recipe piranha-polio

Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis

Homepage:

https://github.com/polio-nanopore/piranha

License:

GPL3 / GPL-3.0-only

Recipe:

/piranha-polio/meta.yaml

package piranha-polio

versions:

1.3.1-0,  1.3-0,  1.2.5-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.1.2-0,  1.1.1-0,  1.1-0, 

1.3.1-0,  1.3-0,  1.2.5-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.1.2-0,  1.1.1-0,  1.1-0,  1.0.13-0,  1.0.12-0,  1.0.10-0,  1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.4-0

depends bcftools:

>=1.11

depends biopython:

depends coreutils:

>=9.1

depends mafft:

depends mako:

>=1.2

depends medaka:

>=1.7.1

depends minimap2:

>=2.17

depends numpy:

<=1.23.5

depends pandas:

depends pysam:

depends python:

<3.10

depends samtools:

>=1.11

depends snakemake-minimal:

depends snipit:

depends tabix:

>=1.11

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 piranha-polio

and update with::

   mamba update piranha-polio

To create a new environment, run:

mamba create --name myenvname piranha-polio

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/piranha-polio:<tag>

(see `piranha-polio/tags`_ for valid values for ``<tag>``)

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