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

2.4.1-0,  2.4-0,  2.3.5-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.beta2-0,  2.2.0-0,  2.1.4-1, 

2.4.1-0,  2.4-0,  2.3.5-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.beta2-0,  2.2.0-0,  2.1.4-1,  2.1.4-0,  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.*

• biopython >=1.70,<2

• click >=7

• cookiecutter

• git

• pandas >=0.23,<1

• python >3.6,<3.7

• ruamel.yaml 0.15.99.*

• snakemake >=5.4.5,<=5.9

Required By

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)