recipe bactopia-variants

Methods used by Bactopia for SNP and InDel analysis

Homepage:

https://bactopia.github.io/

Developer docs:

https://github.com/bactopia/bactopia-variants/

License:

MIT

Recipe:

/bactopia-variants/meta.yaml

Links:

biotools: bactopia, doi: 10.1128/mSystems.00190-20

package bactopia-variants

versions:

1.0.1-0,  1.0.0-0

depends coreutils:

depends gsl:

2.6.*

depends openjdk:

11.0.15.*

depends pigz:

depends python:

>=3.6,<3.11

depends rename:

depends sed:

depends snippy:

>=4.6.0

depends snpeff:

>=4.3,<5

depends vcf-annotator:

>=0.7

depends vcflib:

>=1.0.0_rc3,<=1.0.2

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 bactopia-variants

and update with::

   mamba update bactopia-variants

To create a new environment, run:

mamba create --name myenvname bactopia-variants

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/bactopia-variants:<tag>

(see `bactopia-variants/tags`_ for valid values for ``<tag>``)

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