Package Recipe 'artic'

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:

1.9.1-0, 1.9.0-1, 1.9.0-0, 1.8.5-0, 1.8.4-0, 1.8.3-0, 1.8.2-0, 1.8.1-0, 1.8.0-1,

1.9.1-0, 1.9.0-1, 1.9.0-0, 1.8.5-0, 1.8.4-0, 1.8.3-0, 1.8.2-0, 1.8.1-0, 1.8.0-1, 1.8.0-0, 1.7.5-0, 1.7.4-0, 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:

on align_trim >=1.0.2
on bcftools
on biopython
on bwa
on clair3 >=1.0.0,<2.0.0
on clint
on cyvcf2
on htslib
on mafft
on minimap2
on multiqc
on pandas
on primalbedtools >=0.10.1
on pysam
on pytest
on python >=3.7
on requests
on samtools
on seqtk
on tqdm

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install artic

to add into an existing workspace instead, run:

pixi add artic

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install artic

Alternatively, to install into a new environment, run:

conda create -n envname artic

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/artic:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/artic/README.html)