Package Recipe 'panacota'

recipe panacota

Large scale comparative genomics tools: annotate genomes, do pangenome, core/persistent genome, align core/persistent families, infer phylogenetic tree.

Homepage:: https://github.com/gem-pasteur/PanACoTA
Documentation:: https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/
License:: AGPL / GNU Affero General Public v3
Recipe:: /panacota/meta.yaml

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:

on biopython >=1.60
on colorlog
on fastme
on fasttree >=2.1.10
on iqtree >=1.6.12
on mafft
on mash
on matplotlib-base >=2.0.0
on mmseqs2
on ncbi-genome-download >=0.3.0
on numpy >=1.11
on prodigal >=2.6.2
on progressbar2 >=3.18.0
on prokka 1.14.5
on python >=3.6
on quicktree
on scipy
on termcolor

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 panacota

to add into an existing workspace instead, run:

pixi add panacota

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 panacota

Alternatively, to install into a new environment, run:

conda create -n envname panacota

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/panacota:<tag>

(see panacota/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/panacota/README.html)