Package Recipe 'dadaist2'

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:

1.3.1-2, 1.3.1-1, 1.3.1-0, 1.3.0-0, 1.2.5-0, 1.2.4-0, 1.2.1-0, 1.2.0-1, 1.2.0-0,

1.3.1-2, 1.3.1-1, 1.3.1-0, 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:

on bioconductor-dada2 >=1.34.0
on bioconductor-decipher
on bioconductor-microbiome
on bioconductor-phyloseq
on biom-format 2.1.10.*
on click
on clustalo
on cutadapt >=3.4
on fastp
on fasttree
on iqtree
on mafft
on matplotlib-base
on pandas >=1.0
on perl
on perl-fastx-reader >=0.90
on pyfastx
on python >=3.7
on r-matrix >=1.4
on requests
on rich
on rich-click
on scikit-learn
on seaborn
on seqfu
on usearch

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 dadaist2

to add into an existing workspace instead, run:

pixi add dadaist2

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 dadaist2

Alternatively, to install into a new environment, run:

conda create -n envname dadaist2

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/dadaist2:<tag>

(see dadaist2/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.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/dadaist2/README.html)