recipe pneumo-typer

Pneumo-Typer: An integrated tool for simultaneous identification of serotype, sequence type, and capsule genotype in Streptococcus pneumoniae.

Homepage:

https://www.microbialgenomic.cn/Pneumo-Typer.html

Documentation:

https://github.com/Xiangyang1984/Pneumo-Typer

License:

GNU General Public License v3.0 or any later version (GPL-3.0-or-later)

Recipe:

/pneumo-typer/meta.yaml

Pneumo-Typer is a stand-alone perl application, which requires blat, prodigal, NCBI BLAST+, and several perl Modules (GD, GD::SVG) to be installed before use.

package pneumo-typer

versions:

1.0.3-0,  1.0.2-1,  1.0.2-0,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0

depends blast:

depends blat:

depends perl-bioperl-core:

depends perl-gd:

>=2.74

depends perl-gd-svg:

depends perl-svg:

>=2.87

depends prodigal:

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 pneumo-typer

and update with::

   mamba update pneumo-typer

To create a new environment, run:

mamba create --name myenvname pneumo-typer

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/pneumo-typer:<tag>

(see `pneumo-typer/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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