There are a ton of little-upvoted questions about how to address local folders from inside a docker container, but I can't find one that quite matches mine, so here goes another one:
How can I run a docker container, and mount a local folder so that it's accessible by R/RStudio, inside the container?
That sounds kind of like: mounting local home directory in Rstudio docker? and using an approach similar to that, I can start a container and mount a volume:
docker run -d -p 8787:8787 -v $HOME/my_folder:/LOOKATMEEE -e ROOT=TRUE rocker/tidyverse:3.4
and if I run a bash shell in the container, I can see the folder:
docker exec -it 38b2d6ca427f bash
> ls
bin dev home lib LOOKATMEEE mnt proc run srv tmp var boot etc init lib64 media opt root sbin sys usr
# ^ there is is!
But if I go connect to RStudio server at localhost:8787, I don't see it in the files pane, nor does it show up when run list.files() in the R console:
I'm sure I'm missing something basic, but if someone can tell me what that is... thank you!
In this circumstance, R and RStudio have a default working directory of /home/rstudio, two levels down from /, where I was telling docker to mount the folder.
After the docker run command in the question, you can go list.files('/') to see the folder.
If you want your folder to show up in the default working directory for R, as I do, then modify docker run like this:
docker run -d -p 8787:8787 -v $HOME/my_folder:/home/rstudio/LOOKATMEEE -e ROOT=TRUE rocker/tidyverse:3.4
and there it shall be:
Thank you to user alistaire.
This answer is for future generations :)
The concept is a "match" of the resource from the host with the container:
:
The command structure should be like this:
docker run -d -e PASSWORD= -p 8787:8787 -v
: /home/rstudio/ rocker/rstudio
Check the explanation here
Related
I'm working on a read the docs documentation where I use docker. To customize it, I d like to share the css folder between the container and host, in order to avoid building always a new image to see the changes. The goal is, that I can just refresh the browser and see the changes.
I tried something like this, but it doesn't work:
docker run -v ~/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
What is wrong in this command?
The path of the folder I'd like to share is:
Documents/my-documentation/docs/source/_static/css
Thanks for your help!
I'm guessing that the ~ does not resolve correctly. The tilde character ("~") refers to the home directory of your user; usually something like /home/your_username.
In your case, it sounds like your document isn't in this directory anyway.
Try:
docker run -v Documents/my-documentation/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
I have no mac to test with, but I suspect the command should be as below (Documents is a subfolder to inside your home directory denoted by ~)
docker run -v ~/Documents/my-documentation/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
In your OP you mount the host folder ~/docs/source/_static/css, which does not make sense if your files are in Documents/my-documentation/docs/source/_static/css as that would correspond to ~/Documents/my-documentation/docs/source/_static/css
Keep in mind that Docker is still running inside a VM on Mac, so you will need to give a host path that is valid on that VM
What you can do to get a better view of the situation is to start an interactive container where you mount the root file system of the host vm root into /mnt/vm-root. That way you can see what paths are available to mount and how they should be formatted when you pass them using the -v flag to the docker run command
docker run --rm -it -w /mnt/vm-root -v /:/mnt/vm-root ubuntu:latest bash
Well, I'm new at Docker and I need to implement a Shiny app in a Docker Container.
I have the image from https://hub.docker.com/r/rocker/shiny/, that includes Shiny Server, but I don't know how to deploy my app in the server.
I want to deploy the app in the server, install the required packages for my app into the Docker, save the changes and export the image/container.
As I said, I'm new at Docker and I don't know how it really works.
Any idea?
I guess you should start by creating a Dockerfile in a specific folder which would look like something like this :
FROM rocker/shiny:latest
RUN echo 'install.packages(c("package1","package2", ...), \
repos="http://cran.us.r-project.org", \
dependencies=TRUE)' > /tmp/packages.R \
&& Rscript /tmp/packages.R
EXPOSE 3838
CMD ["/usr/bin/shiny-server.sh"]
Then go into this folder and build your image, giving it a name by using this command :
docker build -t your-tag .
Finally, once your image is built you can create a container, and if you don't forget to map the volume and the port, you should be able to find it at localhost:3838 with the following command launched from the folder containing the srv folder :
docker run --rm -p 3838:3838 -v $PWD/srv/shinyapps/:/srv/shiny-server/ -v $PWD/srv/shinylog/:/var/log/shiny-server/ your-tag
As said in the Docker documentation at the following address https://hub.docker.com/r/rocker/shiny/, you might want to launch it in detached mode with -d option and map it with your host's port 80 for a real deployment.
The link(https://hub.docker.com/r/rocker/shiny/) covers how to deploy the shiny server.
Simplest way would be:
docker run --rm -p 3838:3838 rocker/shiny
If you want to extend shiny server, you can write your own Dockerfile and start with shiny image as base image.(https://docs.docker.com/engine/reference/builder/)
Dockerfile:
FROM rocker/shiny:latest
I have a frontend-only web application hosted in Docker. The backend already exists but it has "custom IP" address, so I had to update my local /etc/hosts file to access it. So, from my local machine I am able to access the backend API without problem.
But the problem is that Docker somehow can not resolve this "custom IP", even when the host in written in the container (image?) /etc/hosts file.
When the Docker container starts up I see this error
$ docker run media-saturn:dev
2016/05/11 07:26:46 [emerg] 1#1: host not found in upstream "my-server-address.com" in /etc/nginx/sites/ms.dev.my-company.com:36
nginx: [emerg] host not found in upstream "my-server-address.com" in /etc/nginx/sites/ms.dev.my-company.com:36
I update the /etc/hosts file via command in Dockerfile, like this
# install wget
RUN apt-get update \
&& apt-get install -y wget \
&& rm -rf /var/lib/apt/lists/*
# The trick is to add the hostname on the same line as you use it, otherwise the hosts file will get reset, since every RUN command starts a new intermediate container
# it has to be https otherwise authentification is required
RUN echo "123.45.123.45 my-server-address.com" >> /etc/hosts && wget https://my-server-address.com
When I ssh into the machine to check the current content of /etc/hosts, the line "123.45.123.45 my-server-address.com" is indeed there.
Can anyone help me out with this? I am Docker newbee.
I have solved this. There are two things at play.
One is how it works locally and the other is how it works in Docker Cloud.
Local workflow
cd into root of project, where Dockerfile is located
build image: docker build -t media-saturn:dev .
run the builded image: docker run -it --add-host="my-server-address.com:123.45.123.45" -p 80:80 media-saturn:dev
Docker cloud workflow
Add extra_host directive to your Stackfile, like this
and then click Redeploy in Docker cloud, so that changes take effect
extra_hosts:
'my-server-address.com:123.45.123.45'
Optimization tip
ignore as many folders as possible to speed up process of sending data to docker deamon
add .dockerignore file
typically you want to add folders like node_modelues, bower_modules and tmp
in my case the tmp contained about 1.3GB of small files, so ignoring it sped up the process significantly
It's quite easy to mount a host directory in the docker container.
But I need the other way around.
I use a docker container as a development environment for developing WordPress plugins. This docker container contains everything needed to run WordPress (MySQL, Apache, PHP and WordPress). I mount my plugin src folder from the host in the docker container, so that I can test my plugin during development.
For debugging it would be helpful if my IDE running on the host has read access to the WordPress files in the docker container.
I found two ways to solve the problem but both seem really hacky.
Adding a data volume to the docker container, with the path to the WordPress files
docker run ... -v /usr/share/wordpress/ ...
Docker adds this directory to the path on the host /var/lib/docker/vfs/dir... But you need to look up the actual path with docker inspect and you need root access rights to see the files.
Mounting a host directory to the docker container and copying the WordPress files in the container to that mounted host directory. A symlink doesn't seem to work.
Is there a better way to do that? Without copying files or changing access rights?
Thank you!
Copying the WordPress files to the mounted folder was the solution.
I move the files in the container from the original folder to the mounted folder and use symbolic links to link them back to the original folder.
The important part is, the container can follow symbolic links in the container and but the host can't. So just using symbolic links from the original folder to the mounted folder doesn't work, because the host cannot follow symbolic links in the container!
You can share the files using smb with svendowideits samba container like this:
docker run --rm -v $(which docker):/docker -v /var/run/docker.sock:/docker.sock svendowideit/samba <container name>
It's possible to do if you use volume instead of filesystem path. It's created for you automatically, if it already doesn't exist.
docker run -d -v usr_share_wordpress:/usr/share/wordpress --name your_container ... image
After you stop or remove your container, your volume will be stored on your filesystem with files from container.
You can inspect volume content during lifetime of your_container with busybox image. Something like:
docker run -it --rm --volumes-from your_container busybox sh
After shutdown of your_container you can still check volume with:
docker run -it --rm -v usr_share_wordpress:/usr/share/wordpress busybox sh
List volumes with docker volume ls.
I had a similar need of exposing the files from container to the host. There is an open issue on this as of today. One of the work-arounds mentioned, using binds, is pretty neat; it works when the container is up and running:
container_root=$(docker inspect --format {{.State.Pid}} "$container_name")/root
sudo bindfs --map=root/"$USER" "$container_root/$app_folder" "$host_folder"
PS: I am not sure this is good for production, but it should work in development scenarios!
Why not just do: docker run ... -v /usr/share/wordpress/:/usr/share/wordpress. Now your local /usr/share/wordpress/ is mapped to /usr/share/wordpress in the Docker container and both have the same files. You could also mount elsewhere in the container this way. The syntax is host_path:container_path, so if you wanted to mount /usr/share/wordpress from your host to /my/new/path on the container, you'd just do: docker run ... -v /usr/share/wordpress/:/my/new/path.
I am a bit new to docker and I have been trying to run deploy a meteor container with my meteor application. I have been using the dockerfile and instructions from https://registry.hub.docker.com/u/golden/meteor-dev/
However, I cant run docker run -p 3000:3000 -t -i -v /path/to/meteor/app:/opt/application -w /opt/application meteor-dev because my docker (version 0.5.3) does not recognize the flag (-w) to set the working directory.
Is there some workaround to set the working directory with docker 0.5.3? The work directory is already set in the docker file, but I guess I need to set it again when I run the container.
well, my workaround was to create a bash script that would go to the working directory and call the commands one by one. I created the bash script where my source is located "/path/to/meteor/app" and call docker run -p 3000:3000 -t -i -v /path/to/meteor/app:/opt/application meteor-dev bash /opt/application/start.sh with the bash as command and my script as argument