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58 lines
2.3 KiB
Markdown
58 lines
2.3 KiB
Markdown
# nf-core/configs: PROFILE Configuration
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All nf-core pipelines have been successfully configured for use on the dangpu PROFILE CLUSTER at the
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Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen.
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To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the PROFILE CLUSTER.
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## Modules
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Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below:
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```bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0
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```
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## How to use the nf-core pipelines on PROFILE CLUSTER
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###1. set up .bash_profile
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Add memory restrictions to `.bash_profile`. Use `vim` text editor to edit `.bash_profile` file (or create one if it does not exist in your home directory:
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```
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vi ~/.bash_profile
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```
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paste the following text within the file:
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```
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# personalising the profile: change the value of the variable $abc123 to your own user id
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abc123=def456
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# In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this
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export NXF_OPTS='-Xms1g -Xmx4g'
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# Don't fill up your home directory with cache files
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export NXF_HOME=/projects/dan1/people/${abc123}/cache/nxf-home
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export NXF_TEMP=${SNIC_TMP:-$HOME/glob/nxftmp}
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# Nextflow singularity image cachedir export
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NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${abc123}/cache/singularity-images
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```
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then save the changes and exit the editor. Now you need to activate the `.bash_profile` by logging out and in again to PROFILE CLUSTER or by typing:
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```
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source .bash_profile
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```
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The `$HOME` directory at dangpu has restricted space and should not be used to store cache files. Create those designated cache spaces for nextflow and singularity outside your `$HOME`:
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```
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mkdir $NXF_SINGULARITY_CACHEDIR
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mkdir $NXF_HOME
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```
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### 3. choose a nf-core pipeline and test it with your preferred settings
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```
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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```
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