- recipe panacota
Large scale comparative genomics tools: annotate genomes, do pangenome, core/persistent genome, align core/persistent families, infer phylogenetic tree.
- Homepage:
- Documentation:
https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/
- License:
AGPL / GNU Affero General Public v3
- Recipe:
- package panacota¶
- versions:
1.4.0-0,1.3.1-0,1.2.0-0,1.1.0-0,1.0.1.2-0- depends biopython:
>=1.60- depends colorlog:
- depends fastme:
- depends fasttree:
>=2.1.10- depends iqtree:
>=1.6.12- depends mafft:
- depends mash:
- depends matplotlib-base:
>=2.0.0- depends mmseqs2:
- depends ncbi-genome-download:
>=0.3.0- depends numpy:
>=1.11- depends prodigal:
>=2.6.2- depends progressbar2:
>=3.18.0- depends prokka:
1.14.5- depends python:
>=3.6- depends quicktree:
- depends scipy:
- depends termcolor:
- 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 panacota and update with:: mamba update panacota
To create a new environment, run:
mamba create --name myenvname panacota
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/panacota:<tag> (see `panacota/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/panacota/README.html)
