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: ```

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:

19.0.1-0, 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,

19.0.1-0, 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:

on bbmap >=39.01,<40
on click >=7
on cookiecutter
on graphviz
on mamba
on networkx
on numpy 1.21.*
on pandas >=1.2,<1.5
on pathlib
on pyarrow >=8
on pygments
on python >=3.8,<3.11
on ruamel.yaml >=0.17
on snakemake-minimal >=7.18.1,<7.26

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 metagenome-atlas

to add into an existing workspace instead, run:

pixi add metagenome-atlas

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 metagenome-atlas

Alternatively, to install into a new environment, run:

conda create -n envname metagenome-atlas

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/metagenome-atlas:<tag>

(see metagenome-atlas/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¶

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)