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Installation
- Install Docker Compose
- Download the Proteomic-Data-Manager
- Rename .django_secrets.env_example to .django_secrets.env
- Configure docker-compose.yml
- Run docker-compose up
Screenshots for a step-by-step guide
Now your server should be functional. If you run into any errors see the Troubleshooting Guide
It will be easiest if you follow the [Docker Guide] (https://docs.docker.com/compose/install/).
(In older versions of Windows, if Docker prompts you to set up Windows Subsystem for Linux 2 (WSL 2), you only need to follow steps 4 and 5, not step 6. Once these steps are completed, a system reboot is necessary for the changes to take effect.)
For Windows systems, Docker Desktop must be manually started. You can do this by clicking the Docker Desktop icon, which allows the application to run in the background.
Rename .django_secrets.env_example to .django_secrets.env (don't forget the "." at the beginning of the file name, only delete the "_example" part).
You can configure certain parameters used within the Django app, such as time zone, debug mode, email server, and Jupyter password. 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.
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 may 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 them 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 default names and can point to any location based on your preference and requirements.
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 (Guide) or the Terminal for Mac or Linux (Guide). If you encounter a "file exists" error, simply retrying the command usually resolves the issue.
Screenshots for step by step guide
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.
Now you can access the data manager, to learn how click here How to access the application