- recipe artic
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
- package artic¶
- versions:
1.5.3-0,1.5.2-0,1.5.1-0,1.2.4-1,1.2.4-0,1.2.3-0,1.2.2-0,1.2.1-0,1.2.0-0,1.5.3-0,1.5.2-0,1.5.1-0,1.2.4-1,1.2.4-0,1.2.3-0,1.2.2-0,1.2.1-0,1.2.0-0,1.1.3-1,1.1.3-0,1.1.2-0,1.1.1-1,1.1.1-0,1.1.0_rc2-0- depends bcftools:
- depends biopython:
- depends bwa:
- depends clair3:
- depends clint:
- depends cyvcf2:
- depends htslib:
- depends minimap2:
- depends multiqc:
- depends muscle:
<5.1- depends pandas:
- depends pyfaidx:
0.6.0.*- depends pysam:
- depends pytest:
- depends python:
3.9- depends requests:
- depends samtools:
- 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 artic and update with:: mamba update artic
To create a new environment, run:
mamba create --name myenvname artic
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/artic:<tag> (see `artic/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/artic/README.html)
