Package Recipe 'lotus3'

recipe lotus3

LotuS3 is a lightweight amplicon sequencing pipeline supporting 16S/18S/ITS

Homepage:: https://lotus3.earlham.ac.uk/
Developer docs:: https://github.com/hildebra/LotuS3/
License:: GPL-2.0-only
Recipe:: /lotus3/meta.yaml
Links:: doi: 10.1186/s40168-022-01365-1, biotools: lotus3

package lotus3¶

Versions:

3.03-1, 3.03-0

Depends:

on bioconductor-dada2
on bioconductor-phyloseq
on blast
on cd-hit
on clustalo
on fasttree
on hmmer >=3.1
on infernal
on iqtree
on itsx
on lambda >=3,<4
on lca >=0.25
on mafft
on minimap2
on perl
on perl-getopt-long
on pigz
on r-base
on r-dplyr
on rdp_classifier
on rtk
on sdm 2.18
on swarm
on unzip
on usearch >=12.0_beta,<13
on vsearch
on wget
on zip

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 lotus3

to add into an existing workspace instead, run:

pixi add lotus3

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 lotus3

Alternatively, to install into a new environment, run:

conda create -n envname lotus3

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/lotus3:<tag>

(see lotus3/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/lotus3/README.html)