recipe qimba

Toolkit for metabarcoding analyses

Homepage:

https://github.com/quadram-institute-bioscience/qimba

License:

MIT

Recipe:

/qimba/meta.yaml

package qimba

versions:

0.4.0-0

depends cd-hit:

>=4.8.1

depends click:

>=8.0

depends configparser:

depends cutadapt:

>=3.5

depends dnaio:

>=1.1

depends fastp:

depends fasttree:

>=2.0

depends kraken2:

depends mafft:

>=7.0

depends minimap2:

>=2.1

depends pandas:

>=2.0.0

depends python:

>=3.9

depends seqfu:

>1.20

depends usearch:

depends xopen:

>=2.0

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 qimba

and update with::

   mamba update qimba

To create a new environment, run:

mamba create --name myenvname qimba

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/qimba:<tag>

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

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