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docs/eddie.md
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@ -11,10 +11,10 @@ There is a Slack channel dedicated to eddie users on the MRC IGMM Slack: [https:
To use, run the pipeline with `-profile eddie` (one hyphen). To use, run the pipeline with `-profile eddie` (one hyphen).
This will download and launch the [`eddie.config`](../conf/eddie.config) which has been pre-configured with a setup suitable for the [University of Edinburgh Eddie HPC](https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing). This will download and launch the [`eddie.config`](../conf/eddie.config) which has been pre-configured with a setup suitable for the [University of Edinburgh Eddie HPC](https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing).
The configuration file supports running nf-core pipelines with either a Conda environment or Docker containers running under Singularity. The configuration file supports running nf-core pipelines with Docker containers running under Singularity. Support for Conda will follow.
```bash ```bash
nextflow run nf-core/PIPELINE -profile eddie # ..rest of pipeline flags nextflow run nf-core/PIPELINE -profile eddie,singularity # ..rest of pipeline flags
``` ```
Before running the pipeline you will need to install Nextflow or load it from the module system. Generally the most recent version will be the one you want. Before running the pipeline you will need to install Nextflow or load it from the module system. Generally the most recent version will be the one you want.
@ -30,11 +30,19 @@ To load the most recent version:
module load igmm/apps/nextflow module load igmm/apps/nextflow
``` ```
This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Conda or Singularity for software management. This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Conda or Singularity for software management.
To set up Nextflow on a login node ... TODO To set up Nextflow on a login node ... TODO
## Singularity set-up
Load Singularity from the module system and set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added.
```
module load singularity
export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity/nf-core-rnaseq_v3.0"
```
## Using iGenomes references ## Using iGenomes references
A local copy of the iGenomes resource has been made available on the Eddie HPC so you should be able to run the pipeline against any reference available in the `igenomes.config`. A local copy of the iGenomes resource has been made available on the Eddie HPC so you should be able to run the pipeline against any reference available in the `igenomes.config`.