recipe esviritu

Read mapping pipeline for detection and measurement of human and animal virus pathogens from short read metagenomic environmental or clinical samples.

Homepage:

https://github.com/cmmr/EsViritu

License:

MIT

Recipe:

/esviritu/meta.yaml

Links:

https: :https:`//doi.org/10.1038/s41467-023-42064-1`

package esviritu

versions:

1.0.2-0,  1.0.1-0,  0.2.3-0,  0.2.2-0

depends fastp:

>=0.23.2

depends minimap2:

>=2.21

depends numpy:

depends polars:

depends pysam:

depends python:

>=3.11

depends pyyaml:

depends r-base:

depends r-htmltools:

depends r-magrittr:

depends r-reactable:

depends r-reactablefmtr:

depends r-remotes:

depends r-scales:

depends samtools:

>=1.15

depends seqkit:

requirements:

additional platforms:

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 esviritu

and update with::

   mamba update esviritu

To create a new environment, run:

mamba create --name myenvname esviritu

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/esviritu:<tag>

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

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