recipe mhcnuggets

MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II

Homepage:

http://karchinlab.org/apps/mhcnuggets.html

License:

APACHE / Apache License

Recipe:

/mhcnuggets/meta.yaml

# MHCnuggets

Welcome to MHCnuggets! Presumably you're here to do some peptide-MHC prediction and not because you were [hungry](https://www.mcdonalds.com/us/en-us/product/chicken-mcnuggets-4-piece.html).

### Usage ### For an overview of how to use MHCnuggets please refer to the Jupyter notebook called `user_guide.ipynb` in the repository

### Installation ###

MHCnuggets is `pip` installable as: ```bash pip install mhcnuggets ```

**Required pacakges:**

* numpy * scipy * scikit-learn * tensorflow * keras

You might want to check if the Keras backend is configured to use the Tensforflow backend.

package mhcnuggets

(downloads) docker_mhcnuggets

versions:

2.4.1-0,  2.4.0-0,  2.3.2-0,  2.3.1-0,  2.2-0

depends keras:

depends numpy:

depends pandas:

depends python:

3.6.*

depends scikit-learn:

depends scipy:

depends tensorflow:

depends varcode:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install mhcnuggets

and update with::

   mamba update mhcnuggets

To create a new environment, run:

mamba create --name myenvname mhcnuggets

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/mhcnuggets:<tag>

(see `mhcnuggets/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mhcnuggets/README.html)