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Running Chipster in SD Desktop

Chipster is a user-friendly analysis software for high-throughput Life science data such as Visium, single-cell and bulk RNA-seq. Chipster provides a web interface to over 500 analysis tools that can be combined into workflows.

The public Chipster server, available in https://chipster.csc.fi is not intended for processing sensitive data. This document describes how you can install your own Chipster server to an SD Desktop virtual machine for analyzing sensitive data.

Before installation

Installing a Chipster server requires significant storage resources and running it requires plenty of memory. Because of that you should apply for at least 1 TB volume for the virtual machine where you plan to install Chipster. Further, as some applications in Chipster require significant amount of memory the flavor of the SD Desktop virtual machine should medium computation or heavy computation. In SD Desktop, the Chipster server is compatible only with SD Desktop Virtual Machines were Podman is available.

Note that all the users of the SD Desktop machine can use the same Chipster server. In cases where several users use the same server, it is good practice ro assign one user as a Chipster manager that installs and manages the Chipster server.

Installation

The installation process starts by contacting CSC servicedesk (servicedesk@csc.fi) to get the Chipster installation files available. Include the Share ID of your CSC project to the request.

Once you have access to the installation files, the actual installation process is simple. Open DataGateway connection. Then use SD Software installer to install the CSC tools toolkit. Next open terminal and give command:

chipster-installer.sh
This command starts Chipster installation process that takes 1-2 hours and downloads nearly 200 GB of data to the Volume disk. Once the process has successfully finished you can start your local Chipster server with command:

start-chipster-server
Once the Chipstwer server is running, all users of the SD Desktop VM can use the same Chipster server. Thus this launch command should be executed only by the user that is acting as the Chipster server manager. Running the command again closes the existing server and launches a new one. In normal use the start-chipster-server command is used to start the service after reboot.

Using Chipster server

Running Chipster server can be used by opening Firefox browser inside SD Desktop and the connecting to server address:

http://localhost:8000.

You can login to the local Chipster server using the default user name chipster and password chipster or by using your CSC username as username and password.

For more details about using Chipster service, please study the material in Chipster home page. Keep in mind that Chipster features and tools that utilize external services are not functional in SD Desktop.