recipe pneumocat

PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)

Homepage:

https://github.com/phe-bioinformatics/pneumocat

License:

GPL / GPL-3.0

Recipe:

/pneumocat/meta.yaml

package pneumocat

(downloads) docker_pneumocat

versions:

1.2.1-11.2.1-01.2-31.2-21.2-01.1-0

depends biopython:

depends bowtie2:

depends lxml:

depends numpy:

depends pysam:

depends python:

<3

depends pyyaml:

depends samtools:

>1.3

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 pneumocat

and update with::

   mamba update pneumocat

To create a new environment, run:

mamba create --name myenvname pneumocat

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/pneumocat:<tag>

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

Download stats