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Run multiple DA tools on datasets using Docker Image
Welcome to the Comparison_of_DA_microbiome_methods wiki!
This page describes the use of a Docker image containing multiple microbiome Differential Analysis tools. If you have a working version of Docker installed on your system, you can jump to "Running multiple DA tools with Docker Image"
Docker can be installed on Linux, Mac as well as Windows. Here are a few links to install Docker on these operating systems
https://docs.docker.com/engine/install/ubuntu/
https://docs.docker.com/docker-for-windows/install/
https://docs.docker.com/docker-for-mac/install/
=== Tip to change the docker installation directory (where it stores the generated image) from the default / ===
On Ubuntu, by default, Docker is installed in the "/" folder. Building or pulling and using Docker Images occupies a sizable amount of harddrive space and by default, all these files end up in the "/" area. This runs the risk of clogging up the "/" area. The following is a protocol to change the default storage in Docker from "/" to another folder on a partition that has sufficient space. We will use systemd from Ubuntu to control Docker behaviour
sudo mkdir -p /etc/systemd/system/docker.service.d
sudo nano /etc/systemd/system/docker.service.d/docker-storage.conf
[Service]
ExecStart=
ExecStart=/usr/bin/dockerd -H fd:// --data-root="/path/to/new/docker_storage folder"
sudo systemctl daemon-reload
sudo systemctl restart docker
Check the change in directory by doing the following: It should now point to "/path/to/new/docker_storage folder"
docker info|grep -P "Docker Root Dir"
sudo groupadd docker
sudo gpasswd -a $USER docker
newgrp docker