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

(downloads) docker_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:

  • on libgcc >=13

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

  • on python

  • on zlib

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 simka

to add into an existing workspace instead, run:

pixi add simka

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 simka

Alternatively, to install into a new environment, run:

conda create -n envname simka

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/simka:<tag>

(see simka/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.

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