recipe metaphlan

Metagenomic Phylogenetic Analysis

Homepage:

https://github.com/biobakery/metaphlan

License:

MIT / MIT License

Recipe:

/metaphlan/meta.yaml

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:

4.1.0-0,  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, 

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 bioconductor-microbiome:

depends biom-format:

depends biopython:

depends blast:

>=2.6.0

depends bowtie2:

>=2.3.0

depends dendropy:

depends hclust2:

depends matplotlib-base:

depends muscle:

>=3.8.1551

depends numpy:

depends pandas:

depends phylophlan:

>=3.1

depends pysam:

depends python:

>=3.7

depends r-ape:

depends r-base:

>=4

depends r-biocmanager:

depends r-compositions:

depends r-essentials:

depends r-optparse:

depends r-rbiom:

depends raxml:

>=8.2.10

depends requests:

depends samtools:

>=1.9

depends scipy:

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 metaphlan

and update with::

   mamba update metaphlan

To create a new environment, run:

mamba create --name myenvname metaphlan

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/metaphlan:<tag>

(see `metaphlan/tags`_ for valid values for ``<tag>``)

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