From 414dba5693e6649f0f6632530a06f94dd2e9a518 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 5 Mar 2025 17:22:57 +0100
Subject: [PATCH] Add Dockerfile

---
 .Rbuildignore            |  2 ++
 DESCRIPTION              |  1 -
 Dockerfile               | 12 ++++++++++++
 README.md                | 15 +++++++++++----
 docker/app.R             |  2 ++
 docker/shiny-server.conf | 11 +++++++++++
 6 files changed, 38 insertions(+), 5 deletions(-)
 create mode 100644 Dockerfile
 create mode 100644 docker/app.R
 create mode 100644 docker/shiny-server.conf

diff --git a/.Rbuildignore b/.Rbuildignore
index 590a58f..5f1e7f6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,4 @@
+^docker$
 ^scripts$
+^Dockerfile$
 ^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
index ae89a86..4f4e98a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,6 @@ Imports:
     gprofiler2,
     markdown,
     rclipboard,
-    readr,
     shiny,
     shinyWidgets
 Suggests:
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..9c6da4a
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,12 @@
+FROM rocker/shiny:4.4
+
+COPY . /tmp/package/
+
+RUN Rscript -e 'install.packages("pak")' && \
+    Rscript -e 'pak::local_install("/tmp/package/")'
+
+COPY docker/app.R /srv/shiny-server/ubigen/app.R
+COPY docker/shiny-server.conf /etc/shiny-server/shiny-server.conf
+
+EXPOSE 3464
+CMD ["/usr/bin/shiny-server"]
diff --git a/README.md b/README.md
index 2a503ec..aa33612 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,9 @@ genes. It is publicly available at
 This repository contains an R package including the input data, the methods and
 the code for the interactive web interface.
 
-## Installation
+## Installation and Usage
+
+### Local
 
 You can install the development version of `ubigen` using:
 
@@ -15,11 +17,9 @@ You can install the development version of `ubigen` using:
 pak::pkg_install("git::https://gitlab.uni-rostock.de/ep135/ubigen.git")
 ```
 
-## Usage
-
 You only need one function to get started. It will run the application and
 serve the graphical user interface which can be viewed using your preferred
-web browser.
+web browser:
 
 ```r
 ubigen::run_app()
@@ -28,6 +28,13 @@ ubigen::run_app()
 For additional information on using the R package, take a look at the built-in
 documentation (`?ubigen::run_app`).
 
+### Server
+
+Docker images for deploying Ubigen on a server are available on Docker Hub at
+[johrpan/ubigen](https://hub.docker.com/r/johrpan/ubigen). They expose the web
+application at port 3464. We recommend setting up a reverse proxy to enable
+TLS.
+
 ## License
 
 This program is free software: you can redistribute it and/or modify it under
diff --git a/docker/app.R b/docker/app.R
new file mode 100644
index 0000000..4aaeedc
--- /dev/null
+++ b/docker/app.R
@@ -0,0 +1,2 @@
+# This file is needed for Shiny Server to recognize Ubigen's shiny app.
+ubigen::app()
\ No newline at end of file
diff --git a/docker/shiny-server.conf b/docker/shiny-server.conf
new file mode 100644
index 0000000..bb9052e
--- /dev/null
+++ b/docker/shiny-server.conf
@@ -0,0 +1,11 @@
+run_as shiny;
+
+server {
+  listen 3464;
+
+  location / {
+    site_dir /srv/shiny-server/ubigen;
+    log_dir /var/log/shiny-server;
+    directory_index off;
+  }
+}