- recipe soi
Orthology Index (OrthoIndex or OI) determines the orthology of a syntenic block.
- Homepage:
- License:
GPL / GPL-3.0-or-later
- Recipe:
- package soi¶
- versions:
1.2.3-0,1.2.0-0- depends biopython:
>=1.81- depends blast:
>=2.14.1- depends diamond:
>=2.1.8- depends drmaa:
- depends entrez-direct:
>=16.2- depends iqtree:
>=2.2.5- depends lazy-property:
>=0.0.1- depends mafft:
>=7.520- depends matplotlib-base:
- depends mcl:
>=22.282- depends mmseqs2:
>=14.7e284- depends muscle:
>=3.8.1551- depends networkx:
>=3.1- depends newick_utils:
- depends orthofinder:
>=2.5.5- depends pal2nal:
- depends pp:
>=1.6.4.4- depends psutil:
- depends python:
>=3- depends raxml-ng:
>=1.2.0- depends trimal:
- depends xopen:
>=1.1.0- 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 soi and update with:: mamba update soi
To create a new environment, run:
mamba create --name myenvname soi
with
myenvnamebeing 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/soi:<tag> (see `soi/tags`_ for valid values for ``<tag>``)
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Link to this page¶
Render an 
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[](http://bioconda.github.io/recipes/soi/README.html)
