Myriad Configuration
All nf-core pipelines have been successfully configured for use on UCL’s myriad cluster University College London.
To use, run the pipeline with -profile ucl_myriad. This will download and launch the ucl_myriad.config which has been pre-configured with a setup suitable for the myriad cluster.
Using Nextflow on Myriad
Before running the pipeline you will need to configure Apptainer and install+configure Nextflow.
Apptainer
This can be done with the following commands:
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 .bash_profile file in your home directory (e.g. /home/<YOUR_ID>/.bash_profile):
# Set all the Apptainer environment variables
export APPTAINER_CACHEDIR=/home/<YOUR_ID>/Scratch/.apptainer/
export APPTAINER_TMPDIR=/home/<YOUR_ID>/Scratch/.apptainer/tmp
export APPTAINER_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.apptainer/localcache
export APPTAINER_PULLFOLDER=/home/<YOUR_ID>/Scratch/.apptainer/pullNextflow
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).
## Download Nextflow-all
curl -s https://get.nextflow.io | bash
NXF_VER=XX.XX.X
nextflow -self-update
chmod a+x nextflow
mv nextflow ~/bin/nextflowThen make sure that your bin PATH is executable, by placing the following line in your .bash_profile:
export PATH=$PATH:/home/<YOUR_ID>/binConfig file
params {
config_profile_description = 'University College London Myriad cluster'
config_profile_contact = 'Chris Wyatt (ucbtcdr@ucl.ac.uk)'
config_profile_url = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/'
}
executor {
name = 'sge'
}
apptainer.runOptions = "-B ${HOME},${PWD}"
process {
//NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
penv = 'smp'
//PROVIDE EXTRA PARAMETERS AS CLUSTER OPTIONS
clusterOptions = "-S /bin/bash"
}
executor
contact
