recipe mashpit

Sketch-based surveillance platform

Homepage:

https://github.com/tongzhouxu/mashpit

License:

GPL2 / GPL-2.0-or-later

Recipe:

/mashpit/meta.yaml

package mashpit

versions:

0.9.7-0,  0.9.6-0,  0.9.2-0

depends biopython:

1.78.*

depends dask:

>=2024.1

depends flask:

>=3.0

depends ncbi-datasets-cli:

>=16.10

depends ncbi-datasets-pylib:

>=16.6.0

depends numpy:

>=1.19.5

depends pandas:

>=1.1.5

depends phytreeviz:

depends python:

>=3.8

depends requests:

depends scikit-bio:

depends scipy:

>=1.0

depends screed:

>=1.0.5

depends sourmash:

>=4.6.1

depends tqdm:

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 mashpit

and update with::

   mamba update mashpit

To create a new environment, run:

mamba create --name myenvname mashpit

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/mashpit:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mashpit/README.html)