Installation

Installation

Requirements

• Python 3.7+ (profile order matters, so insertion-ordered dicts are required). CI covers 3.9 through 3.13; 3.7 and 3.8 are past end of life and are not exercised.
• Biopython, which pip installs for you.

Nothing else. No external PCR tool, no aligner, no database to download.

pip

pip install brucetyper

That puts a brucetyper command on your path:

brucetyper --version
brucetyper -i genomes/ -o results/

conda

conda install -c conda-forge -c bioconda brucetyper

mamba resolves the same thing considerably faster:

mamba install -c conda-forge -c bioconda brucetyper

Or set the channels up once, which is what Bioconda recommends, and drop the -c flags from every later install:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install brucetyper

The recipe is noarch, so the one build serves every platform conda supports.

pipx

A command line tool in its own isolated environment, which keeps Biopython out of your user site-packages:

pipx install brucetyper
brucetyper -i genomes/ -o results/

From a clone

For development, or to run a version that has not been released:

git clone https://github.com/duceppemo/brucetyper
cd brucetyper
pip install -e .

-e installs in place, so edits to brucetyper/assays.py take effect without reinstalling, which is the usual reason to work from a clone.

Without installing at all, a clone also runs directly, which is how every example in this wiki worked before the package existed:

pip install biopython
python bruce_ladder.py -i genomes/ -o results/

bruce_ladder.py is a three line shim at the repository root that dispatches to brucetyper.cli. It takes exactly the same arguments as the brucetyper command and is kept so that the older invocation, and the bruce_rates.py and suis_rates.py workflows, keep working. It is not part of the installed package.

Checking the install

$ brucetyper --version
brucetyper 1.1.0

The test suite is shipped inside the source distribution, so a release can be verified without a clone:

pip download --no-binary :all: --no-deps brucetyper
tar xzf brucetyper-*.tar.gz
cd brucetyper-*/
python -m unittest discover -s tests

One test is skipped there: the shim lives at the repository root and is not in the distribution.

What is installed

brucetyper	The command, equivalent to python bruce_ladder.py from a clone
brucetyper.assays	Every primer and expected band size. The only place either is defined
brucetyper.insilico_pcr	Primer matching and amplicon finding
brucetyper.genotype	Sizes to canonical bands to a call

brucetyper.assays is importable, so the profiles can be read or patched from your own code:

from brucetyper import assays
print(assays.PROFILES['bruce']['RB51'])

See Usage for the options and the reports, and Methods for how a call is made.