recipe bactopia

Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

Homepage

https://bactopia.github.io/

Developer docs

https://github.com/bactopia/bactopia/

License

MIT

Recipe

/bactopia/meta.yaml

Links

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

package bactopia

Versions

1.6.0-1,  1.6.0-0,  1.5.6-0,  1.5.5-0,  1.5.4-1,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.1-0, 

1.6.0-1,  1.6.0-0,  1.5.6-0,  1.5.5-0,  1.5.4-1,  1.5.4-0,  1.5.3-0,  1.5.2-0,  1.5.1-0,  1.5.0-0,  1.4.11-1,  1.4.11-0,  1.4.10-0,  1.4.9-0,  1.4.8-0,  1.4.7-0,  1.4.6-0,  1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.2.4-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.1-0

Depends

• ariba

• beautifulsoup4

• biopython

• blast >=2.10.1

• bowtie2 <2.4.0

• cd-hit

• conda

• coreutils

• executor

• lxml

• mash

• ncbi-amrfinderplus

• ncbi-genome-download

• nextflow

• pysam >=0.15.3

• python >3.6

• requests

• sed

• unzip

• wget

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bactopia

and update with:

conda update bactopia

or use the docker container:

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

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

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/bactopia/README.html)