Installation

Installation

BrucellaID needs Python 3.10 or newer, MASH and BBTools (which provides seal.sh, and Java with it). Neither MASH nor BBTools is on PyPI, so they come from bioconda; BrucellaID itself needs nothing but the Python standard library. Two output formats need a package each, and neither is required: xlsxwriter for the legacy xlsx report (--xlsx) and reportlab for the PDF quality assurance report (--pdf). The HTML version of that report holds the same information and needs nothing.

pip, with the tools from conda (recommended)

conda create -n brucellaid -c conda-forge -c bioconda mash "gsl=2.7.0" bbmap "python>=3.10"
conda activate brucellaid
pip install brucellaid
brucellaid --version

The gsl=2.7.0 pin is not cosmetic: the bioconda builds of mash 2.3 are linked against libgsl.so.25, while their recipe accepts gsl 2.7.1, which provides libgsl.so.27. Without the pin, mash may fail to start with error while loading shared libraries: libgsl.so.25. See Troubleshooting.

The optional output formats: pip install 'brucellaid[xlsx]', pip install 'brucellaid[pdf]', or pip install 'brucellaid[all]' for both. With conda, conda install -c conda-forge xlsxwriter reportlab.

conda, in one command — not yet

conda create -n brucellaid -c conda-forge -c bioconda brucellaid    # once the recipe is merged

This will bring MASH and BBTools with it, and is the shortest way in. The recipe is awaiting review on bioconda; until it is merged the command above finds nothing, so use pip as above. The same goes for the ready-made container: biocontainers builds one from the bioconda package, so there is none yet.

From a clone

git clone https://github.com/duceppemo/BrucellaID
cd BrucellaID
conda env create -f environment.yml
conda activate brucellaid
pip install --no-deps -e .
pytest            # optional: 392 tests

python -m brucellaid works too, and takes the same arguments as the brucellaid command.

Docker or Singularity

Once the bioconda recipe is merged, biocontainers builds an image from it automatically:

docker run --rm -v "$PWD":/data quay.io/biocontainers/brucellaid:<tag> brucellaid -i /data/reads -o /data/results

The tag will be listed on biocontainers.pro. Until then, build your own from the pip install above, or run BrucellaID from a clone.

What is installed

The package ships its reference data and the logo of the reports, about 3.9 MB in all, 3.5 MB of it the extended sketch:

File	What it is
references_extended.msh	The MASH sketch of the 432 Brucella reference genomes a run uses by default from 2.0
references_extended.tsv	What each of those genomes is: code, species, biovar, strain, NCBI accession
references.msh	The MASH sketch of vSNP's 16 Brucella reference genomes, reached with --reference-set vsnp
references.tsv	What each of those genomes is: vSNP species code, species, biovar, strain, NCBI accessions
mlst_alleles.fasta	The 309 alleles of the nine MLST loci
mlst_profiles.tsv	The 122 sequence types
mlst_st_species.tsv	The species of each sequence type, from PubMLST's isolate database
logo.svg, logo.png	The logo the quality assurance reports carry

--reference-set picks between the two packaged sketches, and --sketch, --references, --alleles, --profiles and --st-species take files of your own instead (see Usage).