CS cluster Configuration
All nf-core pipelines have been successfully configured for use on UCL’s CS cluster University College London.
To use, run the pipeline with -profile ucl_cscluster. This will download and launch the ucl_cscluster.config which has been pre-configured with a setup suitable for the CS cluster.
Using Nextflow on CS cluster
Before running the pipeline you will need to configure Singularity and install+configure Nextflow.
Singularity
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 CS cluster. 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 Singularity environment variables
export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/.singularity/
export SINGULARITY_TMPDIR=/home/<YOUR_ID>/.singularity/tmp
export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/.singularity/localcache
export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/.singularity/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
nextflow -self-update
NXF_VER=XX.XX.X
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 CS cluster'
config_profile_contact = 'Simon Murray (simon . murray AT ucl . ac . uk)'
config_profile_url = 'https://hpc.cs.ucl.ac.uk/'
}
executor {
name = 'sge'
}
singularity.runOptions = "-B ${HOME},${PWD}"
process {
//NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
penv = 'smp'
//ADD MEMORY TO CLUSTEROPTIONS
clusterOptions = { "-S /bin/bash -l tmem=${task.memory.mega}M,h_vmem=${task.memory.mega}M" }
}
executor
contact
