recipe skder

skDER & CiDDER: efficient & high-resolution dereplication methods for microbial genomes

Homepage:

https://github.com/raufs/skDER

License:

BSD / BSD-3-Clause license

Recipe:

/skder/meta.yaml

package skder

versions:

1.2.8-1,  1.2.8-0,  1.2.7-0,  1.2.6-0,  1.2.5-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-1, 

1.2.8-1,  1.2.8-0,  1.2.7-0,  1.2.6-0,  1.2.5-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-1,  1.2.1-0,  1.1.1-0,  1.0.10-0,  1.0.9-0,  1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.1-1,  1.0.1-0,  1.0-0

depends biopython:

depends cd-hit:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends matplotlib-base:

depends ncbi-genome-download:

depends pandas:

depends pyrodigal:

depends python:

>=3.10,<3.11.0a0

depends python-igraph:

depends python_abi:

3.10.* *_cp310

depends seaborn:

depends setuptools:

depends skani:

depends wget:

requirements:

additional platforms:

linux-aarch64

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 skder

and update with::

   mamba update skder

To create a new environment, run:

mamba create --name myenvname skder

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/skder:<tag>

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

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