Package Recipe 'metaphlan' — Bioconda documentation

recipe metaphlan

Metagenomic Phylogenetic Analysis.

Homepage:: biobakery/metaphlan
Documentation:: biobakery/MetaPhlAn
License:: MIT / MIT
Recipe:: /metaphlan/meta.yaml
Links:: doi: 10.1038/nmeth.2066, biotools: metaphlan, usegalaxy-eu: metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data with species level resolution. From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

package metaphlan#

Versions:

4.2.6-0, 4.2.5-0, 4.2.4-0, 4.2.3-0, 4.2.2-0, 4.2.1-0, 4.2.0-0, 4.1.2-0, 4.1.1-0,

4.2.6-0, 4.2.5-0, 4.2.4-0, 4.2.3-0, 4.2.2-0, 4.2.1-0, 4.2.0-0, 4.1.2-0, 4.1.1-0, 4.1.0-0, 4.0.6-0, 4.0.5-0, 4.0.4-0, 4.0.3-0, 4.0.2-0, 4.0.1-0, 4.0.0-0, 3.1.0-0, 3.0.14-0, 3.0.13-0, 3.0.12-0, 3.0.11-0, 3.0.10-0, 3.0.9-0, 3.0.8-0, 3.0.7-2, 3.0.7-1, 3.0.7-0, 3.0.6-0, 3.0.5-0, 3.0.4-1, 3.0.4-0, 3.0.3-0, 3.0.2-0, 3.0.1-0, 3.0-4, 3.0-3, 3.0-2, 3.0-1, 3.0-0, 3.0.0.alpha-1, 3.0.0.alpha-0, 2.8.1-1, 2.8.1-0

Depends:

on bioconductor-microbiome
on biom-format
on biopython
on blast
on bowtie2 >=2.3.0
on cmseq
on dendropy
on h5py
on hclust2
on matplotlib-base
on minimap2 >=2.26
on muscle >=3.8.1551
on numpy
on pandas
on phylophlan
on pysam
on python >=3.7
on r-ape
on r-base >=4
on r-biocmanager
on r-compositions
on r-essentials
on r-optparse
on r-rbiom
on raxml >=8.2.10
on requests
on samtools
on scipy

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 metaphlan

to add into an existing workspace instead, run:

pixi add metaphlan

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 metaphlan

Alternatively, to install into a new environment, run:

conda create -n envname metaphlan

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/metaphlan:<tag>

(see metaphlan/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/metaphlan/README.html)