Package Recipe 'metagenome-atlas'

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
Links: doi: 10.1101/737528

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

2.6a2-0, 2.6a1-0, 2.5.0-0, 2.4.5-0, 2.4.4-0, 2.4.3-0, 2.4.2-0, 2.4.1-0, 2.4-0,

2.6a2-0, 2.6a1-0, 2.5.0-0, 2.4.5-0, 2.4.4-0, 2.4.3-0, 2.4.2-0, 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
biopython >=1.70,<2
click >=7
cookiecutter
git
pandas >1
python >3.6,<3.8
ruamel.yaml 0.15.99.*
snakemake >=6.1

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)