recipe simka

Simka and simkaMin are de novo comparative metagenomics tools. Simka represents each dataset as a k-mer spectrum and computes several classical ecological distances between them. SimkaMin outputs approximate (but very similar) results by subsampling the kmer space and requires much less computational resources.

Homepage:

https://github.com/GATB/simka

License:

AGPL-3.0-or-later

Recipe:

/simka/meta.yaml

Links:

biotools: Simka, doi: 10.7717/peerj-cs.94, doi: 10.1093/bioinformatics/btz685

package simka

versions:

1.5.3-5,  1.5.3-4,  1.5.3-3,  1.5.3-2,  1.5.3-1,  1.5.3-0,  1.5.2-0,  1.5.1-0,  1.5.0-0, 

1.5.3-5,  1.5.3-4,  1.5.3-3,  1.5.3-2,  1.5.3-1,  1.5.3-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.0-0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends python:

depends zlib:

requirements:

additional platforms:

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 simka

and update with::

   mamba update simka

To create a new environment, run:

mamba create --name myenvname simka

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/simka:<tag>

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

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