout:

my-asset/
├── dxasset.json
├── Makefile
└── resources/

Build it in an isolated platform worker:

dx build_asset "my-asset"

Set the asset distribution and release to match the app. For multi-region apps, provide an asset available in each target region.

Docker images

The Ubuntu 24.04 and 20.04 AEEs support the native Docker CLI. For production, prefer:

1. Pin an image by immutable digest.

2. docker save it to a tarball.

3. Upload the tarball or include it in an asset.

4. Use docker load in the app.

This avoids a runtime registry dependency and can eliminate broad network access. If a private registry must be used, provide credentials as an explicit input or protected project object. Anyone with VIEW access to that project may be able to read those credentials, so use a narrowly scoped pull-only credential and confirm the project's membership.

Access Requirements

Start with no external network:

{
  "access": {
    "network": []
  }
}

For an app with default permissions, the platform clones declared inputs into its temporary workspace, grants the job CONTRIBUTE only there, and clones declared outputs back to the launch project. Omit project and allProjects unless the app must directly read, modify, or delete existing project objects. Applet defaults differ (project defaults to VIEW), so still declare only the minimum access its behavior requires.

Request only what the app needs:

• network: explicit host allowlist; avoid ["*"]

• project: launch-project level

• allProjects: access to other user projects

• developer: ability to create/modify or use unpublished apps

Project access fields accept VIEW, UPLOAD, CONTRIBUTE, or ADMINISTER. Omit a field when no extra permission is required; "NONE" is not a supported value.

Effective project access never exceeds the launching user's access. Broad allProjects, ADMINISTER, developer, and unrestricted network permissions need explicit justification.

For an HTTPS app, configure httpsApp separately and define the required shared access. Do not expose a service that returns credentials or protected data without its own authorization checks.

Validation Checklist

• JSON parses and contains no comments.

• name and app version follow platform constraints.

• Inputs and outputs have unique names and correct classes.

• App manifests include version, inputSpec, and outputSpec.

• AEE is Ubuntu 24.04 or intentionally retained 20.04.

• No deprecated top-level resource placement is used.

• Every configured region has compatible assets and resources.

• Instance types are available now in each region.

• Retry policy targets transient/recoverable errors.

• Timeout and launch-time cost limits are defined.

• Dependencies are pinned and integrity-controlled.

• Network and project access are least privilege.

• dx build succeeds in a non-production project before publication.