- recipe esviritu
EsViritu: Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
- Homepage:
- License:
MIT
- Recipe:
- Links:
- package esviritu¶
- versions:
0.2.3-0,0.2.2-0- depends bedtools:
2.30.0.*- depends bioawk:
1.0.*- depends biopython:
- depends blast:
>=2.13.0- depends bwa-mem2:
2.2.1.*- depends coverm:
0.6.1.*- depends dashing:
1.0.*- depends fastani:
>=1.3- depends fastp:
>=0.23.2- depends minimap2:
>=2.21- depends numpy:
- depends python:
>=3.8- depends r-base:
- depends r-data.table:
- depends r-dplyr:
- depends r-htmltools:
- depends r-knitr:
- depends r-lubridate:
- depends r-rcolorbrewer:
- depends r-reactable:
- depends r-reactablefmtr:
- depends r-readxl:
- depends r-remotes:
- depends r-scales:
- depends r-stringr:
- depends r-viridis:
- depends samtools:
>=1.9- depends scipy:
- depends seqfu:
>=1.17.1- depends seqkit:
2.4.0.*- depends tqdm:
- 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 esviritu and update with:: mamba update esviritu
To create a new environment, run:
mamba create --name myenvname esviritu
with
myenvnamebeing 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>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/esviritu/README.html)
