The Docker image for this project is still being actively developped and is not intended for unsupervised use.
The Docker image has been tested on the ubuntu v16.04 operating system. To run any of the GUIs in the pipeline, there are some additional steps before running the image.
This document assumes Docker is already installed on your machine, you are using a linux machine, and that you understand some basic functionality of the terminal.
Before getting started, ensure that you have a directory to use as the output location of the pipeline. All files will be outputted here. This shall be known as the DATA_DIRECTORY. Ensure that there is at least 1TB of free space in your DATA_DIRECTORY per new brain (this space will fill up gradually over the course of the pipeline). It is recommended that this directory be empty and reserved only for the outputs of the pipeline.
Here is an example of a good DATA_DIRECTORY: /media/john/external_drive_1/atlas_root
Open a new terminal window. Enter in the commands below into your terminal while you are logged into your user account and push enter after each line. It will create a directory called "atlas_docker_demo" in your home folder and copy the shell script "run_docker.sh" into it.
Command 1:
Run each of the four following commands by copying them one at a time, pasting them into a terminal, and pushing enter.
cd ~mkdir -p ./atlas_docker_demo/cd ./atlas_docker_demo/curl -O "https://raw.githubusercontent.com/ActiveBrainAtlas/MouseBrainAtlas_dev/master/doc/docker/run_docker.sh" "./run_docker.sh"
Next we will want to run the script we just downloaded, named "run_docker.sh". Before attempting to run the Docker container, it will first verify that you have Docker installed as well as the latest Docker Image for this project. If either are not installed, they will be automatically installed. Please replace "$DATA_DIRECTORY" with the actual data directory you have chosen as described above.
Command 2:
source run_docker.sh $DATA_DIRECTORY
This will need several minutes to run as it downloads and runs the Docker Image. You will know it has finished successfully when a GUI is displayed prompting to either "continue a brain" or "start a new brain" through the pipeline.
Using the GUI:
Note: The docker container has a completely seperate filesystem from the computer you are using! Here I will list the locations of important files inside the docker container filesystem:
/app/MouseBrainAtlas_dev/: contains this repository/mnt/data/: This is linked to your real computer's DATA_DIRECTORY (the one you entered in above)/mnt/computer_root/: This is linked to your real computer's root directory. (equivalent to/on your real computer) This allows you to access any and all files located in your filesystem.