- recipe panaroo
panaroo - an updated pipeline for pangenome investigation
- Homepage:
- Documentation:
https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart
- License:
MIT / MIT
- Recipe:
- package panaroo¶
- versions:
1.5.1-0,1.5.0-0,1.4.2-0,1.4.1-0,1.4.0-0,1.3.4-0,1.3.3-0,1.3.2-0,1.3.0-0,1.5.1-0,1.5.0-0,1.4.2-0,1.4.1-0,1.4.0-0,1.3.4-0,1.3.3-0,1.3.2-0,1.3.0-0,1.2.10-0,1.2.9-0,1.2.8-0,1.2.7-0,1.2.4-0,1.2.3-0,1.2.2-1,1.2.2-0,1.2.0-0,1.1.2-0,1.1.0-0,1.0.0-0- depends biocode:
- depends biopython:
- depends cd-hit:
- depends dendropy:
- depends gffutils:
- depends intbitset:
- depends joblib:
- depends mafft:
- depends mash:
- depends matplotlib-base:
- depends mkl:
- depends networkx:
- depends numba:
- depends numpy:
- depends plotly:
- depends prank:
- depends prokka:
- depends python:
>=3.6- depends python-edlib:
- depends scikit-learn:
- depends scipy:
- depends tqdm:
- requirements:
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 panaroo and update with:: mamba update panaroo
To create a new environment, run:
mamba create --name myenvname panaroo
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/panaroo:<tag> (see `panaroo/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/panaroo/README.html)
