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