recipe sonicparanoid

SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models

Homepage:

https://gitlab.com/salvo981/sonicparanoid2

Documentation:

https://gitlab.com/salvo981/sonicparanoid2/-/wikis/home

License:

GPL / GPL-3.0-only

Recipe:

/sonicparanoid/meta.yaml

Links:

doi: 10.1101/2023.05.14.540736, doi: 10.1093/bioinformatics/bty631, biotools: SonicParanoid

package sonicparanoid

versions:

2.0.8-0,  2.0.7-0,  1.3.8-4,  1.3.8-3,  1.3.8-2,  1.3.8-1,  1.3.8-0,  1.3.7-0,  1.3.6-1, 

2.0.8-0,  2.0.7-0,  1.3.8-4,  1.3.8-3,  1.3.8-2,  1.3.8-1,  1.3.8-0,  1.3.7-0,  1.3.6-1,  1.3.6-0,  1.0.14-4,  1.0.14-3,  1.0.14-2,  1.0.14-1,  1.0.14-0,  1.0.13-0

depends biopython:

>=1.83

depends blast:

>=2.12.0

depends diamond:

>=2.0.12

depends filetype:

>=1.2.0

depends gdown:

>=5.2.0

depends gensim:

>=4.2.0

depends libgcc-ng:

>=12

depends mcl:

>=14.137

depends mmseqs2:

>=13.45111

depends mypy:

>=1.10.0

depends numpy:

>=1.22.4,<2.0a0

depends pandas:

>=2.2.0

depends psutil:

>=6.0.0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends scikit-learn:

>=1.5.0

depends scipy:

<1.13

depends smart-open:

>=7.0.1

depends tqdm:

>=4.66.0

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 sonicparanoid

and update with::

   mamba update sonicparanoid

To create a new environment, run:

mamba create --name myenvname sonicparanoid

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/sonicparanoid:<tag>

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

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