Package Recipe 'tafinder3d'

recipe tafinder3d

Toxin-antitoxin system identification with 3D structure-based searching

Homepage:: https://github.com/schmigle/TAfinder3D
License:: MIT
Recipe:: /tafinder3d/meta.yaml

TAfinder3D identifies Types I-VIII toxin-antitoxin loci in bacterial genomes using sequence homology (MMseqs2), domain detection (HMMER), and 3D structure-based searching (Foldseek with GPU acceleration).

package tafinder3d¶

Versions:

1.0.7-0

Depends:

on biopython
on foldseek
on hmmer >=3.4
on mmseqs2
on numpy >=2.0
on pandas >=2.0
on prodigal >=2.6
on prodigal-gv
on protobuf
on python >=3.9,<3.13
on pytorch
on sentencepiece
on transformers

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 tafinder3d

to add into an existing workspace instead, run:

pixi add tafinder3d

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 tafinder3d

Alternatively, to install into a new environment, run:

conda create -n envname tafinder3d

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/tafinder3d:<tag>

(see tafinder3d/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.

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/tafinder3d/README.html)