recipe artic

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

Homepage:

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

License:

MIT

Recipe:

/artic/meta.yaml

package artic

versions:

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, 

1.2.4-1,  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 artic-porechop:

>=0.3.2pre

depends artic-tools:

depends bcftools:

depends biopython:

depends bwa:

depends clint:

depends htslib:

depends keras-preprocessing:

>=1.1.2

depends longshot:

depends medaka:

>=1.10.0

depends minimap2:

>=2.26

depends multiqc:

depends muscle:

3.8.*

depends nanopolish:

>=0.14.0

depends pandas:

depends pip:

depends pyfaidx:

0.6.0.*

depends pysam:

depends pytest:

depends python:

depends pyvcf:

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 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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