I have a shiny application which I have containerised with Docker. Within the shiny application I use the shinyFiles library to allow the user to choose and upload a directory.
My server.R file looks something like this:
shinyServer(function(input, output, clientData, session) {
volumes <- c("Home (~)" = '~', "Current directory" = getwd(), "Root (/)" = '/')
shinyDirChoose(input, 'resultsLocation', roots=volumes, session=session)
})
and my ui.R file looks something like this:
library(shiny)
library(shinyFiles)
shinyUI(fluidPage(
shinyDirButton('resultsLocation', 'Browse...', title = 'Select a directory')
))
This is fine if I run the app locally through R, however, if I build and run the docker container, the user cannot access their local volumes, and instead are stuck within the docker container.
I followed this guide to set up my docker container (with the addition of running chmod +x shiny-server.sh to make the file executable) and everything other than the volumes is working. My Dockerfile looks like this:
# Install R version 3.6.0
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# Install R packages that are required
RUN R -e "install.packages('shiny')"
RUN R -e "install.packages('shinyFiles')"
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 3838
# EXPOSE 3838
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
# Allow permissions
RUN chown -R shiny:shiny /srv/shiny-server
CMD ["/usr/bin/shiny-server.sh"]
And I build and run the container with:
docker build -t shiny_docker_test . ; docker run -p 3838:3838 shiny_docker_test
So, my question is: how can I access my local filesystem/volumes through the dockerised shiny app with shinyFiles? I'm sure there is a simple solution, but I am new to all of this stuff.
Use docker volume feature. For example:
In command line -v is used to map container directories with host directories
docker -v full_path_on_host:full_path_inside_container
Similarly, there is VOLUME keyword for same stuff while working on docker file.
Related
I am deploying Shiny-server in container. By default Shiny-server listens on port 3838, here is piece from shiny-server.conf
# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
# Define a server that listens on port 3838
server {
listen 3838;
I would like to change this port to 80. I obviously can launch container instance, login to it, and change it, but I would like to change it in Dockerfile.
FROM rocker/shiny:3.5.1
RUN apt-get update && apt-get install libcurl4-openssl-dev libv8-3.14-dev -y &&\
mkdir -p /var/lib/shiny-server/bookmarks/shiny
# Download and install library
RUN R -e "install.packages(c('shinydashboard', 'shinyjs', 'V8'))"
# copy the app to the image COPY shinyapps /srv/shiny-server/
COPY "reports" "/srv/shiny-server/sample-apps/reports/"
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /srv/shiny-server/
EXPOSE 80
CMD ["/usr/bin/shiny-server.sh"]
Is there command line option for final line in Dockerfile?
Add
RUN sed -i -e 's/\blisten 3838\b/listen 80/g' /path/to/shiny-server.conf
So perhaps ending up with:
FROM rocker/shiny:3.5.1
RUN apt-get update && apt-get install libcurl4-openssl-dev libv8-3.14-dev -y &&\
mkdir -p /var/lib/shiny-server/bookmarks/shiny
# Download and install library
RUN R -e "install.packages(c('shinydashboard', 'shinyjs', 'V8'))"
# copy the app to the image COPY shinyapps /srv/shiny-server/
COPY "reports" "/srv/shiny-server/sample-apps/reports/"
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /srv/shiny-server/
RUN sed -i -e 's/\blisten 3838\b/listen 80/g' /path/to/shiny-server.conf
EXPOSE 80
CMD ["/usr/bin/shiny-server.sh"]
(I know multiple layers can be inefficient if not compacted, over to you if you want to combine the sed line with the previous RUN command. You might want to combine more of those RUN lines, if that's a concern.)
Documentation for rocker/rstudio docker container.
I am able to get up and running in rstudio using Docker with the following set up in a directory:
Dockerfile:
FROM rocker/tidyverse:latest
docker-compose:
version: "3.5"
services:
ide-rstudio:
build:
context: .
ports:
- 8787:8787
environment:
ROOT: "TRUE"
PASSWORD: test
Now, if I enter this dir in the terminal and type: docker-compose build followed by docker-compose up -d and then navigate to localhost:8787 I see the rstudio login screen. So far so good.
I would like to add shiny to the same container per the documentation (as opposed to using a separate shiny image).
On the documentation I link to at the top it says:
Add shiny server on start up with e ADD=shiny
docker run -d -p 3838:3838 -p 8787:8787 -e ADD=shiny -e PASSWORD=yourpasswordhere rocker/rstudio
shiny server is now running on localhost:3838 and RStudio on localhost:8787.
Since I'm using docker-compose I updated my docker-compose file to this:
version: "3.5"
services:
ide-rstudio:
build:
context: .
ports:
- 8787:8787
- 3838:3838
environment:
ROOT: "TRUE"
ADD: "shiny"
PASSWORD: test
Now, when I go to the terminal like before and type: docker-compose build followed by docker-compose up -d I again see the rstudio login page at localhost:8787. However, if I go to localhost:3838, I see Firefox' 'connection was reset' page. It looks like nothing is there.
How can I add shiny to my container per the instructions?
It seems the image is missing shiny installer. If you run the same compose file without -d and using rocker/rstudio:3.2.0 image you will see in logs that shiny is installing. It failed to install for me (there was a problem with missing file /usr/local/lib/R/site-library/littler/examples/install2.r) but I found the script which installs the thing. For some reason the script does not exist in rocker/tidyverse:latest (I have no idea why, you'd better ask the maintainer) and ADD=shiny has no effect.
I managed to get things working by injecting that script into rocker/tidyverse:latest and here is how you can do it. Save the following as a file named add:
#!/usr/bin/with-contenv bash
ADD=${ADD:=none}
## A script to add shiny to an rstudio-based rocker image.
if [ "$ADD" == "shiny" ]; then
echo "Adding shiny server to container..."
apt-get update && apt-get -y install \
gdebi-core \
libxt-dev && \
wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb && \
install2.r -e --skipinstalled shiny rmarkdown && \
cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/ && \
rm -rf /var/lib/apt/lists/* && \
mkdir -p /var/log/shiny-server && \
chown shiny.shiny /var/log/shiny-server && \
mkdir -p /etc/services.d/shiny-server && \
cd /etc/services.d/shiny-server && \
echo '#!/bin/bash' > run && echo 'exec shiny-server > /var/log/shiny-server.log' >> run && \
chmod +x run && \
adduser rstudio shiny && \
cd /
fi
if [ $"$ADD" == "none" ]; then
echo "Nothing additional to add"
fi
Then either add the following to your Dockefile:
COPY add /etc/cont-init.d/add
RUN chmod +x /etc/cont-init.d/add
or apply execution permission locally and mount it during runtime. To do this run the following locally:
chmod +x add
and add this to docker-compose.yml:
services:
ide-rstudio:
volumes: # this line and below
- ./add:/etc/cont-init.d/add
I built a basic R shiny app and wanted to dockerize it on an Ubuntu 18.04 VM.
I followed this blog.
and got the following situation:
R app
app.R
library(shiny)
# Define UI for application that draws a histogram
ui <- fluidPage(
# Application title
titlePanel("Old Faithful Geyser Data"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
sliderInput("bins",
"Number of bins:",
min = 1,
max = 50,
value = 30)
),
# Show a plot of the generated distribution
mainPanel(
plotOutput("distPlot")
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
output$distPlot <- renderPlot({
# generate bins based on input$bins from ui.R
x <- faithful[, 2]
bins <- seq(min(x), max(x), length.out = input$bins + 1)
# draw the histogram with the specified number of bins
hist(x, breaks = bins, col = 'darkgray', border = 'white')
})
}
# Run the application
shinyApp(ui = ui, server = server)
Dockerfile
# Install R version 3.4
FROM r-base:3.4.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Add shiny user
RUN groupadd shiny \
&& useradd --gid shiny --shell /bin/bash --create-home shiny
# Download and install ShinyServer (latest version)
#RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
# VERSION=$(cat version.txt) && \
# wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
# gdebi -n ss-latest.deb && \
# rm -f version.txt ss-latest.deb
# Install R packages that are required
# TODO: add further package if you need!
RUN R -e "install.packages(c('shiny'), repos='http://cran.rstudio.com/')"
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 80
EXPOSE 80
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
# allow permission
RUN sudo chown -R shiny:shiny /srv/shiny-server
#RUN chown shiny:shiny /var/lib/shiny-server
CMD ["/usr/bin/shiny-server.sh"]
shiny-server.conf
# Define the user we should use when spawning R Shiny processes
run_as shiny;
# Define a top-level server which will listen on a port
server {
# Instruct this server to listen on port 80. The app at dokku-alt need expose PORT 80, or 500 e etc. See the docs
listen 80;
# Define the location available at the base URL
location / {
# Run this location in 'site_dir' mode, which hosts the entire directory
# tree at '/srv/shiny-server'
site_dir /srv/shiny-server;
# Define where we should put the log files for this location
log_dir /var/log/shiny-server;
# Should we list the contents of a (non-Shiny-App) directory when the user
# visits the corresponding URL?
directory_index on;
}
}
shiny-server.sh
#!/bin/sh
# Make sure the directory for individual app logs exists
mkdir -p /var/log/shiny-server
chown shiny.shiny /var/log/shiny-server
exec shiny-server >> /var/log/shiny-server.log 2>&1
The directory structure is
- app/app.R
- Dockerfile
- shiny-server.sh
- shiny-server.conf
I use the docker
Docker version 18.09.9, build 1752eb3
and build it using
sudo docker build -t test .
but when running it I get
sudo docker run test
docker: Error response from daemon: OCI runtime create failed: container_linux.go:345: starting container process caused "exec: \"/usr/bin/shiny-server.sh\": permission denied": unknown.
ERRO[0001] error waiting for container: context canceled
I looked through the various forums mentioning this issue and tried changing permissions.
I am quite puzzled as it seemed to me that this case was a basic example.
==== Edition after comment ====
I have changed the ownership and the permission of the .sh file
sudo chown shiny:shiny shiny-server.sh
sudo chmod u+ shiny-server.sh
rebuilt the image
sudo docker build -t test .
reran it
sudo docker run test
but then it does nothing, no error or message of any type, just going to the next line.
I'm trying to run my shiny app in a docker container.
My app folder structure is like this:
myApp (directory)
-app (directory)
--ui.R
--server.R
--global.R
--style.css
--mydata.xlsx
--mydata2.rds
--functions.R (contains functions I use in app)
-Dockerfile
-shiny-server.conf
-shiny-server.sh
I can get into my directory myApp and run shiny locally by doing runApp('app'). my shiny app runs perfectly.
However, when I try to build the image and run it, it give me error.
docker build -t myshinyapp_obs .
docker run -p 80:80 myshinyapp_obs
The application failed to start.
The application exited during initialization.
The docker image building process seems to be fine.
When run it on docker, I got error.
The interesting thing is when I simply copy any app from shiny gallery and put the ui.R and server.R file under the app folder, it works fine!!!
My question is why my app is not working? given the fact:
my app work perfectly locally
After copying shiny example from gallery into the app folder, the example app works fine.
How can that happen? I cannot figure it out. Spent hours trying to make it work but failed.
Below is my Dockfile:
# Install R version 3.6
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# Install R packages that are required
# TODO: add further package if you need!
RUN R -e "install.packages(c('devtools','readxl','tidyverse','rlang','shiny','shinythemes', 'DT'), repos='http://cran.rstudio.com/')"
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 80
EXPOSE 80
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]
I set up an angular development environment using the following Dockerfile (don't try to build this unless you're really enthusiastic, it takes an age).
FROM ubuntu:14.04
# build environment
RUN ["apt-get", "update"]
RUN ["apt-get", "install", "-y", "nodejs", "npm", "git"]
RUN ["ln", "-s", "/usr/bin/nodejs", "/usr/bin/node"]
RUN ["npm", "install", "-g", "yo"]
RUN ["npm", "install", "-g", "bower"]
RUN ["npm", "install", "-g", "grunt-cli"]
WORKDIR /home/angular
ADD ./package.json /home/angular/package.json
ADD ./bower.json /home/angular/bower.json
ADD ./dist /home/angular/dist
RUN ["npm", "install"]
RUN ["bower", "install", "--allow-root"]
# sass depedencies
ENV RUBY_MAJOR 2.2
ENV RUBY_VERSION 2.2.2
ENV RUBY_DOWNLOAD_SHA256 5ffc0f317e429e6b29d4a98ac521c3ce65481bfd22a8cf845fa02a7b113d9b44
# some of ruby's build scripts are written in ruby
# we purge this later to make sure our final image uses what we just built
RUN ["apt-get", "install", "-y", "curl"]
RUN apt-get update \
&& apt-get install -y autoconf bison libgdbm-dev ruby \
&& rm -rf /var/lib/apt/lists/* \
&& mkdir -p /usr/src/ruby \
&& curl -fSL -o ruby.tar.gz "http://cache.ruby-lang.org/pub/ruby/$RUBY_MAJOR/ruby-$RUBY_VERSION.tar.gz" \
&& echo "$RUBY_DOWNLOAD_SHA256 *ruby.tar.gz" | sha256sum -c - \
&& tar -xzf ruby.tar.gz -C /usr/src/ruby --strip-components=1 \
&& rm ruby.tar.gz \
&& cd /usr/src/ruby \
&& autoconf \
&& ./configure --disable-install-doc \
&& make -j"$(nproc)" \
&& make install \
&& apt-get purge -y --auto-remove bison libgdbm-dev ruby \
&& rm -r /usr/src/ruby
# skip installing gem documentation
RUN echo 'gem: --no-rdoc --no-ri' >> "$HOME/.gemrc"
# install things globally, for great justice
ENV GEM_HOME /usr/local/bundle
ENV PATH $GEM_HOME/bin:$PATH
ENV BUNDLER_VERSION 1.10.5
RUN gem install bundler --version "$BUNDLER_VERSION" \
&& bundle config --global path "$GEM_HOME" \
&& bundle config --global bin "$GEM_HOME/bin"
# don't create ".bundle" in all our apps
ENV BUNDLE_APP_CONFIG $GEM_HOME
RUN gem install compass
VOLUME ["/home/me/code/correspondence/client/dist"]
ADD ./ /home/angular
If I run this with:
sudo docker run -it me/angular /bin/bash
I can use grunt build with no problems. Since I haven't attached a volume to dist that build is no use to other containers such as the webserver. But running:
sudo docker run -itv /home/me/code/correspondence/client/dist:/home/angular me/angular /bin/bash
results in the grunt build command no longer being usable in the container:
grunt-cli: The grunt command line interface. (v0.1.13)
Fatal error: Unable to find local grunt.
If you're seeing this message, either a Gruntfile wasn't found or grunt
hasn't been installed locally to your project. For more information about
installing and configuring grunt, please see the Getting Started guide:
http://gruntjs.com/getting-started
The only difference is adding the volume. How does adding the volume result in this different behaviour?
I suppose that's because you have placed some files to /home/angular in image and when you're mounting your volume to the same path (/home/angular), your volume hides original files.
Quote from documentation:
Note: If the path /opt/webapp already exists inside the container’s
image, its contents will be replaced by the contents of /src/webapp on
the host to stay consistent with the expected behavior of mount
Try to mount volume to another directory, /home/angular/dist/client, for instance.