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: ```

mamba 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:

2.19.0-0,  2.18.2-0,  2.18.1-0,  2.18.0-0,  2.17.2-0,  2.17.1-0,  2.17.0-0,  2.16.3-0,  2.16.2-0, 

2.19.0-0,  2.18.2-0,  2.18.1-0,  2.18.0-0,  2.17.2-0,  2.17.1-0,  2.17.0-0,  2.16.3-0,  2.16.2-0,  2.16.1-0,  2.15.2-0,  2.15.1-0,  2.15.0-0,  2.14.3-0,  2.14.2-0,  2.14.0-0,  2.13.1-0,  2.13.0-0,  2.12.0-1,  2.12.0-0,  2.11.1-0,  2.11.0-1,  2.11.0-0,  2.10.0-0,  2.9.1-0,  2.9.0-0,  2.8.2-0,  2.8.1-0,  2.8.0-0,  2.7.0-0,  2.6a4-0,  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:

>=39.01,<40

depends click:

>=7

depends cookiecutter:

depends graphviz:

depends mamba:

depends networkx:

depends numpy:

1.21.*

depends pandas:

>=1.2,<1.5

depends pathlib:

depends pyarrow:

>=8

depends pygments:

depends python:

>=3.8,<3.11

depends ruamel.yaml:

>=0.17

depends snakemake-minimal:

>=7.18.1,<7.26

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install metagenome-atlas

and update with::

   mamba update metagenome-atlas

To create a new environment, run:

mamba create --name myenvname metagenome-atlas

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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/metagenome-atlas/README.html)