recipe strainscan

One efficient and accurate strain-level microbiome composition analysis tool based on reference genomes and k-mers.

Homepage:

https://github.com/liaoherui/StrainScan

License:

MIT / MIT

Recipe:

/strainscan/meta.yaml

package strainscan

(downloads) docker_strainscan

versions:

1.0.14-1,  1.0.14-0,  1.0.13-0,  1.0.10-0,  1.0.3-0

depends bidict:

0.21.3

depends biopython:

1.74

depends numpy:

1.17.3

depends pandas:

1.0.1

depends psutil:

5.9.1

depends python:

3.7.3

depends r-base:

4.0.2

depends scikit-learn:

0.23.1

depends scipy:

1.3.1

depends sibeliaz:

1.2.3

depends treelib:

1.6.1

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 strainscan

and update with::

   mamba update strainscan

To create a new environment, run:

mamba create --name myenvname strainscan

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/strainscan:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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