How to install

Installing the application on Linux is recommended over Windows due to easier installation and better performance. Nowadays, Ubuntu Desktop is user-friendly and not significantly different from Windows. Here is a guide on [How to install Ubuntu Desktop].(https://ubuntu.com/tutorials/install-ubuntu-desktop#1-overview).

Installation in Three Steps:

1. Install Docker Compose following the Official guide.

   (In old version of windows, if Docker required you to set up WSL 2, only need to follow step 4 and step 5, not step 6)

2. Configure the application. After Downloading the repository, extract the file to a local folder, there are two files that need to be configured: .django_secrets.env_example and docker-compose.yml.

   • Rename .django_secrets.env_example to .django_secrets.env (don't forget the "." in the beginning of the file name).
   • Configure docker-compose.yml (docker configure file, optional but highly recommended) using any text editor(e.g., notepad, VS Code, etc.):

     • Configuring the storage locations for your data, including raw files and processed data, involves setting up to four different locations or drives. The primary storage is a required configuration, while the other three - secondary storage, remote storage, and offline storage - are optional but highly recommended to ensure redundancy.

       If the specified folders do not exist, the system will return an error. Thus, to ensure compatibility, all four drives are set to the 'C' drive in a Windows system by default. However, you can change any of these storage locations by modifying the corresponding 'source' field in the 'bind' section (only change the 'source' field, do not alter the 'target' field).

       The format for specifying storage locations differs based on your operating system. For Windows hosts, the format is /d/docker/primary_storage, which corresponds to the location d:/docker/primary_raw. Linux, on the other hand, uses its native format, /user/xxx/documents/primary_raw.

       You can configure up to four storage locations(primary_storage, secondary_storage, remote_storage, offline_storage) for use in the app. If you're not using all of them, you can either comment out the unused ones using "#" or point it to an empty folder (recommended for easy future expansion). The naming conventions for storage locations, such as "remote_storage," do not need to be taken literally. For instance, "remote_storage" does not necessarily have to point to a remote folder. These are merely default names and can point to any location based on your preference and requirements.

     • (Optional, only for advanced users) Only modify other sections as needed (only for advanced users)

   • Configure .django_secrets.env(optional):
     • You have the ability to configure certain parameters used within the Django app, such as time zone, debug mode, email server, Jupyter password, among others. These parameters can be adjusted based on your specific needs. If you're not sure what to set, you can leave them as their default values, or configure them as their names suggest. It's important to ensure that any changes you make align with your system settings and operational requirements.

3. Start the app. After you have configured the necessary files, you can start the app by running the command "docker compose up" in the directory of the extracted folder (usually named Proteomic-Data-Manager-master). You can do this in the Command Prompt for Windows or the Terminal for Mac or Linux. Alternatively, if you have installed Visual Studio Code or another integrated development environment (IDE) with the appropriate extensions, you can right-click the docker-compose.yml file and select "Compose Up". If you encounter any errors, refer to the troubleshooting page for potential solutions and advice.

if installed properly, you should see a screen similar to the following screenshoot.

What's Next? How to access the application