Installation Docker - MeryemAk/dRNASeq GitHub Wiki

  1. Set up Docker on Ubuntu:
# Add Docker's official GPG key:
sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc

# Add the repository to Apt sources:
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "${UBUNTU_CODENAME:-$VERSION_CODENAME}") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update

# Install the latest version of Docker
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin    # When asked 'Do you want to continue', type Y and enter

# Verify that the installation is successful by running the hello-world image
sudo docker run hello-world

# Check if Docker is active
sudo systemctl status docker

More Information about downloading Docker on Ubuntu. image

  1. Clone the Github repository.
git clone https://github.com/MeryemAk/dRNASeq
  1. Build the Docker images.
# 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

# Pull Docker image for bambu
docker pull mathiasverbeke/bambu_runner:latest

  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.