vladkim/rnaseq repository overview

⁠Description

The image hosts Bioconductor's RNA-seq workflow in interactive Jupyter notebook format.

⁠On Mac OS

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/rnaseq sh -c \
"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. Select "rnaseqGene.ipynb". This will open the notebook in a new tab.

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 Linux

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

sudo docker run --rm -it --net=host vladkim/rnaseq sh -c \
"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. Select "rnaseqGene.ipynb". This will open the notebook in a new tab.

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/rnaseq sh -c \
"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: 192.168.59.103:8888 (or alternatively http://<your boot2docker IP>:8888)

2. The link will lead to the Jupyter directory tree. Select "rnaseqGene.ipynb". This will open the notebook in a new tab.

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.

⁠Further Links

Base Docker image for vladkim/rnaseq⁠