.sidecar

Liatir.sidecar.run() executes a binary that is bundled with the Liatir desktop app and captures its stdout, stderr, and exit code.

Use this to run bioinformatics tools (samtools, minimap2, bwa, bcftools, etc.) without requiring the user to install them separately.

Signature

run(name: string, args: string[]): Promise<SidecarResult>

run(name, args=None) -> dict

Example

const result = await Liatir.sidecar.run('samtools', ['--version']);

if (result.ok) {
  console.log(result.stdout);
} else {
  console.error('Exit code:', result.exitCode);
  console.error(result.stderr);
}

result = ctx.liatir.sidecar.run('samtools', ['--version'])

if result['ok']:
    print(result['stdout'])
else:
    print('Exit code:', result['exitCode'])
    print(result['stderr'])

SidecarResult

Field	Type	Description
ok	boolean / bool	true if the process exited with code 0.
stdout	string / str	Captured standard output.
stderr	string / str	Captured standard error.
exitCode	number | null / int | None	Process exit code.
error	string | null / str | None	Error message if the process failed.
durationMs	number / int	Execution time in milliseconds.

NOTE

SidecarResult fields are always camelCase in both Node and Python, because they come from the JSON response of the Liatir bridge.

Available binaries

The following binaries are bundled with Liatir and can be invoked via sidecar:

Binary	Description
samtools	SAM/BAM processing
minimap2	Long-read alignment
bwa	Short-read alignment
bcftools	VCF/BCF manipulation
fastp	FASTQ preprocessing
seqkit	FASTA/FASTQ toolkit
snpeff	Variant annotation

Notes

TIP

Sidecar binaries run in a sandboxed environment. They cannot access arbitrary paths on the host filesystem — use the plugin filesystem (.desktop.fs.pluginFs / .desktop.fs.plugin_fs) to stage input files and read output files.

WARNING

The list of available sidecar binaries depends on the Liatir app version. Always check result.ok / result['ok'] and handle errors gracefully.