- recipe panaroo
panaroo - an updated pipeline for pangenome investigation
- Homepage:
- Documentation:
https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart
- Developer docs:
- License:
MIT / MIT
- Recipe:
- package panaroo¶
- Versions:
1.6.0-0,1.5.2-0,1.5.1-0,1.5.0-0,1.4.2-0,1.4.1-0,1.4.0-0,1.3.4-0,1.3.3-0,1.6.0-0,1.5.2-0,1.5.1-0,1.5.0-0,1.4.2-0,1.4.1-0,1.4.0-0,1.3.4-0,1.3.3-0,1.3.2-0,1.3.0-0,1.2.10-0,1.2.9-0,1.2.8-0,1.2.7-0,1.2.4-0,1.2.3-0,1.2.2-1,1.2.2-0,1.2.0-0,1.1.2-0,1.1.0-0,1.0.0-0- Depends:
on biocode
on biopython
on cd-hit
on dendropy
on gffutils
on intbitset
on joblib
on mafft
on mash
on matplotlib-base
on networkx
on numba
on numpy
on plotly
on prank
on prokka
on python
>=3.6on python-edlib
on scikit-learn
on scipy
on tqdm
- 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 panaroo
to add into an existing workspace instead, run:
pixi add panaroo
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 panaroo
Alternatively, to install into a new environment, run:
conda create -n envname panaroo
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/panaroo:<tag>
(see panaroo/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/panaroo/README.html)
