recipe lotus2

LotuS2 is a lightweight complete 16S/18S/ITS pipeline

Homepage:

http://lotus2.earlham.ac.uk/

Developer docs:

https://github.com/hildebra/lotus2/

License:

GPL-3.0-or-later

Recipe:

/lotus2/meta.yaml

Links:

doi: 10.1186/s40168-022-01365-1, biotools: lotus2

package lotus2

versions:

2.34.1-1,  2.34.1-0,  2.34-0,  2.32-1,  2.32-0,  2.31-0,  2.30-1,  2.30-0,  2.28.1-1, 

2.34.1-1,  2.34.1-0,  2.34-0,  2.32-1,  2.32-0,  2.31-0,  2.30-1,  2.30-0,  2.28.1-1,  2.28.1-0,  2.28-0,  2.25-0,  2.24-0,  2.23-0,  2.22-0,  2.21-0,  2.19-0,  2.17-0,  2.16-0,  2.14-0,  2.12-1,  2.12-0,  2.11-0,  2.09.2-0,  2.09.1-0,  2.09-0,  2.08-0,  2.07-0,  2.06-0,  2.05.1-0,  2.04-1,  2.04-0,  2.02-0,  2.01-1,  2.01-0

depends bioconductor-dada2:

depends bioconductor-phyloseq:

depends blast:

depends cd-hit:

depends clustalo:

depends fasttree:

depends hmmer:

>=3.1

depends infernal:

depends iqtree:

depends itsx:

depends lambda:

>=3,<4

depends lca:

>=0.25

depends mafft:

depends minimap2:

depends perl:

depends perl-getopt-long:

depends pigz:

depends r-base:

depends r-dplyr:

depends rdp_classifier:

depends rtk:

depends sdm:

2.18

depends swarm:

depends unzip:

depends usearch:

>=12.0_beta,<13

depends vsearch:

depends wget:

depends zip:

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 lotus2

and update with::

   mamba update lotus2

To create a new environment, run:

mamba create --name myenvname lotus2

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/lotus2:<tag>

(see `lotus2/tags`_ for valid values for ``<tag>``)

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