recipe cmash

Fast and accurate set similarity estimation via containment min hash (for genomic datasets).

Homepage:

https://github.com/dkoslicki/CMash

License:

BSD / BSD-3-Clause

Recipe:

/cmash/meta.yaml

Links:

doi: 10.1016/j.amc.2019.02.018

package cmash

versions:

0.5.2-0,  0.5.1-1,  0.5.1-0,  0.5.0-0,  0.4.0-0

depends blist:

depends h5py:

depends hydra:

depends khmer:

>=2.1.1

depends marisa-trie:

depends matplotlib-base:

depends numpy:

>=1.14

depends pandas:

>=0.21.1

depends pycairo:

depends python:

depends scipy:

depends screed:

>=0.9

depends six:

requirements:

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 cmash

and update with::

   mamba update cmash

To create a new environment, run:

mamba create --name myenvname cmash

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/cmash:<tag>

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

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