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Local, docker usage

  • "None informaticians / newcomer to bioinformatics" approach using ubuntu [admin rights required]
  • we do not recommend this installation-process(an older version of Docker will be installed. This installation method is not suitable for a cluster), but it is probably the fastest way to get WtP to run
sudo apt-get update
sudo apt install -y default-jre
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/bin/
sudo apt-get install -y docker-ce docker-ce-cli containerd.io
sudo usermod -a -G docker $USER
  • Restart your computer

Conda usage:

conda create -n wtp nextflow==20.07.01 singularity==3.6.1
conda activate wtp
(wtp) $ nextflow run replikation/What_the_Phage -r v1.2.0 --setup ...

now you should be able to run nextflow run replikation/What_the_Phage -r v1.2.0 --setup -profile local,singularity

Test the workflow

  • latest workflow release 
nextflow pull replikation/What_the_Phage
  • for docker (local use) 
nextflow run replikation/What_the_Phage -r v1.2.0 --cores 8 -profile smalltest,local,docker
  • for singularity (slurm use) 
nextflow run replikation/What_the_Phage -r v1.2.0 --cores 8 -profile smalltest,slurm,singularity