Profiles

Where to run snpQT

Profiles control how snpQT runs. Firstly, there are two options that control where modules are run:

• -profile standard
  • snpQT runs modules on a normal computer.
• -profile cluster
  • snpQT runs modules by submitting them to a SLURM queue.

You must pick one of these profiles to run snpQT. Most people will use the standard profile.

To configure the cluster profile you will need to edit the conf/cluster.config file, which is in the snpQT local path.We have configured cluster.config to run on the Northern Ireland High Performance Centre by default:

process {
    executor = 'slurm'
    // default queue for short jobs less than 3 hours
    queue = 'k2-hipri' 
    withLabel: bigmem {
        memory = 128.GB
    errorStrategy = 'retry'
    maxRetries = 2
    queue = { task.attempt == 1 ? 'k2-hipri' : 'k2-medpri' } 
    }
}

You will need to change k2-hipri and k2-medpri to reflect the names of the partitions in your local cluster.

How to run snpQT

Secondly, snpQT has several options to automatically install a lot of bioinformatics software. Most people will use either -profile conda or -profile singularity:

• -profile conda uses Anaconda to automatically install software packages. Every workflow will work well except imputation.
• -profile singularity uses Singularity to automatically provision containers to run software packages. Every workflow will work well.

You will need to have installed Anaconda or Singularity for these profiles to work.

Other profiles, including -profile docker and -profile modules are described further in the advanced guide.

Summary

You will need to pick a combination of profiles listed above to run snpQT, for example -profile standard,conda or -profile cluster,singularity.

If you don't set a profile snpQT assumes that you already have installed and configured all of the bioinformatics software we use in the pipeline, which is quite unlikely.