SciLifeLab Serve allows hosting of web applications built with the Shiny framework. Shiny is primarily used to create apps with R code although it supports Python as well. Shiny apps can contain interactive visualisations, tables, text, analysis tools, and more. By default SciLifeLab Serve uses the open source framework ShinyProxy behind the scenes to ensure that Shiny apps run smoothly.

Introduction

SciLifeLab Serve allows hosting of Shiny apps free of charge to researchers in life sciences working at a Swedish research institution as well as their collaborators abroad. The data and code behind each app hosted on SciLifeLab Serve need to be made publicly available. All apps hosted on SciLifeLab Serve are publicly available through a URL in the form of x.serve.scilifelab.se. Currently, only apps that have been packaged as a Docker container image are supported (see the instructions below for how to do that).

Each Shiny app hosted on SciLifeLab Serve receives 2 vCPU and 4 GB of memory/RAM by default. These can be requested to be increased up to 12 vCPU and 48 GB of memory/RAM if need is demonstrated (this means that you provide an example of a likely user interaction, for example user input, where having higher resources allocated will make a significant difference to performance).

Step-by-step guide

This step-by-step guide will walk you through creating and publishing a Docker container image with your Shiny app, registering on SciLifeLab Serve, creating a project, and, finally, creating an app inside your project. We have not gone into detail explaining each of the tools and settings we used during the process in order to streamline the instructions. We welcome contributions and suggestions for improvement of this guide.

As of now, SciLifeLab Serve only allows to host Shiny applications if they are packaged as Docker images (Docker is a powerful and widespread tool for deployment of applications). Packaging your R shiny application as a Docker image is relatively straightforward, so do not be concerned if you have never done this before. The first steps of this guide will explain in detail how to do just that. If you run into an issue you cannot resolve, the SciLifeLab Serve team is happy to help you with this through a free individual consultation, get in touch with us by e-mailing serve@scilifelab.se.

Step 1. Download and install Docker Desktop

You will need to have Docker Desktop installed on your computer to be able to build an image.

Step 2. Create a Dockerfile for your app

In this example, we will assume that the Shiny app code is located in a file called app.R and that this file as well as the app's dependencies (e.g., associated data) are located in the folder called 'app'. Make sure that your app runs as it should with this structure (for example, if you run it using RStudio). Here is the file structure that we assume:

..
└── app/
│   ├── app.R
│   ├── dataset1.csv
│   └── dataset2_folder/

Docker images are built from sets of instructions given in a so-called Dockerfile. Create a file called Dockerfile (the name of the file should be exactly 'Dockerfile' and it should not have any file extension) using any text editor you have and insert the code below or simply download this example. Place this file in the parent folder of the folder 'app'.

FROM rocker/shiny:latest

RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get install -y git libxml2-dev libmagick++-dev && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Command to install standard R packages from CRAN; enter the list of required packages for your app here
RUN Rscript -e 'install.packages(c("shiny","tidyverse","BiocManager"))'

# Command to install packages from Bioconductor; enter the list of required Bioconductor packages for your app here
RUN Rscript -e 'BiocManager::install(c("Biostrings"),ask = F)'

RUN rm -rf /srv/shiny-server/*
COPY /app/ /srv/shiny-server/

USER shiny

EXPOSE 3838

CMD ["/usr/bin/shiny-server"]

Here is what your file structure should look like after you create the new files.

..
├── app/
│   ├── app.R
│   ├── dataset1.csv
│   └── dataset2_folder/
└── Dockerfile

Let us look at how you can customize the Dockerfile for your own app. In this example two packages were installed from the standard R packages: shiny and tidyverse. This was done in the line RUN Rscript -e 'install.packages(c("shiny","tidyverse"))'. Add your own packages here as needed by your app. In addition, one package was installed from Bioconductor - Biostrings. This was done in the line RUN Rscript -e 'BiocManager::install(c("Biostrings"),ask = F)'. Add your Bioconductor packages here.

The folder app and its contents are copied into the image in the line COPY /app/* /srv/shiny-server/. If you use a different folder name, change the folder names in this line and lines below. If some of the dependecies of the app are located in different folders these other folders should be copied into the image separately.

You can see our example app with these files in this GitHub repository.

Step 3. Build a Docker image

Ensure that Docker Desktop is running. Open Terminal (or Windows Terminal) and navigate to the folder where your app files and the Dockerfile are located.

cd path/to/your/folder

Run the Docker command to build your image as shown below. Replace your-image-name with your own image name. Note that the dot at the end of the command is important. Please note that building the image may take a while. NB: this step does not yet work for recent (2020 and later) Mac computers with M1 and M2 chips (last updated: 2023-09-26). If you do not have access to another computer we recommend using GitHub Actions to build your image (described below).

docker build -t your-image-name:your-image-tag .

Once the process is complete, your newly created image should appear on Docker Desktop under the Images. Alternatively, run the following command in the Terminal to inspect images on your computer. You should see your image in the list.

docker image ls

In order to test that the image you just built works you need to run a container from this image. To do that, run the following command in the Terminal.

docker run --rm -p 3838:3838 your-image-name:your-image-tag

If everything went as it should, you should now be able to navigate to http://localhost:3838/ in your browser and see and interact with your Shiny app.

Step 4. Publish your Docker image

You have now built and tested an image for your Shiny app on your computer. In order to be able to host this image on SciLifeLab Serve it needs to be published in a so-called image registry. Below, we show how to publish your image manually on DockerHub or automatically on DockerHub or GitHub every time you make an update , this is our recommended method (this method uses GitHub Actions).

Option 1: Manually publishing an image

Register on DockerHub and sign in with your account on Docker Desktop app.

Next, re-build your image as described above, this time including your DockerHub username in the image name, as shown below. It is important that each new version of your app has a unique image tag. You can use v1, version124, date, or any other versioning that you like.

docker build -t <your-dockerhub-username>/<your-image-name>:<your-image-tag> .

Once the image is built and visible on Docker Desktop, pick "Push to Hub" among the options for your app image. This should publish your image on https://hub.docker.com/r/<your-dockerhub-username>/<your-image-name>:<your-image-tag>. For example, our example app is available on https://hub.docker.com/r/scilifelabdatacentre/shiny-adhd-medication-sweden:20240117-062028 (one of the image tags that we have). Please note that your image should stay publicly available even after your app is published on Serve because it will be fetched with regular intervals.

Option 2: Automatically publishing an image

The Docker image can be built and published automatically using GitHub Actions every time you push a change to your repository containing the app code. We recommend setting up this workflow as it will minimize the need for you to do things manually every time you make a change in your app.

The repository of our example Shiny app contains an example of how to set up GitHub actions for publishing on DockerHub or on GitHub packages. See the folder .github/workflows for the two examples. Copy one of these into your own repository into the same folder and customize if needed.

For the DockerHub workflow to work with your own repository you will need to: change the repository name to your own repository; change the image name to your own image (use the following format: <your-dockerhub-username>/<your-image-name>); add DOCKERHUB_USERNAME and DOCKERHUB_TOKEN to the repository secrets (see repository settings), the token is obtained from the DockerHub account settings.

For the GitHub packages workflow to work with your own repository you do not need to make any changes. Keep in mind that the Docker image needs to be publicly available for SciLifeLab Serve to see it, the images on GitHub are not always public by default.

In both cases the workflow to build and publish an image will be triggered on push to the main branch. Each image will be published with the date and time of publication as a unique tag. To learn more about how GitHub actions work here and how you can furher customize them please see the official documentation.

Step 5. Create a user account on SciLifeLab Serve

If you do not already have a user account on SciLifeLab Serve, create an account.

Step 6. Create a project

Every app and model has to be located within a project. Projects that you have created/been granted access to can be found under My projects page.

You need to be logged in to create a project. To create a project, click on the corresponding button on that page. Choose Default project template. The name and description of the project are visible only to you and those who you grant access to the project. Once the project is created, you will be taken to the project dashboard where you can create different types of apps.

Step 7. Create an app

In order to host a Shiny App click the Create button on the Shiny App card. Then enter the following information in the form:

• Name: Name of the app that will be displayed on the Public apps page.
• Description: Provide a brief description of the app, will also be displayed on the Public apps page.
• Subdomain: This is the subdomain that the deployed app will be available at (e.g., a subdomain of r46b61563 would mean that the app would be available at r46b61563.serve.scilifelab.se). If no subdomain name is entered, a random name will be genrated by default. By clicking on New you can specify the custom subdomain name of your choice (provided that it is not already taken). This subdomain will then appear in the Subdomain options and the subdomain will appear in the format 'name-you-chose.serve.scilifelab.se'.
• Permissions: The permissions for the project. There are four levels of permissions for an app: 1. Private: The app can only be accessed by the user that created the app (sign in required). Please note that we only allow the permissions to be set to Private temporarily, while you are developing the app. Eventually each app should be published publicly. 2. Project: All members of the project where the app is located will be able to access the app (sign in required). Please note that we only allow the permissions to be set to Project temporarily, while you are developing the app. Eventually each app should be published publicly. 3. Link Anyone with the URL can access the app but this URL will not be publicly listed anywhere by us (this option is best in case you want to share the app with certain people but not with everyone yet). 4. Public: Anyone with the URL can access the app and the app will be displayed under Public apps page.
• Source code URL: Provide a URL where source code of your app can be accessed. This can, for example, be a link to GitHub repository, an entry on Zenodo or Figshare or another repository. If your source code is stored with a DOI, provide a link starting with https://doi.org/.
• Hardware: Amount of CPU and RAM dedicated to your app. By default there is only one option that is sufficient for most users; get in touch with us if your app needs more hardware resources.
• Port: The port that the Shiny server runs on (usually 3838). Note that we only allow ports in the range 3000-9999.
• Image: Name and tag of the image on DockerHub or full url to the image on a different repository. Note that each version of your app should have a unique tag. Once an image with a certain tag has been deployed once it will no longer be possible to change this version without a new tag.

For our example app, the settings look as shown in the image below.

.

After you create your app, you will be taken to the Project overview again, and should see your app in the list of deployed apps. The state will initially show as 'Pending' (shown in an orange label), but should change to 'Running' (shown in a green label). Please note that even after the status is 'Running' it may take up to a couple of minutes for the app to actually start. If you chose "Link" or "Public" permissions, the app can now be accessed by anyone opening the app URL. "Public" apps are also displayed under the "Apps" page on SciLifeLab Serve.

To update your Shiny app, you need to first publish an updated container image with a new tag. Once your updated container image has been published, go the app settings page (click on the "Settings" link), change the tag in the Image field, and press on the Update button on the bottom of the form. To delete the app, press the "Delete" link next to the "Settings" link.

Frequently Asked Questions

I am stuck while following the guide. Can I get help?

Yes, feel free to get in touch with us (serve@scilifelab.se). Please provide a link to your Shiny app code and data (for example, to your GitHub repository) in your email so that we can best help you.

Can my app be hosted at a top-level domain, such as www.example.org?

Yes, it is possible. Your app will then be available at both x.serve.scilifelab.se and your own example.org. To do this, you will need to purchase a domain name yourself and set up DNS settings that you will get from us. Get in touch with us (serve@scilifelab.se) so that we can arrange this for you.

Can my app contain sensitive data?

No, SciLifeLab Serve does not support hosting of apps with sensitive data.

How many users can use my app simultaneously?

Currently, we do not have a specific enforced limit on the number of concurrent users. We try to accomodate as many users as possible but cannot at this point make promises about a minimum number of users.

Can different users see each other's work/data inside my Shiny app?

No, they cannot. SciLifeLab Serve launches a new copy of your app for each new user that opens it. Different users do not have access to each others' copies. Each user's copy is deleted as soon as the user closes their browser tab.

How much CPU and RAM/memory does Serve allocate to my app?

Please find the default allocation in the text of this page above. If you would like for your app to be allocated more than the default amount of resources, get in touch with us (serve@scilifelab.se) with a motivation.

What resource allocations will my app need on Serve?

You can always deploy your app with default resource allocations and observe its performance, most apps do not need more than the default allocations. If your app is not performing well and you are unsure how to test what it needs, let us know and we can help you.

Why is my app slower on Serve than on my laptop?

If your app is slower on Serve than on your own laptop, it probably needs to be assigned more resources to function well. Get in touch with the us on serve@scilifelab.se and describe your situation.

I updated the image in the app settings, why do I still see the old version?

We require that each version of your app has a unique Docker image tag. When an app has been deployed once using an image with a certain tag it will no longer be possible to fetch an updated image with an identical tag. Therefore, you need to publish your image with a new unique tag and change the image address in the app settings to include this new tag. In other words, instead of using "image:latest" for all of your versions you should be using unique tags for each version, e.g. "image:v3" or "image:20240125". Still seeing the same version despite publishing your Docker image with a new tag? Send us an email to serve@scilifelab.se, and we can take a look what went wrong in that case.

Can I keep my app private while my article/conference submission is under review?

Yes, it is possible to publish an app in such a way that only those with a URL can open it. To do that, choose "Link" option in the Permissions field of the app settings. In this case those who you share the link with (for example, reviewers of your article) will be able to open it but not anyone else.

Can I host a private app for my research group?

No, each app on SciLifeLab Serve needs to be made public eventually. The apps can only stay private while you are still developing it or while it is under peer review.

How do I update or delete my app after it has been published?

Please find the answer in the text of this page.

Can I delete/hide my Docker image after my app is published?

No, the Docker images need to stay available at all times. SciLifeLab Serve is regularly fetching the image again. If it is not available, your app will stop working.

Where can I see logs of what my Shiny application is doing?

Currently, the logs displayed on SciLifeLab Serve for Shiny apps only have limited value. It is not currently possible to see the logs from the Shiny application itself, only from the software that lies between Serve and the Shiny application. Hence, we advice to use your own computer to debug and resolve issues as described below. If your application is running smoothly on your own computer when you run it as described above, it should also run without issues on Serve.

When running your Docker image on your computer, there are two things you can look at. One of these are the logs of the container in general which show what the whole container is doing. The easiest way to do it is to simply click on "Details" in the Docker Desktop application. Here you should see that the application has been launched and is available at port 3838 or if there was an issue.

Another log you can look at is actually all the output from the currently runnin Shiny app. This is like seeing the output when the Shiny app runs in RStudio. For that, in your Docker Desktop find the option to go into Terminal for that container. In there you need to navigate to var/log/shiny-server folder (for example, run 'cd var/log/shiny-server'). There you should see files with logs of running your application (for example, run 'ls'). You can open and read them (for example, run 'cat name.log').

Can I see how many users are accessing my application?

At the moment we do not track such statistics. We plan to implement this at some point in the future.

Can I embed my app on another website using an inline frame (iframe)?

Yes, you can do that. We do not restrict embedding of the apps hosted on SciLifeLab Serve into other websites.