recipe bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.

Homepage:

https://github.com/oschwengers/bakta

Documentation:

https://github.com/oschwengers/bakta/blob/v1.11.0/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/bakta/meta.yaml

Links:

biotools: bakta, usegalaxy-eu: bakta, doi: 10.1099/mgen.0.000685, doi: 10.5281/zenodo.4247252

package bakta

versions:

1.11.0-0,  1.10.4-1,  1.10.4-0,  1.10.3-0,  1.10.2-0,  1.10.1-0,  1.10.0-0,  1.9.4-0,  1.9.3-0, 

1.11.0-0,  1.10.4-1,  1.10.4-0,  1.10.3-0,  1.10.2-0,  1.10.1-0,  1.10.0-0,  1.9.4-0,  1.9.3-0,  1.9.2-1,  1.9.2-0,  1.9.1-0,  1.9.0-0,  1.8.2-1,  1.8.2-0,  1.8.1-0,  1.8.0-0,  1.7.0-1,  1.7.0-0,  1.6.1-0,  1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.2-0,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.3-0,  1.3.1-0,  1.3.0-0,  1.2.4-1,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.1-0,  1.1-0,  1.0.4-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0-0,  0.5-0,  0.4-0,  0.3.2-0,  0.3.1-0,  0.3-0

depends alive-progress:

3.0.1

depends aragorn:

>=1.2.41

depends biopython:

>=1.78

depends blast:

>=2.14.0

depends diamond:

>=2.1.10

depends infernal:

>=1.1.4

depends ncbi-amrfinderplus:

>=4.0.3

depends piler-cr:

depends pycirclize:

>=1.7.0

depends pyhmmer:

>=0.10.15

depends pyrodigal:

>=3.5.0

depends python:

>=3.9,<3.12

depends pyyaml:

>=6.0

depends requests:

>=2.25.1

depends trnascan-se:

>=2.0.11

depends xopen:

>=1.5.0

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 bakta

and update with::

   mamba update bakta

To create a new environment, run:

mamba create --name myenvname bakta

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/bakta:<tag>

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

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