Ubuntu 18.04 with bismark installed

The image contains a full install of bismark, including all necessary dependencies. I am not part of the bismark team - I just made this image.

In detail, the image is set up with:

• Ubuntu 18.04
• samtools v1.9.0
• bowtie v2.3.5
• bismark v0.21.0

To run bismark you can do the following (this will mount the directory /in of the container to the current working directory on your local machine, and allow you to access files in this directory and any sub-directories):

$ docker run --rm -v $(pwd):/home/in -w /in chrishah/bismark:v0.21.0 bismark

You can also enter the container environment and work within it. All executables should be in the PATH.

$ docker run -it --rm -v $(pwd):/in -w /in chrishah/bismark:v0.21.0 /bin/bash