Several typo fixes an improvements

packages/website/docs/admin/user-guide/upload-assembly.md

@@ -18,7 +18,7 @@ Apollo3.
    ![alt text](image-1.png)
 
    - Upload gff3 file containing annotation along with sequence. If we want to
-     upload annotations along with the sequence, we needc to select
+     upload annotations along with the sequence, we need to select
      `Also load features from GFF3 file`.
 
    ![alt text](image-2.png)

packages/website/docs/getting-started/try-it-out/01-setting-up.md

@@ -19,59 +19,11 @@ unzip data.zip
 rm data.zip
 ```
 
-You'll now have a folder called `data/` in your directory.
-
-## Setting up the Apollo CLI
-
-The Apollo CLI is used to configure and load data into Apollo. We'll need a
-config file for our CLI configuration. For simplicity, we'll create an empty
-file called `config.yml` in a new directory.
-
-```sh
-mkdir cli
-touch cli/config.yml
-```
-
-We'll use Docker to run the Apollo CLI. To avoid having to re-type the Docker
-commands, we use this function:
-
-```sh
-function apollo() {
-  docker \
-    run \
-    --rm \
-    --interactive \
-    --add-host host.docker.internal=host-gateway \
-    --volume ./cli:/root/.config/apollo-cli \
-    --volume ./data:/data \
-    ghcr.io/gmod/apollo-cli \
-    "$@"
-}
-```
-
-Paste and run the above command in your terminal to create the function, then
-run `apollo version` in your terminal. You should see something like this
-output:
-
-```
-$ apollo --version
-@apollo-annotation/cli/0.1.20 linux-x64 node-v18.20.4
-```
-
-:::tip
-
-If you're familiar with installing Node.js packages you can install the Apollo
-CLI instead of using Docker.
-
-```bash npm2yarn
-npm install -g @apollo-annotation/cli
-```
-
-:::
+You'll now have two directories called `data/` and `jbrowse_data/`.
 
 ## Running Apollo
 
-Create a file called `config.yml` and paste the following contents into the
+Create a file called `compose.yml` and paste the following contents into the
 file:
 
 ```yml title="compose.yml"
@@ -90,6 +42,7 @@ services:
       ALLOW_GUEST_USER: true
       GUEST_USER_ROLE: admin
       ALLOW_ROOT_USER: true
+      ROOT_USER_NAME: root
       ROOT_USER_PASSWORD: password
       JWT_SECRET: local_testing_only
       SESSION_SECRET: local_testing_only
@@ -170,6 +123,6 @@ volumes:
   uploads: null
 ```
 
-Now in the terminal, run `cd apollo3-annotation/` and `docker compose up`.
-Apollo is now running! You can use <kbd>Ctrl</kbd> + <kbd>C</kbd> to stop it
-when you are done.
+Now in the terminal, run `docker compose up`. You should see a stream of logs
+from the Docker containers. If you do, Apollo is now running! You can use
+<kbd>Ctrl</kbd> + <kbd>C</kbd> in the terminal to stop Apollo when you are done.

packages/website/docs/getting-started/try-it-out/02-loading-data.md

@@ -1,12 +1,62 @@
 # Loading data
 
+## Setting up the Apollo CLI
+
+The Apollo CLI is used to configure and load data into Apollo. We'll need a
+config file for our CLI configuration. For simplicity, we'll create an empty
+file called `config.yml` in a new directory.
+
+```sh
+mkdir cli
+touch cli/config.yml
+```
+
+We'll use Docker to run the Apollo CLI. To avoid having to re-type the Docker
+commands, we use this function:
+
+```sh
+function apollo() {
+  docker \
+    run \
+    --rm \
+    --interactive \
+    --add-host host.docker.internal=host-gateway \
+    --volume ./cli:/root/.config/apollo-cli \
+    --volume ./data:/data \
+    ghcr.io/gmod/apollo-cli \
+    "$@"
+}
+```
+
+Paste and run the above command in your terminal to create the function, then
+run `apollo version` in your terminal. You should see something like this
+output:
+
+```
+$ apollo --version
+@apollo-annotation/cli/0.1.20 linux-x64 node-v18.20.4
+```
+
+:::tip
+
+If you're familiar with installing Node.js packages you can install the Apollo
+CLI instead of using Docker.
+
+```bash npm2yarn
+npm install -g @apollo-annotation/cli
+```
+
+:::
+
+## Configuring the Apollo CLI
+
 Open a new terminal in the same directory where you ran the setup commands. To
 use the Apollo CLI, we need to configure it with the information for the running
 Apollo installation. You can have multiple profiles configured, but we will use
 a single default profile. Run these commands:
 
 ```sh
-apollo config address http://localhost/apollo
+apollo config address http://host.docker.internal/apollo
 apollo config accessType root
 apollo config rootCredentials.username root
 apollo config rootCredentials.password password
@@ -16,6 +66,8 @@ apollo login
 If you need to log in again, run `apollo logout` first, or use
 `apollo login --force`.
 
+## Adding assemblies
+
 The next step is to add an assembly. We're going to use use trimmed-down
 assembly that only includes a single chromosome. This is so that the data is
 small enough to be self-contained inside this repository, without the need for
@@ -34,7 +86,7 @@ apollo assembly \
   --assembly 'Schistosoma mansoni'
 ```
 
-Now that we have an assembly, lets add the annotations we want to curate. They
+Now that we have an assembly, let's add the annotations we want to curate. They
 are stored in a GFF3 file. Run this command to import the annotations:
 
 ```sh
@@ -44,6 +96,8 @@ apollo feature \
   --assembly 'Schistosoma mansoni'
 ```
 
+## Adding annotations
+
 Next we're going to add a second assembly and set of annotations. This assembly
 is from the related species Schistosoma haematobium. Run these two commands to
 add the assembly and annotations:
@@ -62,6 +116,8 @@ apollo feature \
   --assembly 'Schistosoma haematobium'
 ```
 
+## Adding evidence tracks
+
 Apollo is now set up to be able to annotate these genomes. In order to help with
 the annotation, though, it's often useful to include evidence tracks. Apollo is
 built on top of JBrowse 2, so we'll add these evidence tracks to the underlying