Running the Annotation Tool

Running the Annotation Tool#

There are really three parts to running the annotation software: starting the annotation tool the first time, starting it subsequent times, and connecting to the tool once it’s been started. The first time you start the software, you’ll need to perform some steps on GitHub then use Git to clone a repository. You’ll then download an image using the Docker command. Subsequent times that you start the software will be largely the same, but you’ll skip all the Git and GitHub steps, and you won’t have to wait while the docker image is downloaded.

Running the Annotation Tool the First Time#

The first time you run the annotation tool, you’ll need to start by performing some steps on GitHub. The annotation tool is contained in a GitHub repository, which we’ll also use to keep track of the annotations you draw. You’ll need to start by forking this repository so that you have your own copy of it in which you’ll deposit your annotations.

To fork the repository (or “repo”), start by logging into GitHub then following these steps.

Navigate to the repository for the DrawFAVA project: https://github.com/nbenlab/drawFAVA
In the upper right portion of this page is a sequence of buttons, one of which is called “Fork”. Press this button, which should take you to a page titled “Create a new fork”. (If you can’t find the button, just go to this link.)
Make sure that your GitHub user ID is selected in the “Owner” field then press the big green “Create fork” button at the bottom.

The above steps should result in your own fork of the project’s repository; this copy of the repository can be found by navigating to its GitHub page: https://github.com/{{YOUR GITHUB USERNAME}}/drawFAVA. For example, if your GitHub username were noahbenson, then your repository would be at https://github.com/noahbenson/drawFAVA.

Once you have created your fork, the following steps must be run in a shell. In these steps, the variable {{REPO PARENT PATH}} is used several times; this refers to the directory (folder) that you decide to put the project’s repository in on your computer. For example, on a Mac, you might choose to put the project repository (which itself is a directory) on your desktop. In this case, your repo parent path would be ~/Desktop. If you aren’t sure where to put it, then it is fine to use just ~ as your repo parent path.

```
cd "{{REPO PARENT PATH}}"
```
See the paragraph immediately above regarding the repository’s parent path. For example, if your repository’s parent path is ~/Documents, you would enter:
cd "~/Documents"
```
git clone git@github.com:{{YOUR GITHUB USERNAME}}/drawFAVA
```
For example, if your GitHub username were noahbenson, you would enter:
git clone git@github.com:noahbenson/drawFAVA

This command will print out some text but it should not print an error message. If this is your first time running the command, it may print a message that mentions fingerprints and asks you to confirm if you are sure you know who you are communicating with. This is a standard message that is printed in case someone between you and GitHub is impersonating GitHub, and, as long as you have a reputable internet service provider (ISP), isn’t usually anything to worry about. If you are worried about your ISP, then you can look up the codes at GitHub’s website. If not, then it is safe to just type yes to this prompt.

Warning

It is possible to clone GitHub repositories using their https://github.com/... addresses instead of their git@github.com:... addresses, and some GitHub users prefer to use them. We have not configured Git to use https authentication, so that method will not work here unless you have separately configured it.

If you typed the git clone command as instructed above, you don’t need to worry about this.
```
cd drawFava
```
```
docker compose up
```
In order for this command to work, you must have Docker installed, and the Docker engine or Docker daemon must be running. The first time you run this command, it will take a significant amount of time as it needs to download a large virtual machine image that contains all of the project data. On subsequent runs of this command, you won’t need to wait for the download.