Installation Docker - MeryemAk/dRNASeq GitHub Wiki

  1. Set up Docker on Linux:
# Install Docker
sudo dnf install docker

# Start & enable Docker
sudo systemctl start docker
sudo systemctl enable docker

# Verify if docker is running correctly
sudo systemctl status docker      # --> active (running)

  1. Clone the Github repository.

  2. Build the Docker images for nanocomp and nanopack.

# Build Docker image for nanocomp
# Move into the nanocomp folder
cd dRNASeq/nanocomp
# Execute the following command to build the Docker image
docker build -t nanocomp:v1 .       # Takes approximately 30 minutes

# Build Docker image for nanopack
# Move into the nanopack folder
cd dRNASeq/nanopack
# Execute the following command to build the Docker image
docker build -t nanopack:v1 .       # Takes approximately 45 minutes

  1. The data to be analyzed must also be placed in the dRNASeq folder. For details on the required input folder structure, refer to the mandatory parameters under Usage Nextflow.

  2. Before running the workflow for the first time, pull the Nextflow Docker image from Docker Hub. If you have already downloaded the image, you can skip this step and proceed to step 4.

docker pull nextflow/nextflow:21.04.3
  1. Start the nextflow container. Don't forget to replace "nameoffolder" with your own folder name.
docker run -it --workdir $PWD -v /var/run/docker.sock:/var/run/docker.sock -v $HOME/"nameoffolder":$HOME/"nameoffolder" nextflow/nextflow:21.04.3 /bin/bash
  1. You are now inside the Nextflow container, and the workflow is ready to be executed. Each tool runs in its own separate container, which will be automatically pulled if it is not already available locally when the corresponding process in Nextflow starts.