recipe metaclassifier

MetaClassifier is an integrated pipeline for classifying and quantifying DNA metabarcoding data into taxonomy groups

Homepage:

https://github.com/ewafula/MetaClassifier

License:

GPL3 / GNU General Public v3 (GPLv3)

Recipe:

/metaclassifier/meta.yaml

MetaClassifier is an integrated pipeline for identifying the floral composition of honey using DNA metabarcoding to determine the plants that honey bees visit. MetaClassifier utilizes a database of marker sequences and their corresponding taxonomy lineage information to classify high-throughput metabarcoding sample sequencing reads data into taxonomic groups and quantify taxon abundance. MetaClassifier can also be employed in other studies that utilize barcoding, metabarcoding, and metagenomics techniques to characterize richness, abundance, relatedness, and interactions in ecological communities.

package metaclassifier

(downloads) docker_metaclassifier

Versions:

1.0.1-0,  v1.0.1-0

Depends:

  • on numpy >=1.18.1

  • on pandas >=1.2.2

  • on pear >=0.9.6

  • on python >=3.7

  • on seqtk >=1.3

  • on vsearch >=2.15.2

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 metaclassifier

to add into an existing workspace instead, run:

pixi add metaclassifier

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 metaclassifier

Alternatively, to install into a new environment, run:

conda create -n envname metaclassifier

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/metaclassifier:<tag>

(see metaclassifier/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.

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