recipe neofox

Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descriptors

Homepage:

https://github.com/tron-bioinformatics/neofox

Documentation:

https://neofox.readthedocs.io/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/neofox/meta.yaml

Links:

doi: 10.1093/bioinformatics/btab344

package neofox

versions:

1.2.2-0,  1.1.0-0

depends betterproto:

>=1.2.5,<1.3.0

depends biopython:

>1.80

depends blast:

depends dask:

>=2024.0.0,<=2024.6.3

depends distributed:

>=2024.0.0,<=2024.6.2

depends faker:

>=13.13.0,<13.14.0

depends logzero:

>=1.5.0

depends mock:

>=4.0.3,<4.1.0

depends numpy:

>=1.24,<1.27

depends pandas:

>=2.1,<2.3

depends poetry:

1.8.2

depends pysam:

>0.20

depends python:

3.11

depends python-dotenv:

>=0.12.0,<0.13.0

depends scipy:

>=1.10.0

depends xmltodict:

>=0.12.0,<0.13.0

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 neofox

and update with::

   mamba update neofox

To create a new environment, run:

mamba create --name myenvname neofox

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/neofox:<tag>

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

Notes

NeoFox has some required and optional third party dependencies that have a non commercial use license. These dependencies can be installed following the guidelines here https://neofox.readthedocs.io/en/latest/02_installation.html#step-by-step-guide-without-docker. Furthermore, NeoFox requires to install some reference data, the installation process is described here https://neofox.readthedocs.io/en/latest/02_installation.html#configuration-of-the-reference-folder

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