recipe orthologer

Establish orthology among fasta files.

Homepage:

https://orthologer.ezlab.org

Documentation:

https://orthologer.ezlab.org/#on-orthodb-data

Developer docs:

https://gitlab.com/ezlab/orthologer_container

License:

GPL3 / GPL3

Recipe:

/orthologer/meta.yaml

Links:

biotools: orthologer, doi: 10.1093/nar/gkac996, PMID: 36350662

Map genes to OrthoDB as well as finding orthology among a set of fasta files.

package orthologer

(downloads) docker_orthologer

versions:

3.5.0-03.4.2-03.4.1-03.4.0-03.3.2-03.3.1-0

depends _openmp_mutex:

>=4.5

depends bash:

>=4.1

depends biopython:

depends blast:

depends busco:

>=5.7.0

depends cd-hit:

depends diamond:

depends libgcc:

>=12

depends libgomp:

depends libstdcxx:

>=12

depends mmseqs2:

depends numpy:

depends python:

>=3.4

depends rsync:

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 orthologer

and update with::

   mamba update orthologer

To create a new environment, run:

mamba create --name myenvname orthologer

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/orthologer:<tag>

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

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