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 utilize 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 will run on future workers.

See Cloud Workstation in 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 will be packaged, uploaded to the platform, and then unpackaged in the root directory \ of the worker. In our 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 will be placed in the worker’s root directory /:

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

We are able to access the SAMtools command because the respective binary is visible from the default $PATH variable. The directory /usr/bin/ is part of the $PATH variable, so in our script we can reference the samtools command directly:

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