recipe bactopia

Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

Homepage:

https://bactopia.github.io/

Developer docs:

https://github.com/bactopia/bactopia/

License:

MIT

Recipe:

/bactopia/meta.yaml

Links:

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

package bactopia

versions:

3.2.0-0,  3.1.0-0,  3.0.1-1,  3.0.1-0,  3.0.0-0,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.3-0, 

3.2.0-0,  3.1.0-0,  3.0.1-1,  3.0.1-0,  3.0.0-0,  2.2.0-0,  2.1.1-0,  2.1.0-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.7.1-0,  1.7.0-0,  1.6.5-1,  1.6.5-0,  1.6.4-0,  1.6.3-0,  1.6.2-2,  1.6.2-1,  1.6.2-0,  1.6.1-0,  1.6.0-1,  1.6.0-0,  1.5.6-0,  1.5.5-0,  1.5.4-1,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.11-1,  1.4.11-0,  1.4.10-0,  1.4.9-0,  1.4.8-0,  1.4.7-0,  1.4.6-0,  1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.2.4-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.1-0

depends bactopia-py:

1.5.0.*

depends conda:

>=22.11.0

depends coreutils:

depends mamba:

>=1.1.0

depends nextflow:

>=23,<24

depends python:

>=3.9,<3.13

depends sed:

depends wget:

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 bactopia

and update with::

   mamba update bactopia

To create a new environment, run:

mamba create --name myenvname bactopia

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:<tag>

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

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