crukcibioinformatics/crossmap repository overview

⁠CrossMap Docker image

Dockerfile used to create a Docker image for converting genome coordinates between different assemblies using CrossMap⁠.

⁠Building the Docker image

To build the Docker image run the following command within the directory containing the Dockerfile:

docker build --tag="crukcibioinformatics/crossmap" .

⁠Obtaining a pre-built image

Alternatively, a pre-built image can be obtained from Docker Hub⁠ as follows:

docker pull crukcibioinformatics/crossmap

⁠Usage

To show the usage instructions for CrossMap:

docker run --rm crukcibioinformatics/crossmap CrossMap.py

The following shows how to convert a set of intevals in a BED format file from the mm9 mouse assembly to mm10 using a chain file obtained from UCSC⁠.

docker run --rm -v ${PWD}:/work -w /work crukcibioinformatics/crossmap CrossMap.py bed mm9ToMm10.over.chain.gz targets.mm9.bed targets.mm10.bed