> ## Documentation Index
> Fetch the complete documentation index at: https://opensre.com/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# Snakemake
> 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.
In that case, run the following command:
```bash theme={null}
sudo tracer init --token
```
Go to our [onboarding](https://app.tracer.cloud/dashboard) to get your own personal token
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 theme={null}
snakemake -j 16
```
or launch the Tracer demo workflow:
```bash theme={null}
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.
Watch your pipeline run in the Tracer dashboard
View real-time metrics, resource usage, and performance insights for your pipeline runs.
Each rule in your Snakefile will appear as a timeline step, with detailed performance and cost breakdowns.
