- recipe etoki
EToKi (Enterobase Tool Kit) includes methods related to Enterobase data analysis pipelines
- Homepage:
- License:
GPL3 / GNU General Public v3 (GPLv3)
- Recipe:
- package etoki¶
- versions:
1.2.3-0- 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:
1.21.6.*- depends pandas:
- depends perl-lyve-set:
- depends piler-cr:
- depends pilon:
- depends psutil:
- depends python:
>=3.6- depends rapidnj:
- depends raxml:
- depends raxml-ng:
- depends samtools:
- depends scikit-learn:
- depends scipy:
- depends simbac:
- depends spades:
>=3.15- depends trf:
- 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 etoki and update with:: mamba update etoki
To create a new environment, run:
mamba create --name myenvname etoki
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/etoki:<tag> (see `etoki/tags`_ for valid values for ``<tag>``)
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Link to this page¶
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