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fixing paths and adding slurm info
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wclose authored Oct 29, 2019
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4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -60,7 +60,9 @@ conda env create -f envs/clusterTutorial.yaml
```
conda activate clusterTutorial
```
8. Before running any jobs on the cluster, don't forget to change the `ACCOUNT` and `EMAIL` fields in the [cluster profile configuration](config/cluster.json) and the [cluster submission script](code/clusterSnakemake.pbs).
8. Before running any jobs on the cluster, don't forget to change the `ACCOUNT` and `EMAIL` fields in the following files for whichever cluster you're using:
* PBS: [cluster profile configuration](config/pbs-torque/cluster.json) and the [cluster submission script](code/clusterSnakemake.pbs)
* Slurm: [cluster profile configuration](config/slurm/cluster.json) and the [cluster submission script](code/clusterSnakemake.sh)

9. Run the Snakemake workflow. **Note**: If you wish to rerun the workflow after having it successfully complete, use the `--forcerun` or the `--forceall` flags or just delete the `results/` directory by running `snakemake clean`.
- To run it locally on the login node:
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