- recipe wgfast
The whole genome focused array SNP typing (WG-FAST) pipeline
- Homepage:
- License:
GPL / GPL v3
- Recipe:
- package wgfast¶
- Versions:
1.0.4-0,1.0.3-2,1.0.3-1,1.0.3-0- Depends:
on bbmap
on biopython
on bwa
on click
on dendropy
on ete3
on logbook
on mash
on nasp
on ncbitk
on pandas
on pathos
on picard
on python
>=3on qt
on raxml
on retrying
on samtools
on snakemake
>=5
- 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 wgfast
to add into an existing workspace instead, run:
pixi add wgfast
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 wgfast
Alternatively, to install into a new environment, run:
conda create -n envname wgfast
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/wgfast:<tag>
(see wgfast/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/wgfast/README.html)
