fooliu/macs2 repository overview

⁠Official MACS2 v2.2.7.1 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 Python3.8 docker image, and the other based on official Python3.8-slim docker image. Only if space is a concern, and you keep using Python3.8-slim docker for all the Python 3.8 applications, pull the slim one.

To pull the regular MACS2 image:

docker pull fooliu/macs2

To pull the MACS2 image based on Python3.8-slim

docker pull fooliu/macs2:py37-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

• Python3.8 docker image 3.8
• pip install numpy version 1.17, cython 0.29, and pytest 4.6
• git clone MACS codes from github master branch then run setup.py

⁠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.