recipe parsnp

Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.

Homepage:

https://github.com/marbl/parsnp

Documentation:

https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html

License:

custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE

Recipe:

/parsnp/meta.yaml

package parsnp

versions:

2.1.4-0,  2.1.3-0,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.0.6-0,  2.0.5-0,  2.0.4-0,  2.0.3-0, 

2.1.4-0,  2.1.3-0,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.0.6-0,  2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-1,  2.0.2-0,  1.7.4-2,  1.7.4-1,  1.7.4-0,  1.7.3-0,  1.7.2-0,  1.7.1-1,  1.7.1-0,  1.7.0-0,  1.6.2-1,  1.6.2-0,  1.6.1-1,  1.6.1-0,  1.6.0-0,  1.5.6-1,  1.5.6-0,  1.5.4-1,  1.5.4-0,  1.5.3-0,  1.5.2-1,  1.5.2-0,  1.5.1-0,  1.5.0-4,  1.5.0-3,  1.5.0-2,  1.5.0-1,  1.5.0-0,  1.2-0

depends biopython:

depends fastani:

depends fasttree:

depends harvesttools:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends mash:

depends numpy:

depends openmp:

depends phipack:

depends pyspoa:

depends python:

>=3.7

depends raxml:

depends tqdm:

depends zlib:

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 parsnp

and update with::

   mamba update parsnp

To create a new environment, run:

mamba create --name myenvname parsnp

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/parsnp:<tag>

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

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