recipe mashmap

A fast approximate aligner for long DNA sequences.

Homepage:

https://github.com/marbl/MashMap

Documentation:

https://github.com/marbl/MashMap/blob/v3.1.3/README.md

License:

Custom

Recipe:

/mashmap/meta.yaml

Links:

biotools: mashmap, usegalaxy-eu: mashmap, doi: 10.1101/2023.05.16.540882, doi: 10.1093/bioinformatics/bty597, doi: 10.1007/978-3-319-56970-3_5

package mashmap

versions:

3.1.3-2,  3.1.3-1,  3.1.3-0,  3.1.2-0,  3.1.1-0,  3.1.0-0,  3.0.6-0,  3.0.5-0,  3.0.4-0, 

3.1.3-2,  3.1.3-1,  3.1.3-0,  3.1.2-0,  3.1.1-0,  3.1.0-0,  3.0.6-0,  3.0.5-0,  3.0.4-0,  3.0.2-0,  3.0.1-1,  3.0.1-0,  3.0-0,  2.0-8,  2.0-7,  2.0-6,  2.0-5,  2.0-4,  2.0-3,  2.0-2,  2.0-1,  2.0-0,  1.0-1,  1.0-0

depends gsl:

>=2.7,<2.8.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends openblas:

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

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 mashmap

and update with::

   mamba update mashmap

To create a new environment, run:

mamba create --name myenvname mashmap

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/mashmap:<tag>

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

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