Setup for CLIMB users

Set up civet3 environment

  1. Clone the civet3 repository with git clone https://github.com/cov-ert/civet3.git && cd civet3
  2. conda env create -f environment.yml
  3. conda activate civet3
  4. pip install .

Recommended: Set up environment variables

This sets the default background data directory to the latest output of datapipe. Alternatively, the directory can be specified with -d/--datadir or supplied in a config file.


  • Add the following to your .bash_profile

    • CIVET_DATADIR=/cephfs/covid/bham/results/msa/latest/civet3
    export CIVET_DATADIR
    CIVETMODE='CLIMB'
    export CIVETMODE

  • Run:

    • source .bash_profile

    Check the install worked

    Type (in the civet3 environment):

    echo $CIVET_DATADIR
    civet -v
    civet --art

    You should see the path supplied, the version of civet and the civet logo printed printed respectively.

    Troubleshooting install

    If you get an error message similar to command not found: civet

    1. Double check you are in the civet3 environment with conda activate civet3
    2. Then try pip uninstall civet and then re-install with pip install .