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52 lines
2.3 KiB
Markdown
52 lines
2.3 KiB
Markdown
# nf-core/configs: Myriad Configuration
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All nf-core pipelines have been successfully configured for use on UCL's myriad cluster [University College London](https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/).
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To use, run the pipeline with `-profile ucl_myriad`. This will download and launch the [`ucl_myriad.config`](../conf/ucl_myriad.config) which has been pre-configured with a setup suitable for the myriad 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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## Using Nextflow on Myriad
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Before running the pipeline you will need to install and configure Nextflow and Singularity.
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### Singularity
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This can be done with the following commands:
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```bash
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## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
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module add java/openjdk-11/11.0.1
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module add singularity-env/1.0.0
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```
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Then set the correct configuration of the cache directories, where <YOUR_ID> is replaced with you credentials which you can find by entering `whoami` into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home/<YOUR_ID>/.bashrc):
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```bash
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# Set all the Singularity cache dirs to Scratch
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export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
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export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
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export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
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export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
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# Bind your Scratch directory so it is accessible from inside the container
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export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
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```
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### Nextflow
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Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`).
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```bash
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## Download Nextflow-all
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curl -s https://get.nextflow.io | bash
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NXF_VER=22.10.0
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nextflow -self-update
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chmod a+x nextflow
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mv nextflow ~/bin/nextflow
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```
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Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:
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```bash
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export PATH=$PATH:/home/<YOUR_ID>/bin
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```
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