Merge pull request #1 from iambaim/add_info

Update instructions

instructions.md

@@ -5,89 +5,119 @@ Assuming that you can only use rootless Docker and that Docker is installed on t
 
 1. Ask IT to assign you **sub-UIDs** and **sub-GIDs** on the server.
 2. Run:
-   ```bash 
+   ```console
    dockerd-rootless-setuptool.sh install
    ```
 3. Some IMR servers uses NFS share for users HOME directory. Rootless Docker won't work with this. Find any physical disks (e.g., `/localscratch`) and run this command:
-   ```bash
+   ```console
    rm -R ~/.local/share/docker
    mkdir -p /localscratch/${USER}/.local/share/docker
    ln -s /localscratch/${USER}/.local/share/docker ~/.local/share/docker
    ```
 4. Run Docker daemon at backend:
-   ```bash
+   ```console
    screen -dmS dockerd bash -c "export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock && dockerd-rootless.sh"
    ```
 5. Test your docker installation:
-   ```bash
+   ```console
    export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock
    docker run hello-world
    ```
 
 ## 1. Install Docker Compose
 1. Prepare your local environment:
-   ```bash
+   ```console
    echo 'export PATH=$HOME/local/bin:$PATH' >> $HOME/.bash_profile
    echo 'export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock' >> $HOME/.bash_profile
    source $HOME/.bash_profile
    ```
    Note that the you only need to do the `source...` command once. The `.bash_profile` content will be executed on every user login.
 2. Run the installation command:
-   ```bash
+   ```console
    curl -L "https://github.com/docker/compose/releases/download/1.29.2/docker-compose-$(uname -s)-$(uname -m)" -o ~/local/bin/docker-compose
    chmod +x ~/local/bin/docker-compose
    ```
    Note that newer version might be available. You can check it here: https://docs.docker.com/compose/install/
 3. Check if Docker Compose is properly installed using this command:
-   ```bash
+   ```console
    docker-compose version
    ```
 
 ## 2. Run Bioticexplorer
 1. Clone `bioticexplorer-docker` repo:
-   ```bash
+   ```console
    git clone https://github.com/iambaim/bioticexplorer-docker.git
    ```
 2. Bring up the Bioticexplorer
-   ```bash
+   ```console
    cd bioticexplorer-docker
    docker-compose up -d
    ```
 3. Setup user crontab for nightly database updates:
-   ```bash
+   ```console
    echo '0 0 * * * export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock && export PATH=/home/${USER}/local/bin:$PATH && export COMPOSE_INTERACTIVE_NO_CLI=1 && cd' $(pwd) '&& ./script/db-update.sh > '$(pwd)'/run.log 2>&1' > tmp-crontab
    
    crontab tmp-crontab
    ```
    Note that the above assumes that we run the automated updates every 00:00 hour in the server time.
 4. Populate database for the first time:
-   ```bash
+   ```console
    screen -dmS firstrun bash -c "export DOCKER_HOST=unix://$XDG_RUNTIME_DIR/docker.sock && ./script/db-update.sh"
    ```
 5. Sit back or relax while the database is being created for the first time. Or you can follow the progress by running:
-   ```bash 
+   ```console
    screen -r firstrun
    ```
    Don't forget to do `Ctrl-a-d` to detach from the screen.
 
 6. Meanwhile, the server should be reachable via the address `<server>:8080` and `<server>:8080/notebook` for the R Jupyter notebook server.
 
-## 3. Troubleshooting
-1. If the server is misbehaving, you can restart them using:
-   ```bash
+## 3. Updating BioticExplorer and BioticExplorerServer apps (and the Docker image)
+
+1. Ensure you have pushed all the necessary changes into the official BioticExplorer and BioticExplorerServer repositories (by default, the image will get them from https://github.com/MikkoVihtakari/BioticExplorer and https://github.com/MikkoVihtakari/BioticExplorerServer). See the `Dockerfile` content.
+
+2. Note down your own Docker Hub repository that will host your image. Previously this was `iambaim/bioticexplorer` (https://hub.docker.com/r/iambaim/bioticexplorer). You can use any name you want, just remember to update the `docker-compose.yml` file to change the source location of the image.
+
+3. Build the image. TIPS: Building the image will take some time. Using `screen` is a good idea:
+   ```console
+   cd bioticexplorer-docker
+   docker build -t mikkovihtakari/bioticexplorer:latest .
+   ```
+   You can use any username/repository and version (e.g., `mikkovihtakari/bioticexplorer:2.1`). However, don't forget to to update the `docker-compose.yml` file or just stick to using `latest` for version.
+
+4. After the image building is complete, push the image to the Docker Hub (login first if you haven't done that):
+   ```console
+   docker login -u mikkovihtakari
+   ...
+
+   docker push mikkovihtakari/bioticexplorer:latest
+   ```
+
+5. Check your Docker Hub page to ensure that the image has been uploaded.
+
+6. If you want to force the running server to use the latest image (again, don't forget to  double check the `docker-compose.yml` file content):
+   ```console
+   cd bioticexplorer-docker
+   docker-compose pull
+   docker-compose up -d
+   ```
+
+# Troubleshooting
+1. If the server is misbehaving, you can restart it using:
+   ```console
    cd bioticexplorer-docker
    docker-compose down
    ...
    docker-compose up -d
    ```
 
 2. We can follow the server live logs using this command:
-   ```bash
+   ```console
    docker-compose logs -f
    ```
 
 3. To edit the live bioticexplorer server, use this command: 
-   ```bash
+   ```console
    docker-compose exec -u root bioticexplorer bash
    ```
    After that you can go to `/BioticExplorer` directory and edit the files using `vim`. Use this in combination with the live logs to pinpoint any of the server errors.