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README.md

Official MACS2 v2.1.2 docker

MACS2 is a bioinformatics algorithm to analyze ChIP-seq datasets.

Get Started

Pull the image

Currently, there are two types of MACS2 images, one based on official Python2.7 docker image, and the other based on official Python2.7-slim docker image. Only if space is a concern, and you keep using Python2.7-slim docker for all the Python 2.7 applications, pull the slim one.

To pull the regular MACS2 image:

docker pull fooliu/macs2

To pull the MACS2 image based on Python2.7-slim

docker pull fooliu/macs2:py27-slim

Analyze your data

Example of analyzing ChIP-seq data in the CURRENT directory

Let's assume you pulled the regular MACS2 image. If not, change the image name accordingly. First, cd to the working directory containing ChIP-seq alignment files such as chip-seq-file.bam and control-seq-file.bam. Then

docker run -v $PWD:/data/ fooliu/macs2 callpeak -t /data/chip-seq-file.bam -c /data/control-seq-file.bam -n test-run --outdir /data/

The first part -v $PWD:/data/ will mount the CURRENT directory $PWD to /data/ in the container, so please don't forget to add /data/ to the path of input files with -t and/or -c, and don't forget to set the --outdir option to /data/. The final outputs will be directly written into the CURRENT directory. Extra MACS2 options can be modified or added after docker run -v $PWD:/data/ fooliu/macs2. The ENTRYPOINT (or the default command when run the container) has been set as macs2.

Built with

  • Python2.7 docker image 2.7.15
  • pip install numpy version 1.15.4
  • pip install MACS2 version 2.1.2

Author

This Docker image is maintained and uploaded by Tao Liu [email protected]. MACS2 is actively maintained on Github, many users contribute codes and suggestions.