recipe fargene

Fragmented Antibiotic Resistance Gene iENntifiEr takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output

Homepage:

https://github.com/fannyhb/fargene

License:

MIT

Recipe:

/fargene/meta.yaml

package fargene

versions:

0.1-4,  0.1-3,  0.1-2,  0.1-0

depends biopython:

>=1.68

depends clustalo:

depends emboss:

depends hmmer:

depends matplotlib:

depends numpy:

depends pip:

depends prodigal:

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends pyyaml:

depends seqtk:

depends spades:

depends trim-galore:

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 fargene

and update with::

   mamba update fargene

To create a new environment, run:

mamba create --name myenvname fargene

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/fargene:<tag>

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

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