recipe bactopia-teton

Methods used by Bactopia for taxonomic classification

Homepage:

https://bactopia.github.io/

Developer docs:

https://github.com/bactopia/bactopia-teton/

License:

MIT

Recipe:

/bactopia-teton/meta.yaml

Links:

biotools: bactopia, doi: 10.1128/mSystems.00190-20

package bactopia-teton

versions:

1.1.1-0,  1.1.0-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0

depends bracken:

>=2.8

depends coreutils:

depends fastq-scan:

>=1.0.1

depends gsl:

2.6.*

depends hostile:

>=0.1.0

depends kraken2:

>=2.1.3

depends krakentools:

>=1.2

depends krona:

>=2.8.1

depends pandas:

depends pigz:

depends python:

>=3.6,<3.11

depends sed:

depends sizemeup:

>=1.2.3

depends sra-human-scrubber:

>=2.2

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 bactopia-teton

and update with::

   mamba update bactopia-teton

To create a new environment, run:

mamba create --name myenvname bactopia-teton

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/bactopia-teton:<tag>

(see `bactopia-teton/tags`_ for valid values for ``<tag>``)

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