recipe genefior

Genefíor: A customisable and multi-tool approach for gene detection

Homepage:

https://github.com/NickJD/Genefior

License:

GPL-3.0-only

Recipe:

/genefior/meta.yaml

Genefíor orchestrates multiple alignment tools (BLAST, DIAMOND, Bowtie2, BWA, Minimap2 and MMseqs2) to search DNA and protein sequences against AMR and user-provided databases with transparent, coverage-based validation.

package genefior

versions:

0.6.0-0

depends blast:

>=2.17.0

depends bowtie2:

>=2.5.4

depends bwa:

>=0.7.19

depends diamond:

>=2.1.13

depends minimap2:

>=2.30

depends mmseqs2:

depends python:

>=3.10

depends samtools:

>=1.19.2

depends seqtk:

>=1.4

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 genefior

and update with::

   mamba update genefior

To create a new environment, run:

mamba create --name myenvname genefior

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/genefior:<tag>

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

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