recipe skmer

Assembly-free and alignment-free tool for estimating genomic distances between genome-skims

Homepage:

https://github.com/shahab-sarmashghi/Skmer

License:

BSD / BSD-3-Clause

Recipe:

/skmer/meta.yaml

package skmer

versions:

3.3.0-0,  3.2.1-0,  3.1.0-1,  3.1.0-0,  3.0.2-1,  3.0.2-0,  3.0.1-1,  3.0.1-0,  3.0.0-0, 

3.3.0-0,  3.2.1-0,  3.1.0-1,  3.1.0-0,  3.0.2-1,  3.0.2-0,  3.0.1-1,  3.0.1-0,  3.0.0-0,  2.0.2-3,  2.0.1-0,  2.0.0-0,  1.1.0-1,  1.1.0-0,  1.0.0-0

depends kmer-jellyfish:

2.3

depends mash:

2.3

depends numpy:

depends pandas:

depends python:

depends scipy:

depends seqtk:

1.3

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 skmer

and update with::

   mamba update skmer

To create a new environment, run:

mamba create --name myenvname skmer

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/skmer:<tag>

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

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