recipe orthologer

Ortholog detection for comparative genomics and fast functional annotation behind OrthoDB and BUSCO.

Homepage:

https://orthologer.ezlab.org

Documentation:

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

Developer docs:

https://gitlab.com/ezlab/orthologer_container

License:

GPL3 / GPL-3.0-or-later

Recipe:

/orthologer/meta.yaml

Links:

biotools: orthologer, doi: 10.1093/nar/gkae987, PMID: 39535043

Ortholog detection for comparative genomics and fast functional annotation behind OrthoDB and BUSCO.

package orthologer

(downloads) docker_orthologer

versions:

3.7.1-03.5.0-13.5.0-03.4.2-03.4.1-03.4.0-03.3.2-03.3.1-0

depends _openmp_mutex:

>=4.5

depends bash:

>=4.1

depends biopython:

depends blast:

depends boost-cpp:

depends busco:

>=5.7.0

depends cd-hit:

depends diamond:

depends ete3:

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends mmseqs2:

depends numpy:

depends python:

>=3.11,<3.12.0a0

depends python_abi:

3.11.* *_cp311

depends rsync:

depends spdlog:

>=1.12.0,<1.13.0a0

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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