recipe barcodeforge

A CLI tool for generating pathogen-specific barcodes for Freyja.

Homepage:

https://github.com/andersen-lab/BarcodeForge

Documentation:

https://andersen-lab.github.io/Freyja/src/wiki/custom_barcodes.html

License:

BSD / BSD-2-Clause

Recipe:

/barcodeforge/meta.yaml

package barcodeforge

versions:

1.1.1-0,  1.1.0-0,  1.0.0-0

depends augur:

>=31.1.0

depends biopython:

>=1.78

depends dendropy:

>=4.5.2

depends ete4:

>=4.3.0

depends matplotlib-base:

>=3.10.3

depends numpy:

>=1.20.0

depends pandas:

>=1.3.0

depends pathlib:

>=1.0.1

depends python:

>=3.10

depends rich:

>=10.0.0

depends rich-click:

>=1.6.0

depends seaborn:

>=0.13.2

depends six:

>=1.16.0

depends ucsc-fatovcf:

depends usher:

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 barcodeforge

and update with::

   mamba update barcodeforge

To create a new environment, run:

mamba create --name myenvname barcodeforge

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/barcodeforge:<tag>

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

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Render an badge with the following MarkDown:

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