recipe chewiesnake

ChewieSnake is a snakemake workflow that performs cgMLST allele calling for a set of assembled genomes using chewBBACA.

Homepage:

https://gitlab.com/bfr_bioinformatics/chewieSnake

License:

BSD-3

Recipe:

/chewiesnake/meta.yaml

package chewiesnake

versions:

3.0.0-2,  3.0.0-1,  3.0.0-0

depends bioconductor-biobase:

>=2.46

depends bioconductor-biostrings:

>=2.54

depends bioconductor-ggtree:

>=2.0.0

depends biopython:

1.76.*

depends chewbbaca:

2.0.12.*

depends fastp:

0.19.5.*

depends grapetree:

2.1.*

depends kmc:

3.1.0.*

depends pandoc:

>=2.11

depends python:

>=3.6

depends r-ape:

5.*

depends r-base:

>=3.6.3

depends r-dendextend:

>=1.14

depends r-dt:

depends r-knitr:

depends r-optparse:

depends r-plotly:

depends r-reshape2:

depends r-rmarkdown:

depends r-tidyverse:

>=1.3

depends shovill:

1.1.0.*

depends snakemake:

>=5.30

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 chewiesnake

and update with::

   mamba update chewiesnake

To create a new environment, run:

mamba create --name myenvname chewiesnake

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/chewiesnake:<tag>

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

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