- recipe parsnp
Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.
- Homepage:
- Documentation:
https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html
- License:
custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE
- Recipe:
- package parsnp¶
- Versions:
2.1.5-0,2.1.4-0,2.1.3-0,2.1.2-0,2.1.1-1,2.1.1-0,2.0.6-0,2.0.5-0,2.0.4-0,2.1.5-0,2.1.4-0,2.1.3-0,2.1.2-0,2.1.1-1,2.1.1-0,2.0.6-0,2.0.5-0,2.0.4-0,2.0.3-0,2.0.2-1,2.0.2-0,1.7.4-2,1.7.4-1,1.7.4-0,1.7.3-0,1.7.2-0,1.7.1-1,1.7.1-0,1.7.0-0,1.6.2-1,1.6.2-0,1.6.1-1,1.6.1-0,1.6.0-0,1.5.6-1,1.5.6-0,1.5.4-1,1.5.4-0,1.5.3-0,1.5.2-1,1.5.2-0,1.5.1-0,1.5.0-4,1.5.0-3,1.5.0-2,1.5.0-1,1.5.0-0,1.2-0- Depends:
on biopython
on fastani
on fasttree
on harvesttools
on libgcc
>=13on libstdcxx
>=13on libzlib
>=1.3.1,<2.0a0on mash
on numpy
on openmp
on phipack
on pyspoa
on python
>=3.7on raxml
on tqdm
on zlib
- 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 parsnp
to add into an existing workspace instead, run:
pixi add parsnp
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 parsnp
Alternatively, to install into a new environment, run:
conda create -n envname parsnp
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/parsnp:<tag>
(see parsnp/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/parsnp/README.html)
