recipe genomad

Identification of mobile genetic elements

Homepage:

https://portal.nersc.gov/genomad/

Developer docs:

https://github.com/apcamargo/genomad/

License:

BSD / Lawrence Berkeley National Labs BSD variant license

Recipe:

/genomad/meta.yaml

Links:

biotools: genomad

package genomad

(downloads) docker_genomad

versions:
1.8.1-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.7.6-0,  1.7.5-0,  1.7.4-0,  1.7.3-0,  1.7.2-0, 

1.8.1-0,  1.8.0-2,  1.8.0-1,  1.8.0-0,  1.7.6-0,  1.7.5-0,  1.7.4-0,  1.7.3-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.1-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.0-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.0-0

depends aragorn:

depends keras:

>=2.7,<3

depends mmseqs2:

14.7e284.*

depends numba:

>=0.57

depends numpy:

>=1.21

depends pyrodigal-gv:

>=0.3.1

depends python:

>=3.8

depends python-crfsuite:

depends rich-click:

>=1.4

depends taxopy:

>=0.4.0

depends tensorflow:

>=2.7,<2.16

depends xgboost:

>=1.6

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 genomad

and update with::

   mamba update genomad

To create a new environment, run:

mamba create --name myenvname genomad

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/genomad:<tag>

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

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