recipe amptk

AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.

Homepage:

https://github.com/nextgenusfs/amptk

Documentation:

http://amptk.readthedocs.io/

License:

BSD / BSD-2-Clause

Recipe:

/amptk/meta.yaml

Links:

doi: 10.7717/peerj.4925

package amptk

versions:

1.6.0-0,  1.5.5-0,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.1-1,  1.5.1-0,  1.5.0-0,  1.4.2-1, 

1.6.0-0,  1.5.5-0,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.1-1,  1.5.1-0,  1.5.0-0,  1.4.2-1,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.0-0,  1.2.4-1,  1.2.4-0,  1.2.2-0,  1.2.0-0,  1.1.3-0

depends bioconductor-dada2:

>=1.12.1

depends bioconductor-phyloseq:

depends biom-format:

depends biopython:

depends distro:

depends fasttree:

depends mafft:

depends matplotlib-base:

depends minimap2:

depends natsort:

depends numpy:

depends pandas:

depends pigz:

depends psutil:

depends pyfastx:

>=0.8.0

depends python:

>=3

depends python-edlib:

>=1.2.1

depends r-base:

depends r-dt:

depends r-htmltools:

depends r-plotly:

depends requests:

depends seaborn:

depends vsearch:

>=2.15.0

requirements:

additional platforms:

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 amptk

and update with::

   mamba update amptk

To create a new environment, run:

mamba create --name myenvname amptk

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/amptk:<tag>

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

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