bushlab/phaser repository overview

⁠Introduction

This container contains an installation of phASER, phASER Gene AE, phASER Annotate and phASER-POP, with Scipy, Numpy, bedtools, samtools, tabix, Cython, pysam and htslib.

This container has been built with Condaforge with the Mambaforge installer.⁠

There is also an installation of Jupyter for scientific computing.

⁠Running the container

docker run -it --rm -p 9999:9999 bushlab/phaser:latest

Once inside the container, the mamba environment needs to be activated with the command mamba activate phaser_env.

⁠References

Castel, S. E., Mohammadi, P., Chung, W. K., Shen, Y. & Lappalainen, T. Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Nat Commun 7, 12817 (2016).

phASER can be found here.⁠