Package Recipe 'anvio-minimal'

recipe anvio-minimal

An interactive analysis and visualization platform for omics data

Homepage:: https://merenlab.org/software/anvio/
Documentation:: https://anvio.org/learn/
Developer docs:: https://github.com/merenlab/anvio
License:: GPL3 / GPL-3.0-or-later
Recipe:: /anvio-minimal/meta.yaml
Links:: biotools: anvio, doi: 10.1038/s41564-020-00834-3

package anvio-minimal¶

Versions:

9-0, 8-0, 7.1-0, 7-0, 6.2-1, 6.2-0, 6.1-1, 6.1-0, 6-0,

9-0, 8-0, 7.1-0, 7-0, 6.2-1, 6.2-0, 6.1-1, 6.1-0, 6-0, 5.5.0-0, 5.4.0-0, 5.3.0-0, 5.2.0-1, 5.2.0-0

Depends:

on biopython
on bottle
on colored
on django
on ete3
on illumina-utils
on matplotlib-base
on mistune
on multiprocess
on networkx
on numba
on numpy <=1.24
on pandas 1.4.4
on paste
on plotext
on psutil
on pulp 2.7.0
on pyani 0.2.10
on pymupdf
on pyrodigal-gv
on pysam
on python 3.10.*
on reportlab
on requests
on rich-argparse
on scikit-learn 1.2.2
on scipy
on six
on snakemake-minimal 5.10.0
on sqlite >=3.31.1
on statsmodels
on tabulate
on tomli 2.2.1

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 anvio-minimal

to add into an existing workspace instead, run:

pixi add anvio-minimal

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 anvio-minimal

Alternatively, to install into a new environment, run:

conda create -n envname anvio-minimal

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/anvio-minimal:<tag>

(see anvio-minimal/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/anvio-minimal/README.html)