recipe etoki

EToKi (Enterobase Tool Kit) includes methods related to Enterobase data analysis pipelines



GPL3 / GNU General Public v3 (GPLv3)



package etoki

(downloads) docker_etoki



depends bbmap:

depends blast:

depends bowtie2:

depends bwa:

depends click:

depends curl:

depends diamond:

depends ete3:

depends fasttree:

depends flye:

depends gatk:

depends kraken2:

depends last:

depends megahit:

depends mmseqs2:

depends nextpolish:

depends numba:

depends numpy:


depends pandas:

depends perl-lyve-set:

depends piler-cr:

depends pilon:

depends psutil:

depends python:


depends rapidnj:

depends raxml:

depends raxml-ng:

depends samtools:

depends scikit-learn:

depends scipy:

depends simbac:

depends spades:


depends trf:



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 etoki

and update with::

   mamba update etoki

To create a new environment, run:

mamba create --name myenvname etoki

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<tag>

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

Download stats