- 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:
on bbmap
on blast
on bowtie2
on bwa
on click
on curl
on diamond
on ete3
on fasttree
on flye
on gatk
on kraken2
on last
on megahit
on mmseqs2
on nextpolish
on numba
on numpy
1.21.6.*on pandas
on perl-lyve-set
on piler-cr
on pilon
on psutil
on python
>=3.6on rapidnj
on raxml
on raxml-ng
on samtools
on scikit-learn
on scipy
on simbac
on spades
>=3.15on trf
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install etoki
to add into an existing workspace instead, run:
pixi add etoki
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install etoki
Alternatively, to install into a new environment, run:
conda create -n envname etoki
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/etoki:<tag>
(see etoki/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/etoki/README.html)
