tracer-cloud--opensre/docs/integrations/snakemake.mdx

---
title: "Snakemake"
description: "Monitor Snakemake workflows with Tracer"
---
Tracer integrates with Snakemake to provide pipeline-level observability. It captures per-rule execution times, resource usage, and cross-node performance metrics.

Install the Tracer agent on the machines where Snakemake executes and it will automatically collect detailed metrics from every rule and job. You don’t need to modify your Snakefile or add wrappers because Tracer passively observes workflow execution at the system level using eBPF.

Whether running locally, on HPC, or in the cloud, Tracer provides real-time visibility into resource usage, execution timelines, and performance bottlenecks across the workflow.

## Why use Tracer in combination with Snakemake

Snakemake reports high-level progress, but Tracer explains why rules take time or fail:

- View CPU, memory, and I/O usage per rule
- Identify bottlenecks or inefficient resource requests
- Attribute cost per sample or rule
- Trace nested shell commands and containers automatically
- Correlate logs and metrics across distributed environments

## Getting Started

### Prerequisites

- Working Snakemake installation
- Tracer installed on [your operating system](/environments/overview)

### Just run your pipeline, Tracer will automatically attach

If Tracer is already installed on your operating system, you only need to enable the Tracer agent for pipelines that have not been run with Tracer before.<br/>
In that case, run the following command:

```bash
sudo tracer init --token <your-token>
```
<Info> Go to our [onboarding](https://app.tracer.cloud/dashboard) to get your own personal token</Info>

When running this command, you will be asked to name your pipeline for clear labeling in the dashboard.

## Examples

Run a Snakemake pipeline under Tracer:

```bash
snakemake -j 16
```

or launch the Tracer demo workflow:

```bash
sudo tracer demo
```

Once the pipeline starts, open the Tracer dashboard, and you’ll see each Snakemake rule as a timeline step updating in real time.

<Card href="https://app.tracer.cloud/">
  <img
    className="block dark:hidden"
    src="/images/logo/tracer/Tracer Full Body - Black.png"
    alt="Tracer Logo"
    style={{ width: '10%', height: 'auto', marginBottom: '1rem' }}
  />
  <img
    className="hidden dark:block"
    src="/images/logo/tracer/Tracer Full Body - Black.png"
    alt="Tracer Logo"
    style={{ width: '10%', height: 'auto', marginBottom: '1rem' }}
  />

  <div style={{ fontSize: '1.3rem', fontWeight: '700', marginBottom: '1 rem', color: 'inherit' }}>
    Watch your pipeline run in the Tracer dashboard
  </div>

  <div style={{ color: 'inherit' }}>
    View real-time metrics, resource usage, and performance insights for your pipeline runs.
  </div>
</Card>
Each rule in your Snakefile will appear as a timeline step, with detailed performance and cost breakdowns.