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installation_guide.md

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Last time updated: November 2024

General description

The eSPC webserver is currently hosted through ShinyProxy, with each tool contained in a docker image. To modify an existing app, you need to have proficiency in Python and R.

  1. Clone the Repo and the submodules
git clone https://github.com/SPC-Facility-EMBL-Hamburg/eSPC_biophysics_platform
cd eSPC_biophysics_platform
git submodule update --init --recursive

If you want to try the tools but don't plan to edit the code frequently

  1. Install docker (https://docs.docker.com/engine/install/)
sudo bash updateDocker.bash

To install individual tools (for developers)

Follow the README.md document:

Tool Path
MoltenProt differentialScanningFluorimetryApps/README.md
FoldAffinity differentialScanningFluorimetryApps/README.md
ThermoAffinity microscaleThermophoresisApp/README.md
PhotoMol massPhotometryApp/README.md
Raynals dynamicLightScatteringApp/README.md
ChiraKit circularDichroismApp/README.md

Installation of the whole eSPC platform

To install the eSPC platform in the development machine, follow these instructions:

  1. Clone or download this repo

  2. Install docker (tested with Docker version 27.1.1, https://docs.docker.com/engine/install/)

  3. Install java (tested with openjdk 22.0.2)

  4. Install shinyproxy (tested with shinyproxy3.1.1, https://www.shinyproxy.io/downloads/)

  5. Create the file '/etc/systemd/system/docker.service.d/override.conf' and fill it with the following text:

    [Service]
    ExecStart=
    ExecStart=/usr/bin/dockerd -H unix:// -D -H tcp://127.0.0.1:2375

This file will be used for setting up the Docker systemd service

  1. Modify the file paths shown in application.yml according to your machine
  2. Start the docker service
systemctl daemon-reload
systemctl start docker
  1. Build the docker images
sudo bash updateDocker.bash
  1. To test the correct installation run shinyproxy
java -jar shinyproxy-x.y.z.jar
  1. Open localhost:8080 inside any browser

Additionally, you can enter and inspect each of the docker images by running

docker run -t -i docker_container_name /bin/bash

General code structure

The following tree represents how the files are organised and their purpose:

README.md                                   # Information about the eSPC platform
fresh_install_guide.md                      # Manual to install from scratch the eSPC platform in a new host
updateDocker.bash                           # Script to update the eSPC docker images
application.yml                             # Example configuration file for ShinyProxy
dockerFiles/                                # Contains the docker files to build the docker images
dynamicLightScatteringApp/                  # Files for the Raynals app
circularDichroismApp/                       # Files for the ChiraKit app 
differentialScanningFluorimetryApps/        # Files for the FoldAffinity and Moltenprot apps (they share the same docker image)
massPhotometryApp/                          # Files for the PhotoMol app
microscaleThermophoresisApp/                # Files for the ThermoAffinity app
templates                                   # HTML and CSS files, user documentation files, and images 
   |-- custom                               
   |   |-- app.html                         # Template file used by ShinyProxy to render the user interface of a Shiny web application
   |   |-- assets                           
   |   |   |-- apps_user_documentation      # User documentation PDFs
   |   |   |-- css                          
   |   |   |   |-- custom.css               # Used to customize the visual appearance of a Shiny web application
   |   |   |-- img                          # Images of the apps (now presented at spc.embl-hamburg.de)
   |   |-- index.html                       # Front page of the eSPC platform