recipe metagenome-atlas

ATLAS - Three commands to start analysing your metagenome data

Homepage

https://github.com/metagenome-atlas

Documentation

https://metagenome-atlas.rtfd.io

Developer docs

https://github.com/metagenome-atlas/atlas

License

BSD / BSD-3-Clause

Recipe

/metagenome-atlas/meta.yaml

Atlas is a easy to use metagenomic pipeline 

# Quick Start

Three commands to start analysing your metagenome data: ```

conda install -c bioconda -c conda-forge metagenome-atlas atlas init –db-dir databases path/to/fastq/files atlas run

``` All databases and dependencies are installed on the fly in the directory `db-dir`. You want to run these three commands on the example_data on the GitHub repo. If you have more time, then we recommend you configure atlas according to your needs.

- check the `samples.tsv` - edit the `config.yaml` - run atlas on any cluster system

For more details see documentation.

package metagenome-atlas

Versions

2.1.3-0, 2.1.1-0, 2.0.6-1, 2.0.5-1, 2.0.4-1, 2.0.3-1, 2.0.1-1, 2.0.1-0

Depends bbmap

>=37.78

Depends biopython

>=1.70

Depends click

>=7

Depends git

Depends pandas

>=0.23

Depends python

>3.6,<3.7

Depends ruamel.yaml

>=0.15

Depends snakemake

>=5.4.5,<6

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install metagenome-atlas

and update with:

conda update metagenome-atlas

or use the docker container:

docker pull quay.io/biocontainers/metagenome-atlas:<tag>

(see metagenome-atlas/tags for valid values for <tag>)

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/metagenome-atlas/README.html)