nf-core/configs: ucl_myriad
University College London Myriad cluster
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 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.
Using Nextflow on Myriad
Before running the pipeline you will need to install and configure Nextflow and Singularity.
Singularity
This can be done with the following commands:
## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
module add java/openjdk-11/11.0.1
module add singularity-env/1.0.0
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):
# Set all the Singularity cache dirs to Scratch
export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
# Bind your Scratch directory so it is accessible from inside the container
export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
Nextflow
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=22.10.0
nextflow -self-update
chmod a+x nextflow
mv nextflow ~/bin/nextflow
Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:
export PATH=$PATH:/home/<YOUR_ID>/bin
Config 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/'
}
process {
executor='sge'
penv = 'smp'
}
params {
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 36
max_time = 72.h
// igenomes_base = 's3://ngi-igenomes/igenomes/'
}
// optional executor settings
executor {
queueSize = 10
submitRateLimit = '1 sec'
}
singularity {
enabled = true
autoMounts = true
}
executor
contact
