I need to download some free plugins from wordpress website and move that folders to plugins folder via command property in the docker-compose
Is there any way to execute shell script after the docker compose is completed?
> command: apt-get install -y curl curl -SL
https://downloads.wordpress.org/plugin/advanced-custom-fields.5.7.12.zip
or a bash script for this?
The documentation says:
The command can also be a list, in a manner similar to dockerfile:
command: ["bundle", "exec", "thin", "-p", "3000"]
You can:
docker-compose run <your_service> apt-get install -y curl
docker-compose run <your_service> curl -SL https://downloads.wordpress.org/plugin/advanced-custom-fields.5.7.12.zip
You can even do it in 1 command but I'm guessing the installation is one off and you might include that in your image ;)
Hope this helps.
Related
I'm trying to install wp plugins by executing script right after the wordpress image is built.
Here is my Dockerfile:
FROM wordpress
# Update aptitude with new repo
RUN apt-get update
# Install software
RUN apt-get install -y sudo vim curl less git python-dev python3.5
# Add WP-CLI
RUN curl -o /bin/wp-cli.phar https://raw.githubusercontent.com/wp-cli/builds/gh-pages/phar/wp-cli.phar
COPY wp-su.sh /bin/wp
RUN chmod +x /bin/wp-cli.phar /bin/wp && chown www-data:www-data /bin/wp-cli.phar /bin/wp
# Copy scripts into the image
COPY install.py /usr/src/wordpress
COPY plugins.json /usr/src/wordpress
COPY wait-for-it.sh /usr/src/wordpress
RUN chmod +x /usr/src/wordpress/install.py
RUN chmod +x /usr/src/wordpress/plugins.json
RUN chmod +x /usr/src/wordpress/wait-for-it.sh
COPY --chown=www-data:www-data uploads/ /usr/src/wordpress/wp-content/uploads
# Cleanup
RUN apt-get clean
RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ENTRYPOINT ["/usr/src/wordpress/wait-for-it.sh", "db:3306", "--", "python" , "/usr/src/wordpress/install.py" ]
CMD ["apache2-foreground"]
Once the scripts runs I get the following error:
Error: This does not seem to be a WordPress installation.
Pass --path=`path/to/wordpress` or run `wp core download`.
I tried doing what the error suggested but it did not work. The wordpress installation from my understanding should be located at /usr/src/wordpress along with all the scripts I copied into it. Is what I'm doing correct ? Should it even be possible to do what I'm attempting ? Any help would be appreciated.
Note: This image is run from docker-compose.yml
UPDATE:
Looks to me like the reason for the above error is because the wordpress installation isn't there yet and by specifying the entrypoint I think I'm overwriting the entry point that is provided by the official wp image in which wordpress installation is copied into /var/www/html directory at runtime. Not sure how to get around this.
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 wanted to have a Widget to view and edit the time range from within dashboards of kibana. So after lot of research i found a plugin as Kibana-time-plugin. Ref: https://github.com/nreese/kibana-time-plugin
Currently i am using kibana 5.4.0 in my local. After installing the plugin i have tried "bower install" as per the command specified in git page. But getting an error as :-
$ bower install
/usr/bin/env: ‘node’: No such file or directory
And even if Kibana is not running and giving an error as below attached image:-
kibana5.4.0
Can anyone Guide me on this ?
Thanks in Advance !!!!!!!!!!!!!!!
I think the optimization failures may be due to file permissions, the plugin files need to be accessible by the kibana user. Specifically check this instruction:
Installing plugins with linux packages
Here is a complete script that worked for me. I am new to Kibana and Kibana plugins so any feedback appreciated. Two important notes:
1) I am pulling the zip file from S3 so you will need to edit that.
2) Be sure to restart kibana afterwards and check the logs
#!/bin/bash
# install nodejs and npm
sudo curl --silent --location https://rpm.nodesource.com/setup_6.x | sudo bash -
sudo yum install -y nodejs
sudo npm install -g bower
# copy the plugin zip and unzip it and fix the name
cd /usr/share/kibana/plugins
sudo aws s3 cp s3://<YOUR-BUCKET>/kibana-time-plugin-master.zip .
sudo unzip kibana-time-plugin-master.zip
sudo mv kibana-time-plugin-master kibana-time-plugin
# install the plugin
cd /usr/share/kibana/plugins/kibana-time-plugin
sudo sed -i -e 's/5.0.0/5.4.2/' package.json
sudo chown -R kibana:kibana *
sudo mkdir -p /home/kibana
sudo chown -R kibana:kibana /home/kibana
sudo -u kibana bower install
I'm migrating my standard environment app to flexible environment in GAE and facing issues.
app.yaml snippet
runtime: custom
env: flex
api_version: 1
threadsafe: true
handlers:
- url: /.*
script: main.app
Dockerfile
FROM gcr.io/google_appengine/python-compat-multicore
RUN apt-get update -y
RUN apt-get install -y python-pip build-essential libssl-dev libffi-dev python-dev libxml2-dev libxslt1-dev xmlsec1
RUN apt-get install -y curl unzip
RUN curl https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz > /tmp/google-cloud-sdk.tar.gz
RUN mkdir -p /usr/local/gcloud
RUN tar -C /usr/local/gcloud -xvf /tmp/google-cloud-sdk.tar.gz
RUN /usr/local/gcloud/google-cloud-sdk/install.sh
RUN curl https://storage.googleapis.com/appengine-sdks/featured/google_appengine_1.9.40.zip > /tmp/google_appengine_1.9.40.zip
RUN unzip /tmp/google_appengine_1.9.40.zip -d /usr/local/gae
ENV PATH $PATH:/usr/local/gcloud/google-cloud-sdk/bin
ENV PATH $PATH:/usr/local/gae/google_appengine/
COPY . /app
WORKDIR /app
ENV MODULE_YAML_PATH app.yaml
RUN pip install -r requirements.txt
issue while running gcloud app deploy(stack trace)
File "/env/local/lib/python2.7/site-packages/google/appengine/ext/vmruntime/vmconfig.py", line 63, in BuildVmAppengineEnvConfig
escaped_appid = appid.replace(':', '_').replace('.', '_')
AttributeError: 'NoneType' object has no attribute 'replace'
Is there anything which I'm missing in dockerfile? What are the other configuration changes which should be done such that there is not much application level code changes. Is it advidsable to use webapp2 in flexible environment
We're working on a better error message, but this is happening because you're trying to use the python-compat-multicore runtime. That runtime is not supported on env:flex, and has been deprecated. We're asking folks to follow this guide to upgrade to runtime:python:
https://cloud.google.com/appengine/docs/flexible/python/migrating
I am looking into docker to distribute a shiny application that also requires RStudio. The primary goal is easy installation at hospitals under Windows. Everything that requires character input into black boxes will certainly fail during installation by non-IT people.
My previous attempts used vagrant, but installing vagrant alone proved to be a hurdle.
The rocker repository, has an RStudio and a Shiny , and for my own installation both work together. However, I would like to create a combined application for easier installation.
What is the recommended workflow? Start with RStudio, and manually add Shiny?
Or merge the dockerfiles code from both Rockers, starting with r-base? Or use compose tool?
The point of Docker, in general, is isolation of services so that they can be updated/changed without effecting others. My recommendation would be to use docker-compose, instead. Below is an example docker-compose yaml file that serves both rstudio and shiny on the same server at different subdomains using the incredibly useful docker-gen by Jason Wilder. All R docker images used below are courtesy of Rocker or more directly Rocker Docker Hub. These are very very reliable because, well, Dirk Eddelbeutel and Carl Boettiger made them. In this example I've also included some options for RStudio such as setting a user/pass and whether or not the user has root access. There are more instructions on using the Rocker RStudio image available on this wiki page:
Change the following:
your_user to your username on the server
SOME_USER to your desired RStudio username
SOME_PASS to your desired Rstudio password
*.DOMAIN.tld to your domain, don't forget to add A records for your subdomains.
nginx1:
image: nginx
container_name: nginx
ports:
- "80:80"
- "443:443"
volumes:
- /etc/nginx/conf.d
- /etc/nginx/vhost.d
- /usr/share/nginx/html
- /home/your_user/services/volumes/proxy/certs:/etc/nginx/certs:ro
nginx-gen:
links:
- "nginx1"
image: jwilder/docker-gen
container_name: nginx-gen
volumes:
- /var/run/docker.sock:/tmp/docker.sock:ro
- /home/your_user/services/volumes/proxy/templates/nginx.tmpl:/etc/docker-gen/templates/nginx.tmpl:ro
volumes_from:
- nginx1
entrypoint: /usr/local/bin/docker-gen -notify-sighup nginx -watch -only-exposed -wait 5s:30s /etc/docker-gen/templates/nginx.tmpl /etc/nginx/conf.d/default.conf
rstudio:
links:
- "nginx1"
image: rocker/hadleyverse
container_name: rstudio
ports:
- "8787:8787"
environment:
- VIRTUAL_PORT=8787
- ROOT=TRUE
- VIRTUAL_HOST=rstudio.DOMAIN.tld
- USER=SOME_USER
- PASSWORD=SOME_PASS
shiny:
links:
- "nginx1"
image: rocker/shiny
container_name: shiny
environment:
- VIRTUAL_HOST=shiny.DOMAIN.tld
volumes:
- /home/your_user/services/volumes/shiny/apps:/srv/shiny-server/
- /home/your_user/services/volumes/shiny/logs:/var/log/
- /home/your_user/services/volumes/shiny/packages:/home/shiny/
It's trivial to add more services like a blog, for example, just follow the pattern or search the internet for a docker-compose version of your service and add it.
Interesting question, but I'm not sure I understand the advantage of having the shiny-server and the rstudio-server instances served from the same container.
Is the purpose so that the two containers share the same R libraries (e.g. so a package doesn't need to be installed separately on each) or merely to have one docker container instead of two? Just having to run two docker commands instead of one doesn't seem that onerous, but maybe I'm underestimating.
Sharing the underlying libraries seems like a valid objective though, and I don't think there's an ideal solution available yet.
I feel the most docker-esque solution would be to do this via container orchestration/compose tool as you mention. This is the usual way to combine separate services (e.g. web server and database) without building one on top of the other.
Unfortunately, the tooling for orchestration based on mapping volumes is not nearly as well developed as it is for mapping ports.
Imagine running the rstudio as a volume container:
docker run --name rstudio -v /usr/local/lib/R/site.library rocker/rstudio true
(If you wanted RStudio access at the same time, one could instead run this as:)
docker run --name rstudio -dP -v /usr/local/lib/R/site.library rocker/rstudio
You can then use the the site.library from the rstudio container in place of that on the shiny container with a command like:
docker run --volumes-from rstudio -dP rocker/shiny
Unfortunately, this clobbers the site.library of the shiny container. To work around this, you'd want to mount the library of the rstudio container in a different place, but there's no easy syntax for this like we already have with port links. It can be done though, see:
How to map volume paths using Docker's --volumes-from?
There's an open thread on this issue in the rocker repo too.
I have developed a working single docker for
R
RStudio (server)
Shiny Server (free edition)
I built it exactly for the same reasons mentioned by #Dieter Menne. It may be not ideal for ops, but it great for dev (especially if the team members all use different envs. like mac, windows etc.).
It is on Centos 6 as this is the env. I use at work.
This is the dockerfile:
FROM centos:centos6.7
MAINTAINER enzo smartinsightsfromdata
RUN yum -y install epel-release
RUN yum update -y && yum clean all
# RUN yum reinstall -y glibc-common
RUN yum install -y locales java-1.7.0-openjdk-devel tar
# Misc packages
RUN yum groupinstall -y "Development Tools"
# R devtools pre-requisites:
RUN yum install -y wget git xml2 libxml2-devel curl curl-devel openssl-devel
WORKDIR /home/root
RUN yum install -y R
RUN wget http://cran.r-project.org/src/contrib/rJava_0.9-7.tar.gz
RUN R CMD INSTALL rJava_0.9-7.tar.gz
RUN R CMD javareconf \
&& rm -rf rJava_0.9-7.tar.gz
#-----------------------
# Add RStudio binaries to PATH
# export PATH="/usr/lib/rstudio-server/bin/:$PATH"
ENV PATH /usr/lib/rstudio-server/bin/:$PATH
ENV LANG en_US.UTF-8
RUN yum install -y openssl098e supervisor passwd pandoc
# RUN wget http://download2.rstudio.org/rstudio-server-rhel-0.99.484-x86_64.rpm
# Go for the bleading edge:
RUN wget https://s3.amazonaws.com/rstudio-dailybuilds/rstudio-server-rhel-0.99.697-x86_64.rpm
RUN yum -y install --nogpgcheck rstudio-server-rhel-0.99.697-x86_64.rpm \
&& rm -rf rstudio-server-rhel-0.99.484-x86_64.rpm
RUN groupadd rstudio \
&& useradd -g rstudio rstudio \
&& echo rstudio | passwd rstudio --stdin
RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='http://cran.r-project.org', INSTALL_opts='--no-html')"
RUN wget https://download3.rstudio.org/centos5.9/x86_64/shiny-server-1.4.0.756-rh5-x86_64.rpm
RUN yum -y install --nogpgcheck shiny-server-1.4.0.756-rh5-x86_64.rpm \
&& rm -rf shiny-server-1.4.0.756-rh5-x86_64.rpm
RUN mkdir -p /var/log/shiny-server \
&& chown shiny:shiny /var/log/shiny-server \
&& chown shiny:shiny -R /srv/shiny-server \
&& chmod 777 -R /srv/shiny-server \
&& chown shiny:shiny -R /opt/shiny-server/samples/sample-apps \
&& chmod 777 -R /opt/shiny-server/samples/sample-apps
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
RUN mkdir -p /var/log/supervisor \
&& chmod 777 -R /var/log/supervisor
EXPOSE 8787 3838
CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]
This is how the supervisord.conf file looks like:
[supervisord]
nodaemon=true
logfile=/var/log/supervisor/supervisord.log
pidfile = /tmp/supervisord.pid
[program:rserver]
user=root
command=/usr/lib/rstudio-server/bin/rserver
stdout_logfile=/var/log/supervisor/%(program_name)s.log
stderr_logfile=/var/log/supervisor/%(program_name)s.log
startsecs=0
autorestart=false
[program:shinyserver]
user=root
command=/usr/bin/shiny-server
stdout_logfile=/var/log/supervisor/%(program_name)s.log
stderr_logfile=/var/log/supervisor/%(program_name)s.log
autorestart=false
It is available at my github page: smartinsightsfromdata
I have also developed a working docker for shiny server pro on centos (using shiny server pro temporary edition, valid 45 days only).
Somewhat unfortunately, there is no definite answer, it all depends on how much reusability you would be looking for and whether an upstream base image is well maintained. The is also images size tradeoff, more layers there are, bigger the resulting image gets.