Package Recipe 'autometa' — Bioconda documentation

recipe autometa

Automated extraction of genomes from shotgun metagenomes

Homepage:: KwanLab/Autometa
Documentation:: https://autometa.readthedocs.io/en/latest/
License:: AGPL / AGPL-3.0
Recipe:: /autometa/meta.yaml

An automated binning pipeline for metagenomes, in particular host-associated and highly complex ones. Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research, 2019. DOI: https://doi.org/10.1093/nar/gkz148

package autometa#

Versions:

2.2.3-0, 2.2.2-0, 2.2.1-0, 2.2.0-0, 2.1.0-0, 2.0.3-0, 2.0.2-0, 2.0.1-0, 2.0.0-0

Depends:

on attrs
on bedtools
on biopython >=1.82
on bowtie2
on diamond >=2.0
on gdown
on hmmer
on numba >=0.47
on numpy >=1.13
on pandas >=1.5
on parallel
on prodigal >=2.5
on python >=3.7
on requests
on rsync
on samtools >=1.11
on scikit-bio
on scikit-learn >=1.3
on scipy
on seqkit
on tqdm
on trimap
on tsne
on umap-learn >=0.5

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 autometa

to add into an existing workspace instead, run:

pixi add autometa

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 autometa

Alternatively, to install into a new environment, run:

conda create -n envname autometa

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/autometa:<tag>

(see autometa/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/autometa/README.html)