Package Recipe 'neofox'

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:

1.2.3-0, 1.2.2-0, 1.1.0-0

Depends:

on betterproto >=1.2.5,<1.3.0
on biopython >1.80
on blast
on dask >=2024.0.0,<=2024.6.3
on distributed >=2024.0.0,<=2024.6.2
on faker >=13.13.0,<13.14.0
on logzero >=1.5.0
on mock >=4.0.3,<4.1.0
on numpy >=1.24,<1.27
on pandas >=2.1,<2.3
on poetry 1.8.2
on pysam >0.20
on python 3.11
on python-dotenv >=0.12.0,<0.13.0
on scipy >=1.10.0
on xmltodict >=0.12.0,<0.13.0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install neofox

to add into an existing workspace instead, run:

pixi add neofox

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install neofox

Alternatively, to install into a new environment, run:

conda create -n envname neofox

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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

Download stats¶

Link to this page¶

Render an 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/neofox/README.html)