Precompiled Binary

This tutorial showcases packaging a precompiled binary in the resources/ directory of an app(let).

View full source code on GitHub

Precompiling a Binary

In this applet, the SAMtools binary was precompiled on an Ubuntu machine. A user can do this compilation on an Ubuntu machine of their own, or they can use the Cloud Workstation app to build and compile a binary. On the Cloud Workstation, the user can download the SAMtools source code and compile it in the worker environment, ensuring that the binary runs on future workers.

See Cloud Workstationin the App library for more information.

Resources Directory

The SAMtools precompiled binary is placed in the <applet dir>/resources/ directory. Any files found in the resources/ directory are packaged, uploaded to the Platform, and then extracted in the root directory \ of the worker. In this case, the resources/ dir is structured as follows:

├── Applet dir
│   ├── src
│   ├── dxapp.json
│   ├── resources
│       ├── usr
│           ├── bin
│               ├── < samtools binary >

When this applet is run on a worker, the resources/ directory is placed in the worker's root directory /:

/
├── usr
│   ├── bin
│       ├── < samtools binary >
├── home
│   ├── dnanexus
│       ├── applet script

The SAMtools command is available because the respective binary is visible from the default $PATH variable. The directory /usr/bin/ is part of $PATH, so the script can reference the samtools command directly:

samtools view -c "${mappings_bam_name}" > "${mappings_bam_prefix}.txt"