recipe dadaist2

Command line wrapper to run DADA2 on a set of paired-end reads

Homepage:

https://quadram-institute-bioscience.github.io/dadaist2

Developer docs:

https://github.com/quadram-institute-bioscience/dadaist2

License:

MIT

Recipe:

/dadaist2/meta.yaml

Links:

biotools: dadaist2, doi: 10.3390/ijms22105309

Command line wrapper to run DADA2 on a set of paired-end reads with several exporting tools to generate plots and numerical ecology analyses

package dadaist2

versions:

1.3.0-0,  1.2.5-0,  1.2.4-0,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.2-1, 

1.3.0-0,  1.2.5-0,  1.2.4-0,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.2-1,  1.0.2-0,  1.0.1-1,  1.0.1-0,  0.9.0-0,  0.8.0-0,  0.7.7-1,  0.7.7-0,  0.7.5-0,  0.7.3-2,  0.7.3-1,  0.7.3-0,  0.6.0-1,  0.6.0-0,  0.4.00-2,  0.4.00-1,  0.4.00-0,  0.2.00-0,  0.1.04-0

depends bioconductor-dada2:

>=1.18.0

depends bioconductor-decipher:

depends bioconductor-microbiome:

depends bioconductor-phyloseq:

depends biom-format:

2.1.10.*

depends clustalo:

depends cutadapt:

>=3.4

depends fastp:

depends fasttree:

depends pandas:

>=1.0

depends perl:

depends perl-fastx-reader:

>=0.90

depends python:

>=3.6

depends qax:

depends r-matrix:

1.3-2.*

depends rich:

depends seqfu:

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 dadaist2

and update with::

   mamba update dadaist2

To create a new environment, run:

mamba create --name myenvname dadaist2

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/dadaist2:<tag>

(see `dadaist2/tags`_ for valid values for ``<tag>``)

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