Getting started with sRNAtoolbox Docker
The sRNAtoolbox docker provides the user with a number of preinstalled programs like all sRNAtoolbox tools, Vienna package, bowtie, samtools etc. needed for common small RNA data analysis.
First of all, Docker must be installed. To install Docker in Ubuntu and MacOS please do the following:
1- Install docker
sudo apt update
sudo apt install docker.io
2- Start docker as a service
sudo systemctl start docker
sudo systemctl enable docker
To install Docker Desktop in Windows please follow these instructions.
sRNAtoolbox docker is hosted in Dockerhub so the first step is to pull the image from it:
sudo docker pull ugrbioinfo/srnatoolbox:latest
After this, your sRNAtoolbox docker image is downloaded and now you can launch it:
sudo docker run --hostname sRNAtoolbox --name sRNAtoolbox --user srna --workdir /home/srna -it ugrbioinfo/srnatoolbox:latest /bin/bash
Alternatively, if you want to start the container with shared folders:
sudo docker run --hostname sRNAtoolbox --name sRNAtoolbox --user srna --workdir /home/srna --mount type=bind,source=MACHINE_FOLDER,destination=/shared/shared_folder -it ugrbioinfo/srnatoolbox:latest /bin/bash
After the first use you can exit the container by typing “exit” and stop the container with the following:
sudo docker stop sRNAtoolbox
For further uses:
sudo docker start sRNAtoolbox
sudo docker exec -term=SCREEN -it sRNAtoolbox /bin/bash