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45 lines
1.5 KiB
Markdown
45 lines
1.5 KiB
Markdown
# nf-core/configs: GIS Aquila Configuration
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All nf-core pipelines have been successfully configured for use on the cluster of the GIS (Genome Institute of Singapore (Aquila)).
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To use, run the pipeline with `-profile gis`. This will download and launch the [`gis.config`](../conf/gis.config) which has been pre-configured with a setup suitable for the GIS Aquila cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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## How to use on GIS core
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Before running the pipeline you will need to load Nextflow using the environment module system on GIS Aquila. You can do this by issuing the commands below:
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```bash
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# Login to a compute node
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srun --pty bash
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## Load Nextflow and Singularity environment modules
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module purge
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source /mnt/projects/rpd/rc/init.2017-04
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module load miniconda3
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# Run a nextflow pipeline with dependencies bundled in a conda environment
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set +u
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source activate nfcore-rnaseq-1.0dev
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set -u
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# Run a downloaded/git-cloned nextflow workflow from
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nextflow run \\
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nf-core/workflow \\
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-resume \\
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-profile gis \\
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--email my-email@example.org \\
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-c my-specific.config
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...
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# Or use the nf-core client
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nextflow run nf-core/rnaseq ...
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```
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## Databanks
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A local copy of several genomes are available in `/mnt/projects/rpd/genomes.testing/S3_igenomes/` directory.
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> NB: You will need an account to use the HPC cluster on GIS in order to run the pipeline. If in doubt contact IT or go to [Andreas Wilm](https://github.com/andreas-wilm)
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