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Installation

Note the following instructions are for pre-release installation for bohra version 3

1. Install conda (skip this step if you already have conda installed)

If you do not already have conda installed, you can check out the documentation here. We recommend you install miniforge

2. Setup the bohra environment and install the pipeline co-ordinator

  1. Clone the bohra repository
git clone https://github.com/MDU-PHL/bohra.git
  1. Create the environment and install bohra
cd bohra
conda env create -f environment.yml -n bohra
conda activate bohra
pip3 install .
  1. Test this has worked as expected 
    bohra --help
    Should result in 
Usage: bohra [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  generate-input  Generare input files for the Bohra pipeline.
  init-databases  Check that dependencies are installed correctly.
  install-deps    Install dependencies for Bohra - Highly recommended to...
  run             Run the Bohra pipeline.
  test            Check that bohra is installed correctly and runs as...

3. Install dependencies and setup environment variables

This step will setup conda environments under the path/to/conda/envs/bohra(depending on how you have configured your conda installation).

Additionally, bohra depends upon either a correctly configure kraken2 compatible database. The bohra install-deps command will optionally download the databases for your and also set the appropriate environment variables for you.

  1. Activate your environment from step 2 above 

    conda activate bohra

  2. Run the bohra dependency installation

bohra install-deps (optional add --setup-database )

The initial creation of the conda environments may take some time (~10 - 15 minutes). Once the environments are set up, if you have added the --setup-databases, bohra will try to set up your database environment variables. Although this is not essential it is HIGHLY recommended for ease of running and reproducibility.

Please be aware of the following:

  • If you elect to say no to setting up a KRAKEN2_DEFAULT_DB you will need to provide the --kraken2_db flag each time you run bohra if you wish to do speciation or use any features which depend on species (typing and AMR).

  • If you are happy to use the mlst database that comes bundled with the mlst tool, then you can decline setting the BOHRA_PUBMLST_DB and BOHRA_BLAST_DB.

  • If you already have a kraken2 database you can press 'n' when asked if you want to download. If you select 'y' please make sure that you have enough storage space for the databases. Some are quite large, up to 600 GB (half-terabyte).