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https://github.com/compdatasci/rstudio-desktop

Desktop for R-Studio
https://github.com/compdatasci/rstudio-desktop

desktop-environment docker-image jupyter-notebook rstudio

Last synced: 3 months ago
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Desktop for R-Studio

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README 

        
# Docker Image for RStudio

This Docker image provides the Ubuntu 16.04 environment with X Windows with RStudio and Jupyter Notebook. The X Windows will display in your web browser in full-screen mode. You can use this Docker image on 64-bit Linux, Mac or Windows. It allows you to use the same programming environment regardless which OS you are running on your laptop or desktop.



[![Build Status](https://travis-ci.org/compdatasci/rstudio-desktop.svg?branch=master)](https://travis-ci.org/compdatasci/rstudio-desktop) [![](https://images.microbadger.com/badges/image/compdatasci/rstudio-desktop.svg)](https://microbadger.com/images/compdatasci/rstudio-desktop)



## Preparation

Before you start, you need to first install Python and Docker on your computer by following the steps below.



### Installing Python

If you use Linux or Mac, Python is most likely already installed on your computer, so you can skip this step.



If you use Windows, you need to install Python if you have not yet done so. The easiest way is to install `Miniconda`, which you can download at https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe. During installation, make sure you check the option to make Miniconda the system's default Python.



### Installing Docker

Download the Docker Community Edition for free at https://www.docker.com/community-edition#/download and then run the installer. Note that you need administrator's privilege to install Docker. After installation, make sure you launch Docker before proceeding to the next step.



**Notes for Windows Users**

1. Docker only supports 64-bit Windows 10 Pro or higher. If you have Windows 8 or Windows 10 Home, you need to upgrade your Windows operating system before installing Docker. Stony Brook students can get Windows 10 Education free of charge at https://stonybrook.onthehub.com. Note that the older [Docker Toolbox](https://www.docker.com/products/docker-toolbox) supports older versions of Windows, but it should not be used.

2. After installing Docker, you may need to restart your computer to enable virtualization and Microsoft Hyper-V. Note that you may also need to change the BIOS of your computer to enable hardware virtualization if it was not yet enabled.

3. For security reasons, do not use Docker in the Administrator account, even if you are the sole user on the computer. For Docker version 17.06 or later, your Windows account must be a member of the local group “docker-users” for you to run Docker. To add your account to the group, you need to log into an Administrator account and run `Computer Management`. Open up `Local Users and Groups`, select `Groups`, right click on `docker-users` in the list, and then click on `Add to Group...` to add your username to the group.

4. If you previously installed VMWare or VirtualBox on your Windows computer, they might conflict with Docker. You may get an error message stating that virtualization must be enabled when starting Docker, even though virtualization was already enabled. To resolve the issue, go to Windows Features in the Control Panel, disable Hyper-V and then re-enable it.

5. When you use Docker for the first time, you must change its settings to make the C drive shared. To do this, right-click the Docker icon in the system tray, and then click on `Settings...`. Go to `Shared Drives` tab and check the C drive.

6. Docker for Windows saves the images and data volumes in a shared public folder `C:\Users\Public\Documents\Hyper-V\Virtual Hard Disks\MobyLinuxVM.vhdx`. This is a major security risk because all your images and data can be accessed and modified by other Docker users on the same computer. If you are using a shared Windows computer, make sure you create a private folder such as `C:\Users\YourUserName\Documents\Hyper-V\Virtual Hard Disks` and then go to `Advanced` tab in Docker Settings, and change the `Image and Volume VHD Location` to this folder.



**Notes for Mac Users**

1. Docker Version 17.06.0-ce [has a bug](https://github.com/docker/for-mac/issues/1809) that causes Docker to restart when your computer wakes up from sleep and when your network settings change. As a workaround, change the Proxies setting in Docker's preferences to "No Proxy".

2. On Mac, the clock in Docker would lag when your computer goes to sleep and then wakes up. You can resolve this issue either by restarting Docker after waking up or by installing [sync-docker-time](https://github.com/x11vnc/sync-docker-time).



**Notes for Linux Users**

* Most Linux distributions have a `docker` package. You can use the package installer for your system to install `docker`. Note that on some system (e.g., OpenSUSE), you may need to run the following commands to start up `docker` after installing `docker`:

```

sudo systemctl enable docker

sudo systemctl start docker

```

* After you install Docker, make sure you add yourself to the `docker` group. On Ubuntu, this is done by running the command:

```

sudo adduser $USER docker

```

On other systems, try the following command.

```

sudo usermod -G docker -a $USER 

```

After adding yourself to the `docker` group, you need to log out and log back in before you can use Docker.

## Running the Docker Image

To run the Docker image, first download the script [`rstudio_desktop.py`](https://raw.githubusercontent.com/compdatasci/rstudio-desktop/master/rstudio_desktop.py)

and save it to the working directory where you will store your codes and data. You can download the script using command line: On Windows, start `Windows PowerShell`, use the `cd` command to change to the working directory where you will store your codes and data, and then run the following command:

```

curl https://raw.githubusercontent.com/compdatasci/rstudio-desktop/master/rstudio_desktop.py -outfile rstudio_desktop.py

```

On Linux or Mac, start a terminal, use the `cd` command to change to the working directory, and then run the following command:

```

curl -s -O https://raw.githubusercontent.com/compdatasci/rstudio-desktop/master/rstudio_desktop.py

```



After downloading the script, you can start the Docker image using the command

```

python rstudio_desktop.py -p

```

This will download and run the Docker image and then launch your default web browser to show the desktop environment. The `-p` option is optional, and it instructs the Python script to pull and update the image to the latest version. The work directory by default will be mapped to the current working directory on your host.



If your source code is in a named Docker volume, e.g. `myproject`, you can mount the volume to the `~/project` directory inside the container using the command

```

python rstudio_desktop.py -v myproject

```

and the work directory will be the data volume.



For additional command-line options, use the command

```

python rstudio_desktop.py -h

```



### Running the Docker Image as Jupyter-Notebook Server

Besides using the Docker Image as an X-Windows desktop environment, you can also use it as a Jupyter-Notebook server with the

default web browser on your computer. Simply replace `rstudio_desktop.py` with `rstudio_jupyter.py` in the preceding commands. That is, on Windows run the commands

```

curl https://raw.githubusercontent.com/compdatasci/rstudio-desktop/master/rstudio_jupyter.py -outfile rstudio_jupyter.py

python rstudio_jupyter.py -p

```

or on Linux and Mac run the commands

```

curl -s -O https://raw.githubusercontent.com/compdatasci/rstudio-desktop/master/rstudio_jupyter.py

python rstudio_jupyter.py -p

```

in the directory where your Jupyter notebooks are stored.



### Running the Docker Image Offline

After you have download the Docker image using the `curl` and `python` commands above, you can run the image offline without internet connection using the following command:

```

python rstudio_desktop.py

```

or

```

python rstudio_jupyter.py

```

in the directory where you ran the `curl` command above.



### Stopping the Docker Image

To stop the Docker image, press Ctrl-C twice in the terminal (or Windows PowerShell on Windows) on your host computer where you started the Docker image, and close the tab for the desktop in your web browser.



## Entering Full-Screen Mode for Desktop Environment

For the best experience, use [VNC Viewer](http://realvnc.com/download/viewer) to connect to Docker image with the port and password displayed in the terminal output, which supports the full-screen mode. If you don't have the VNC viewer, you can

also use the full-screen mode in a web browser.



When using a web browser, we recommend *Google Chrome* or *Chromium browser*, which have the same user interface. On Windows or Linux, you can enter full-screen mode by selecting the menu `View --> "Full Screen"` Alternatively, open the Chrome menu (the three vertical dots at the top right) and select the square to the far right of the Zoom buttons (the "+" and "-" buttons). To exit the full-screen mode, press the `F11` key. On Mac, it behaves similarly except that the menu item is named `Enter Full Screen` instead of `Full Screen`, and the keyboard shortcut is `Ctrl-Cmd-f` instead of `F11`. You can also click on the green circle at the top-left corner of *Google Chrome* to enter and exit the full-screen mode. Note that in the full-screen mode, you need to disable `Always Show Toolbar in Full Screen` under the `View` menu of `Google Chrome`, and you can reveal the menu and the toolbar by sliding your mouse to the top of the display.



Alternatively, you can also use the "native" browsers on different platforms.

- On Windows, you can use the native browser *Microsoft Edge*. Toggle on and off the full-screen mode by pressing Win+Shift+Enter (hold down the Windows and Shift keys and press Enter).

- On Mac, you can use the native browser *Safari*, for which you can toggle the full-screen mode by clicking on the green circle at the top-left corner of *Safari* or selecting the `View --> "Enter Full Screen"` menu. To exit the full-screen mode, press `Ctrl-Cmd-f`, or slide your mouse to the top of the display to enable the menus.

- On Linux, the default browser *Firefox* does not hide its address bar in its native full-screen mode. You are recommended to use *Google Chrome* or *Chromium browser* instead. However, you can use *Firefox* for a full-screen viewing mode by clicking on the `Fullscreen` button in the left sidebar of Docker desktop environment. However, this is not recommended for day-to-day use, because *Firefox* would exit this full-screen mode whenever you press `Esc`, which may happen quite often.



If your Docker desktop environment started automatically in a non-recommended browser, you can copy and paste the URL into a recommended browser.

## Tips and Tricks

1. By default, Docker uses two CPU cores and 2GB of memory on Mac and Windows. If you want to run large jobs, you can increase the amount of memory or the number of cores dedicated to Docker. Just click on the Docker icon in the system tray, select `Settings` (or `Preferences` for Mac) and then select the `Advanced` tab to adjust the settings.

2. When using the Docker desktop, the files under `$HOME/.config`, `$HOME/.ssh`, , `$HOME/project`,  `$HOME/shared` and any other

directory that you might have mounted explicitly are persistent. Any change to files in other directories will be lost when the Docker container stops. Use `$HOME/.config` to store the configuration files of the desktop environment. `$HOME/shared` maps to the working directory on the host, and you are recommended to use it or a mounted project directory to store codes and data.

3. The `$HOME/.ssh` directory in the Docker container maps to the `.ssh` directory on your host computer. This is particularly convenient for you to use your ssh-keys for authentications with git repositories (such as github or bitbucket). To use your ssh keys, run the `ssh-add` in a terminal to add your keys to the ssh-agent.

4. You can copy and paste between the host and the Docker desktop through the `Clipboard` box in the left toolbar, which is synced automatically with the clipboard of the Docker desktop. To copy from the Docker desktop to the host, first, select the text in the Docker desktop, and then go to the `Clipboard` box to copy. To copy from host to the Docker desktop, first, paste the text into the `Clipboard` box, and then paste the text in the Docker desktop.

5. To stop the Docker container, do not just close the browser window, because the Docker container would still be running in the background. Instead, you can stop the container using one of the following approaches:

 - Use the `logout` button in the lower-left corner of the Docker desktop,

 - Press Ctrl-C twice in the terminal where you started the python script, or

 - Run the command `docker stop ` in a terminal on the host, and you can find the `Container ID` using the `docker ps -a` command.