Public Repository

Last pushed: 2 years ago
Short Description
ipython notebook + IRkernel + couple of Bioconductor workflows/vignettes
Full Description

Description

The image inherits from dtenenba/jupyter to install ipython notebook, IRkernel and the required dependencies.

On Linux

After pulling the image, start ipython notebook in the container by running in bash:

sudo docker run --rm -it --net=host vladkim/jupyter ipython notebook --profile=nbserver --no-browser --ip=127.0.0.1
  1. After starting the ipython notebook, access the Jupyter directory tree by entering the following URL in your (local) browser: localhost:8888

  2. The link will lead to the Jupyter directory tree. Click on "Rnotebooks" directory and choose a notebook.

  3. You can run code blocks by executing "Shift + Enter" key combination. In most cases you will have to run blocks one after another to produce output without errors or warnings.

On Mac OS X

Open the Jupyter notebook directory tree by running the following command in Docker shell (not Mac's native bash):

docker run --rm -it --net=host vladkim/jupyter ipython notebook --profile=nbserver --no-browser --ip=192.168.99.100

Keep in mind that the --ip=192.168.99.100 is valid only, if you are using docker-machine client (i.e. if you installed Docker on your Mac following the official instructions). If you are using the deprecated boot2docker client, you have to change the IP flag to --ip=192.168.59.103

  1. After starting the ipython notebook, access the Jupyter directory tree by entering the following URL in your (local) browser: 192.168.99.100:8888

  2. The link will lead to the Jupyter directory tree. Click on "Rnotebooks" directory and choose a notebook.

  3. You can run code blocks by executing "Shift + Enter" key combination. In most cases you will have to run blocks one after another to produce output without errors or warnings.

On Windows

Start boot2docker. After the boot2docker virtual machine loaded, pull the image (the download size is about 2 GB). Upon a successful download, run the following command:

docker run --rm -it --net=host vladkim/jupyter ipython notebook --profile=nbserver --no-browser --ip=192.168.59.103

Note that 192.168.59.103 is the default IP address of boot2docker. You can query the boot2docker IP on your machine by:

boot2docker ip

If it is different from the default IP, replace 192.168.59.103 everywhere by your boot2docker IP address.

  1. After starting the ipython notebook, open the following link in your (local) browser:
    http://192.168.59.103:8888/ (or alternatively http://<your boot2docker IP>:8888)

  2. The link will lead to the Jupyter directory tree. Click on "Rnotebooks" directory and choose a notebook.

  3. You can run code blocks by executing "Shift + Enter" key combination. In most cases you will have to run blocks one after another to produce output without errors or warnings.

TO-DO: write about saving image and managing .Rdata

Docker Pull Command
Owner
vladkim

Comments (0)