MHC-Annotation 0.0.2

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MHC-annotation

Tools to annotate haplotypes of MHC with gene and transcript information

Dependencies

There is only a few dependencies which you have to take care of yourself.

conda environment

The easiest way to take of these dependencies is to utilize the environment.yml in this repository to create a conda environment. conda create --name mhca -f environment_mhca.yml

manually

The script assumes that you have minimap2 installed and that it is callable with minimap2 on the command line. There are several ways to install this dependency depending on your environment. Giving two examples:

• sudo apt-get install minimap2
• conda install -c bioconda minimap2

You will also need the python packages biopython and bcbio-gff. You can install them in a conda environment with:

• conda install -c bioconda bcbio-gff
• conda install -c bioconda biopython

Install

Install this package with pip.

pip install MHC-annotation