Public | Automated Build

Last pushed: 7 months ago
Short Description
Docker RStudio container for use in Galaxy as a new interactive environment.
Full Description

Docker RStudio Container

RStudio running in a docker container. This image can be used to integrate RStudio into Galaxy.
A variety of different packages are pre-installed and can be used right away.

This docker container is used by the Galaxy-RStudio project.

Usage

  • Build your own image and run it

    Docker is a pre-requirement for this project. You can build the container with:

    $ docker build -t rstudio-notebook .
    

    The build process can take some time, but if finished you can run your container with:

    $ docker run -p 8787:8787 -v /home/user/foo/:/import/ -t rstudio-notebook
    

    and you will have a running RStudio instance on http://localhost:8787/.

  • Run a pre-built image from the docker registry

    $ docker run -p 8787:8787 -v `pwd`/foo:/import erasche/docker-rstudio-notebook
    

Environment Variables

Several environment variables are available by default, per IE rough standards

Build-Time Variables

Variable Use
RSTUDIO_FULL Build RStudio with the full complement of Bio packages (warning, slow)

Run-Time Variables

Variable Use
GALAXY_WEB_PORT Port on which Galaxy is running, if applicable
CORS_ORIGIN If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
DOCKER_PORT Used in Galaxy Interactive Environments to ensure that proxy routes are unique and accessible
API_KEY Galaxy API Key with which to interface with Galaxy
HISTORY_ID ID of current Galaxy History, used in easing the dataset upload/download process
REMOTE_HOST Unused
GALAXY_URL URL at which Galaxy is accessible
DEBUG Enable debugging mode, mostly for developers

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

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Owner
erasche
Source Repository