Asset Build Process

Understand the structure of an asset source directory and learn how to build an asset bundle.

Asset Directory Structure

A DNAnexus asset can be built using the dx build_asset utility in the DNAnexus SDK, which builds an asset bundle in an isolated environment. The utility expects a directory with the following structure:

asset_name
├── dxasset.json                          # This is the only required file
├── resources
│   └── ...
└── Makefile

To build this asset, run the command dx build_asset asset_name

Each component of the directory is described in detail below.

Asset Metadata

The dxasset.json file contains essential metadata that defines the asset. This file is required to build an asset and therefore must be present in the asset source directory. The following is a sample dxasset.json file:

{
  "name": "asset_name", // Asset bundle name
  "title": "Example Asset", // Human-readable name
  "description": "Libraries required for a tool you've built", // Detailed description of the asset bundle and its contents
  "version": "0.0.1", // Version number
  "distribution": "Ubuntu", // Linux distribution targeted by the asset bundle
  "instanceType": "mem2_ssd1_x4", // Instance type on which the asset bundle will be built
  "release": "24.04", // Linux release version
  "excludeResource": [ // Files and directories that should not be included
    "/src/my.ccp", // Optional asset-bundle exclusion
    "/scripts"
  ],

  "execDepends": [ // Packages on which the asset depends
    {"name": "samtools", "package_manager": "apt"},
    {"name": "pandas","package_manager": "pip"}
  ]
}

Additional Resources

If anything is present in the resources/ subdirectory of the asset directory, it is archived by dx build_asset and unpacked into the root of a clean Ubuntu installation during the asset build process. Files here can be propagated directly into the asset, or they can be used to build other artifacts that are themselves propagated into the asset.

For example, if you have some C or C++ source files that you need to compile so that their binary output can be included in the asset bundle, you can do one of the following:

• Put your source files somewhere in the resources/ directory, such as resources/example_dir/.

• Invoke your build process from the Makefile included in the asset source directory. In the asset build environment, your source files are available in the directory /example_dir.

By default, the PATH in the execution environment (inherited from Ubuntu's defaults) is the following:

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

Makefile

The optional Makefile contains instructions to build and copy additional resources required by the asset. If present in the asset source directory, the Makefile is copied to the working directory /home/dnanexus of the asset build environment and executed. Here is an example Makefile that downloads and installs specific resources:

SHELL=/bin/bash -e -x -o pipefail

VERSION=2.30.0
all:
 apt-get update -y
 apt-get install build-essential git zlib1g zlib1g-dev bzip2 libbz2-dev liblzma-dev wget python python-dev -y
 wget https://github.com/arq5x/bedtools2/releases/download/v${VERSION}/bedtools-${VERSION}.tar.gz
 tar zxvf bedtools-${VERSION}.tar.gz
 cd bedtools2 && make && make install && cd ../
 rm -fr bedtools-${VERSION}.tar.gz bedtools2s

To learn more about the Makefile in general, see the Wikipedia page.

Building an Asset

Assuming the directory asset_name contains a dxasset.json file, you can use the following command to build your asset:

dx build_asset asset_name

A virtual worker starts a new DNAnexus job to provide an isolated build environment in which the following steps are performed:

1. A snapshot is taken of the worker's filesystem. During this process, all the directories, files, and symbolic links are recorded, except those mentioned in the excludeResource field of the dxasset.json file. Files in directories matching the following paths are excluded: /proc*, /tmp*, /run*, /boot*, /home/dnanexus*, /sys*. On Ubuntu 24.04 and 20.04 the paths /bin, /sbin are also excluded as they are symlinks to /usr/bin, /usr/sbin

2. Any packages mentioned in the execDepends field of the dxasset.json are installed in the worker's execution environment.

3. If a resources/ directory is present in the asset source directory, its contents are copied to the root directory / of the worker's execution environment.

4. If a Makefile is present in the asset source directory, it is copied to /home/dnanexus on the worker and executed as sudo make -C /home/dnanexus.

5. A second snapshot of the worker's execution environment is taken.

6. All new and modified files, that is files with different timestamps from those on the earlier snapshot, are packaged in the resulting asset bundle.