I am trying to run a shiny application on an open port on my server. I usually run docker images using command docker run -p 4000:3838 tag_name, assuming that docker container has exposed port, and shiny app is running at this port.
This all works completely fine for any shiny application that is using http. But I need https.
So the Dockerfile I use consists of:
FROM rocker/r-ver:4.0.1
# System libs:
RUN apt-get update
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install -y libssl-dev
RUN apt-get install -y zlib1g-dev
RUN apt-get install -y libxml2-dev
# R packages installed
RUN R -e "install.packages('remotes')"
RUN R -e "remotes::install_version('searchConsoleR')"
RUN R -e "remotes::install_version('googleAuthR')"
# [...] more R libraries are installed
# Copy application files to a dir
RUN mkdir /root/app
COPY . /root/app
# Expose and set run command from dir above
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app', port = 3838, host = '0.0.0.0')"]
Then I execute docker build -t tag_name . and docker run -p 4000:3838 tag_name.
The page is available at http://server.host:4000
However, since I am using Google Login, I need to use https. But when I visit server's https://server.host:4000 I see an error of page not existing.
Can someone please help?
Related
I have created an R Plumber API, and deploy it in a Docker image.
Dockerfile:
ARG R_VERSION=latest
FROM rocker/r-ver:${R_VERSION}
# install the linux libraries needed for plumber
RUN apt-get update -qq && apt-get install -y \
libssl-dev \
libcurl4-gnutls-dev
COPY / /
# Making home & test folders
RUN Rscript required-packages/required-packages.R
# Giving permission to tests to run
RUN chmod +x tests/run_tests.sh
# Run Tests
RUN tests/run_tests.sh
# open port 7575 to traffic
EXPOSE 7575
# when the container starts, start the main.R script
ENTRYPOINT ["Rscript", "./main.R"]
main.R
library(plumber)
r <- plumb("./plumber.R")
r$run(port = 7575, host = "0.0.0.0")
I run the container with the following command.
docker run --rm -p 7575:7575 'container-name'
On the machine, http://localhost:7575/echo works perfectly fine. However, I cannot call the API from an external computer with http://ip_address:7575/echo.
What could be the problem? As far as I know, the 7575 port is open.
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.)
I'm trying to learn how to deploy a shiny app using Shinyproxy, and I'm using the templated "euler app" (from this repo), but the application does not appear when I navigate to http://localhost:4445. Here's the most similar question I could find, but unfortunately not helpful to my issue: link.
Background
All installations seem fine, and I successfully installed Docker and Java.
The Dockerfile and Docker image work locally, no issues there. The command docker run --rm -p 3838:3838 shiny-euler-app works.
Here is my Dockerfile (copied from the repo):
FROM openanalytics/r-base
MAINTAINER Tobias Verbeke "tobias.verbeke#openanalytics.eu"
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev \
libssl1.1
# system library dependency for the euler app
RUN apt-get update && apt-get install -y \
libmpfr-dev
# basic shiny functionality
RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"
# install dependencies of the euler app
RUN R -e "install.packages('Rmpfr', repos='https://cloud.r-project.org/')"
# copy the app to the image
RUN mkdir /root/euler
COPY euler /root/euler
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/euler')"]
As well, Shinyproxy works fine with the default openanalytics/shinyproxy-demo Docker image, as you can see:
Problem
The issue I have is when I try and supply a different Shiny app and its accompanying application.yml. Here is the application.yml file I'm using (I've tried to make it as basic as possible, with no authentication, etc):
proxy:
title: Standalone Docker Engine
port: 4445
authentication: none
docker:
url: http://localhost:2375
specs:
- id: euler
display-name: Euler's number
container-cmd: ["R", "-e", "shiny::runApp('/root/euler')"]
container-image: shiny-euler-app
Unfortunately, when I run java -jar shinyproxy-2.4.2.jar (in the directory which contains the shinyproxy-2.4.2.jar file and the application.yml file) I get this blank webpage:
For some reason, I am able to access the Shinyproxy webpage, but the Dockerized Shiny app does not appear.
Would really appreciate any helpful suggestions on where/how I could try and solve this issue. Thanks!
I have a Docker container running a shiny app (Dockerfile here).
Shiny server logs are output to stdout and application logs are written to /var/log/shiny-server. I'm deploying this container to AWS Fargate and logging applications only display stdout which makes debugging an application when deployed challenging. I'd like to write the application logs to stdout.
I've tried a number of potential solutions:
I've tried the solution provided here, but have had no luck.. I added the exec xtail /var/log/shiny-server/ to my shiny-server.sh as the last line in the file. App logs are not written to stdout
I noticed that writing application logs to stdout is now the default behavior in rocker/shiny, but as I'm using rocker/verse:3.6.2 (upgraded from 3.6.0 today) along with RUN export ADD=shiny, I don't think this is standard behavior for the rocker/verse:3.6.2 container with Shiny add-on. As a result, I don't get the default behavior out of the box.
This issue on github suggests an alternative method of forcing application logging to stdout by way of an environment variable SHINY_LOG_STDERR=1 set at runtime but I'm not Linux-savvy enough to know where that env variable needs to be set to be effective. I found this documentation from Shiny Server v1.5.13 which gave suggestions in which file to set the environment variable depending on Linux distro; however, the output from my container when I run cat /etc/os-release is:
which doesn't really line up with any of the distributions in the Shiny Server documentation, thus making the documentation unhelpful.
I tried adding adding the environment variable from the github issue above in the docker run command, i.e.,
docker run --rm -e SHINY_LOG_STDERR=1 -p 3838:3838 [my image]
as well as
docker run --rm -e APPLICATION_LOGS_TO_STDOUT=true -p 3838:3838 [my image]
and am still not getting the logs to stdout.
I must be missing something here. Can someone help me identify how to successfully get application logs to stdout successfully?
You can add the line ENV SHINY_LOG_STDERR=1 to your Dockerfile (at least, this works with rocker/shiny, not sure about rocker/verse), such as with your Dockerfile:
FROM rocker/verse:3.6.2
## Add shiny capabilities to container
RUN export ADD=shiny && bash /etc/cont-init.d/add
## Install curl and xtail
RUN apt-get update && apt-get install -y \
curl \
xtail
## Add pip3 and other Python packages
RUN sudo apt-get update -y && apt-get install -y python3-pip
RUN pip3 install boto3
## Add R packages
RUN R -e "install.packages(c('shiny', 'tidyverse', 'tidyselect', 'knitr', 'rmarkdown', 'jsonlite', 'odbc', 'dbplyr', 'RMySQL', 'DBI', 'pander', 'sciplot', 'lubridate', 'zoo', 'stringr', 'stringi', 'openxlsx', 'promises', 'future', 'scales', 'ggplot2', 'zip', 'Cairo', 'tinytex', 'reticulate'), repos = 'https://cran.rstudio.com/')"
## Update and install
RUN tlmgr update --self --all
RUN tlmgr install ms
RUN tlmgr install beamer
RUN tlmgr install pgf
#Copy app dir and theme dirs to their respective locations
COPY iarr /srv/shiny-server/iarr
COPY iarr/reports/interim_annual_report/theme/SwCustom /opt/TinyTeX/texmf-dist/tex/latex/beamer/
#Force texlive to find my custom beamer theme
RUN texhash
EXPOSE 3838
## Add shiny-server information
COPY shiny-server.sh /usr/bin/shiny-server.sh
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf
## Add dos2unix to eliminate Win-style line-endings and run
RUN apt-get update -y && apt-get install -y dos2unix
RUN dos2unix /usr/bin/shiny-server.sh && apt-get --purge remove -y dos2unix && rm -rf /var/lib/apt/lists/*
# Enable Logging from stdout
ENV SHINY_LOG_STDERR=1
RUN ["chmod", "+x", "/usr/bin/shiny-server.sh"]
CMD ["/usr/bin/shiny-server.sh"]
I have the following docker file.
FROM ubuntu
RUN apt-get update
EXPOSE 9000:80
# Install nginx
RUN apt-get install -y nginx
# Install Curl
RUN apt-get -qq update
RUN apt-get -qq -y install curl
ENTRYPOINT service nginx start
When I try to run the following commands in a shell script, the docker image is created
and container is started, however, when the shell script exits, the docker container is stopped.
How can I keep the docker container running after the shell script exits ? The idea is to have a running container with nginx running on port 80 that can be accessed from host using port 9000.
Don't run nginx as a background service. Launch it in the foreground as the nginx container on hub.docker.com does:
CMD ["nginx", "-g", "daemon off;"]
With containers, when pid 1 dies, your container dies. It's identical to when you kill pid 1 (init) on any Linux machine.