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 biopython:

>=1.66,<1.78

depends blast:

>=2.2.28

depends prodigal:

>=2.6.1

depends python:

>=3.6

requirements:

additional platforms:

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 tn3_ta_finder

and update with::

   mamba update tn3_ta_finder

To create a new environment, run:

mamba create --name myenvname tn3_ta_finder

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/tn3_ta_finder:<tag>

(see `tn3_ta_finder/tags`_ for valid values for ``<tag>``)

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