recipe mash

Fast sequence distance estimator that uses MinHash.

Homepage:

https://github.com/marbl/Mash

Documentation:

https://mash.readthedocs.io/en/latest

License:

https://github.com/marbl/Mash/blob/master/LICENSE.txt

Recipe:

/mash/meta.yaml

Links:

biotools: mash, usegalaxy-eu: mash_screen, usegalaxy-eu: mash_sketch, doi: 10.1186/s13059-016-0997-x, doi: 10.1186/s13059-019-1841-x

package mash

versions:

2.3-9,  2.3-8,  2.3-7,  2.3-6,  2.3-5,  2.3-4,  2.3-3,  2.3-2,  2.3-1, 

2.3-9,  2.3-8,  2.3-7,  2.3-6,  2.3-5,  2.3-4,  2.3-3,  2.3-2,  2.3-1,  2.3-0,  2.2.2-2,  2.2.2-1,  2.2.2-0,  2.2.1-1,  2.2.1-0,  2.2-0,  2.1.1-0,  2.1-1,  2.1-0,  2.0-3,  2.0-2,  2.0-1,  2.0-0,  1.1-0,  1.0.2-2,  1.0.2-1

depends capnproto:

>=1.0.2,<1.0.3.0a0

depends gsl:

>=2.7,<2.8.0a0

depends libcblas:

>=3.9.0,<4.0a0

depends libgcc:

depends libgcc-ng:

>=12

depends libstdcxx:

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 mash

and update with::

   mamba update mash

To create a new environment, run:

mamba create --name myenvname mash

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/mash:<tag>

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

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