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40 lines
2.4 KiB
Markdown
40 lines
2.4 KiB
Markdown
# nf-core/configs: Sheffield Bioinformatics Core Facility ShARC Configuration
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## Using the SBC_ShARC Institutional Configuration Profile
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To use [`sbc_sharc.config`](../conf/sbc_sharc.config), run nextflow with an nf-core pipeline using `-profile sbc_sharc` (note the single hyphen).
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This will download and launch [`sbc_sharc.config`](../conf/sbc_sharc.config) which has been pre-configured with a setup suitable for the ShARC cluster and will automatically load the appropriate pipeline-specific configuration file.
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The following nf-core pipelines have been successfully configured for use on the the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html):
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- [nf-co.re/atacseq](https://nf-co.re/atacseq)
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- [nf-co.re/chipseq](https://nf-co.re/chipseq)
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- [nf-co.re/rnaseq](https://nf-co.re/rnaseq)
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- [nf-co.re/sarek](https://nf-co.re/sarek)
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When using [`sbc_sharc.config`](../conf/sbc_sharc.config) with the pipelines listed above, the appropriate configuration file from the list below will be loaded automatically:
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- [atacseq sbc_sharc.config](../conf/pipeline/atacseq/sbc_sharc.config)
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- [chipseq sbc_sharc.config](../conf/pipeline/chipseq/sbc_sharc.config)
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- [rnaseq sbc_sharc.config](../conf/pipeline/rnaseq/sbc_sharc.config)
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- [sarek sbc_sharc.config](../conf/pipeline/sarek/sbc_sharc.config)
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The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file might work with other nf-core pipelines as it stands but we cannot guarantee they will run without issue. We will be continuing to create, test and optimise configurations for new pipelines in the future.
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## A Note on Singularity Containers
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The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file supports running nf-core pipelines with Singularity containers; Singularity images will be downloaded automatically before execution of the pipeline.
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When you run nextflow for the first time, Singularity will create a hidden directory `.singularity` in your `$HOME` directory `/home/$USER` which has very very limited (10GB) space available. It is therefore a good idea to create a directory somewhere else (e.g., `/data/$USER`) with more room and link the locations. To do this, run the following series of commands:
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```shell
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# change directory to $HOME
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cd $HOME
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# make the directory that will be linked to
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mkdir /data/$USER/.singularity
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# link the new directory with the existing one
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ln -s /data/$USER/.singularity .singularity
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```
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