recipe rsv-typer

Genotyping RSV samples from nanopore sequencing data

Homepage:

https://github.com/DiltheyLab/RSVTyper

License:

MIT

Recipe:

/rsv-typer/meta.yaml

package rsv-typer

versions:

0.3.0-1,  0.3.0-0,  0.2.0-0,  0.1.0-0

depends absl-py:

1.4.0.*

depends artic:

1.2.1.*

depends longshot:

0.4.5.*

depends minimap2:

>=2.17

depends muscle:

3.8.*

depends nextclade:

2.14.0.*

depends python:

>=3

depends pyvcf:

0.6.8 py36h9f0ad1d_1002

depends samtools:

>=1.10

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 rsv-typer

and update with::

   mamba update rsv-typer

To create a new environment, run:

mamba create --name myenvname rsv-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/rsv-typer:<tag>

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

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