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Document use of NXF_CONDA_CACHEDIR and fix typo in section header
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Me committed Oct 12, 2023
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8 changes: 6 additions & 2 deletions docs/uod_hpc.md
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Expand Up @@ -4,7 +4,7 @@ The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and [sarek](https://nf-c

To use, run the pipeline with `-profile uod_hpc`. This will download and launch the [`uod_hpc.config`](../conf/uod_hpc.config) which has been pre-configured with a setup suitable for the Dundee cluster.

## Using Nextflow on Myriad
## Using Nextflow on Dundee Cluster

Before running the pipeline you will need to install and configure Nextflow. You can do this by issuing the commands below:

Expand All @@ -17,11 +17,15 @@ conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install -c bioconda nextflow

# Specify a cache directory in your /cluster space for conda environments
export NXF_CONDA_CACHEDIR="/cluster/<group_name>/<your_directory>/nxf-conda-cachedir"
```

For convenience, append the activation command to your `.bashrc` file to avoid having to source your conda environment on each log-in:
For convenience, append the `export NXF_CONDA_CACHEDIR` and conda activation commands to your `.bashrc` file to avoid having to run on each log-in:

```bash
echo export NXF_CONDA_CACHEDIR='"/cluster/<group_name>/<your_directory>/nxf-conda-cachedir"' >> ~/.bashrc
echo source '"/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"' >> ~/.bashrc
```

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