recipe confindr

Detect intra- and inter-species bacterial contamination in NGS reads

Homepage:

https://github.com/OLC-Bioinformatics/ConFindr

Documentation:

https://OLC-Bioinformatics.github.io/ConFindr/

License:

MIT / MIT

Recipe:

/confindr/meta.yaml

package confindr

versions:

0.8.1-1,  0.8.1-0,  0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.0-0, 

0.8.1-1,  0.8.1-0,  0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.0-0,  0.5.1-0,  0.5.0-0,  0.4.8-0,  0.4.7-0,  0.4.6-0,  0.4.5-0,  0.4.4-0,  0.4.3-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.4-0,  0.3.3-0,  0.3.2-0

depends bbmap:

>=39.01

depends biopython:

1.81.*

depends kma:

>=1.4.9

depends mash:

>=2.3

depends minimap2:

depends pysam:

>=0.15

depends pytest:

depends python:

>=3.9.15

depends samtools:

>=1.6

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 confindr

and update with::

   mamba update confindr

To create a new environment, run:

mamba create --name myenvname confindr

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/confindr:<tag>

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

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