Package Recipe 'tn3_ta_finder'

recipe tn3_ta_finder

Tn3 transposon and type II toxin-antitoxin finder for bacterial and archaeal genomes

Homepage:: https://github.com/danillo-alvarenga/tn3-ta_finder
License:: AGPL / AGPL-3.0-or-later
Recipe:: /tn3_ta_finder/meta.yaml

Tn3+TA_finder is a program for the automatic prediction of transposable elements of the Tn3 family associated with type II toxin and antitoxin pairs in bacteria and archaea. It compares bacterial and archaeal genome sequences to custom Tn3 transposase+resolvase and type II toxin+antitoxin databases

package tn3_ta_finder¶

Versions:

1.0.1-0

Depends:

on biopython >=1.66,<1.78
on blast >=2.2.28
on prodigal >=2.6.1
on python >=3.6

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 tn3_ta_finder

to add into an existing workspace instead, run:

pixi add tn3_ta_finder

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 tn3_ta_finder

Alternatively, to install into a new environment, run:

conda create -n envname tn3_ta_finder

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/tn3_ta_finder:<tag>

(see tn3_ta_finder/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/tn3_ta_finder/README.html)