Installation

Conda

Install the latest released version using conda:

conda create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.5"

If you’re having issues installing chewBBACA through conda, please verify that you are using conda>=22.11, and enable the libmamba solver, which might speed up the installation process. You can also install mamba and run the following command:

mamba create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.5"

Important

We strongly recommend that users install and use BLAST 2.9.0+ with chewBBACA<=3.3.2. Please open an issue if you find any problems with any of the dependencies.

Pip

Install using pip:

pip3 install chewbbaca

Python dependencies

numpy ~=1.24.3
scipy ~=1.10.1
biopython >=1.79
plotly >=5.8.0
SPARQLWrapper >=2.0.0
requests >=2.27.1
pandas >=1.5.1,<2.1
pyrodigal >=3.0.0 (for chewBBACA >=3.3.0)

Note

These dependencies are defined in the requirements file and should be automatically installed when using conda or pip.

Other dependencies

BLAST >=2.9.0 (we recommend using BLAST 2.9.0+)
Prodigal >=2.6.3 (for chewBBACA <3.3.0)
MAFFT >=7.505 (for schema evaluation only)
FastTree >=2.1.11 (for allele calling evaluation only)

Important

Installation through conda should take care of all dependencies. If you install through pip you need to ensure that you have BLAST, MAFFT, FastTree and Prodigal (for chewBBACA <3.3.0) installed and added to the PATH.

The reports generated by the SchemaEvaluator and AlleleCallEvaluator modules use the React library and the following JavaScript packages:

Material UI for most of the components.

MUI-Datatables for datatables components.

MSA Viewer for the Multiple Sequence Alignmnet.

Phylocanvas.gl for the NJ Tree.

react-plotly.js for the charts.

react-scroll for animating vertical scrolling in the NJ Tree component.

Monaco Editor for React for the read-only code editor that displays the DNA and Protein sequences.

react-markdown and remark-gfm to render markdown.

Note

You do not need to install the JS packages. chewBBACA includes JS bundles that are added to the report directory and are used by the browser.