recipe squeegee

squeegee, de novo computational contamination detection tool for metagenomic samples

Homepage:

https://gitlab.com/treangenlab/squeegee

License:

MIT

Recipe:

/squeegee/meta.yaml

package squeegee

versions:

0.2.0-0,  0.1.3-0

depends biopython:

depends bowtie2:

>=2.3.5

depends kraken:

>=1.1.1

depends mash:

>=2.2.2

depends meryl:

>=1.2

depends numpy:

depends python:

>=3.6

depends samtools:

>=1.11

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 squeegee

and update with::

   mamba update squeegee

To create a new environment, run:

mamba create --name myenvname squeegee

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/squeegee:<tag>

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

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Link to this page

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