recipe singlem

SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. It is able to differentiate closely related species even if those species are from lineages new to science.

Homepage:

https://github.com/wwood/singlem

License:

GPL3 / GNU General Public v3 (GPLv3)

Recipe:

/singlem/meta.yaml

package singlem

versions:

0.16.0-0,  0.15.1-0,  0.15.0-0,  0.14.0-0,  0.13.2-2,  0.13.2-1,  0.13.2-0

depends biopython:

depends bird_tool_utils_python:

>=0.4.1

depends cd-hit:

depends diamond:

>=2.1.7

depends expressbetadiversity:

depends extern:

depends fastalite:

depends fasttree:

depends graftm:

>=0.14.0

depends hmmer:

depends jinja2:

depends krona:

depends mafft:

depends mfqe:

depends ncbi-ngs-sdk:

depends orfm:

depends pandas:

depends pip:

depends polars:

>=0.19.3

depends pplacer:

depends prodigal:

depends pyarrow:

depends pyranges:

depends python:

>=3.7

depends seqmagick:

depends smafa:

>=0.7.0

depends sqlalchemy:

depends sqlite:

depends squarify:

depends sra-tools:

depends tqdm:

depends zenodo_backpack:

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 singlem

and update with::

   mamba update singlem

To create a new environment, run:

mamba create --name myenvname singlem

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/singlem:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

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