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Installation

Starting v0.2.0, the recommended way to install mhcflow is via PyPI:

pip install mhcflow

Note

mhcflow implicitly requires samtools, novoalign, and novoindex binaries to be available in your environment. Currently, mhcflow does not check for the presence of these binaries.

Pre-v0.2.0

Please follow the instructions below if you choose to use the v0.1.0 version.

  • Clone the v0.1.0 branch of the mhcflow repository:
git clone -b v0.1.0 https://github.com/svm-zhang/mhcflow.git

  • For those who want to build the v0.1.0 using boa: The boa project has been archived, and you might want to try its successor rattler-build. However, I was unable to build the v0.1.0 with rattler-build on both the Linux and MacOs (see here). This difficulty is the primary reason I rewrote mhcflow in Python starting with v0.2.0.

    If you manage to get rattler-build working in your environment, you will need to take the following additional steps:

    1. Update the recipe.yaml in the v0.1.0 branch to conform to the rattler-build recipe specification.
    2. Use the rattler-build command instead of boa.

  • If you continue to have trouble building mhcflow with rattler-build, please refer to the Manual section in the INSTALL.md. Additionally, see the runtime requirement section of recipe.yaml for a list of dependencies required to run v0.1.0. The dependency list is illustrated below:

  run:
    - python >=3.8
    - numpy
    - pysam
    - polars
    - tqdm
    - samtools >=1.13
    - picard
    - seqkit

Note

I will provide a Dockerfile at a later point to ease the installation process.