recipe artic

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.

Homepage:

https://github.com/artic-network/fieldbioinformatics

Documentation:

https://artic.readthedocs.io/en/latest

License:

MIT / MIT

Recipe:

/artic/meta.yaml

package artic

versions:

1.7.3-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.5-0,  1.6.4-0,  1.6.3-0,  1.6.2-0,  1.6.1-0, 

1.7.3-0,  1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.5-0,  1.6.4-0,  1.6.3-0,  1.6.2-0,  1.6.1-0,  1.6.0-0,  1.5.8-0,  1.5.7-0,  1.5.6-0,  1.5.5-1,  1.5.5-0,  1.5.4-0,  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:

>=1.0.0

depends clint:

depends cyvcf2:

depends htslib:

depends mafft:

depends minimap2:

depends multiqc:

depends pandas:

depends pysam:

depends pytest:

depends python:

>=3.7

depends requests:

depends samtools:

depends seqtk:

depends tqdm:

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 artic

and update with::

   mamba update artic

To create a new environment, run:

mamba create --name myenvname artic

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/artic:<tag>

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

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