recipe strainr2

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities using metagenomic sequencing reads

Homepage:

https://github.com/BisanzLab/StrainR2

License:

MIT / MIT

Recipe:

/strainr2/meta.yaml

package strainr2

(downloads) docker_strainr2

versions:

2.1.0-1,  2.1.0-0,  2.0.0-1,  2.0.0-0,  1.0.1-1,  1.0.1-0,  1.0.0-1,  1.0.0-0

depends bbmap:

depends fastp:

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-optparse:

depends r-tidyverse:

depends samtools:

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 strainr2

and update with::

   mamba update strainr2

To create a new environment, run:

mamba create --name myenvname strainr2

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/strainr2:<tag>

(see `strainr2/tags`_ for valid values for ``<tag>``)

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