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

• bioconductor-biostrings >=2.54

• bioconductor-ggtree >=2.0.0

• biopython 1.76.*

• chewbbaca 2.0.12.*

• fastp 0.19.5.*

• grapetree 2.1.*

• kmc 3.1.0.*

• pandoc >=2.11

• python >=3.6

• r-ape 5.*

• r-base >=3.6.3

• r-dendextend >=1.14

• r-dt

• r-knitr

• r-optparse

• r-plotly

• r-reshape2

• r-rmarkdown

• r-tidyverse >=1.3

• shovill 1.1.0.*

• snakemake >=5.30

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install chewiesnake

and update with:

conda update chewiesnake

or use the docker container:

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

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

Download stats

Link to this page

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