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Installation

Instructions for installing civet locally

Requirements

civet runs on MacOS and Linux. The conda environment recipe may not build on Windows (and is not supported) but civet can be run using the Windows subsystem for Linux.

  1. Some version of conda, we use Miniconda3. Can be downloaded from here
  2. Access to CLIMB or to a local data directory. More information about this data here

Install civet

  1. git clone https://github.com/COG-UK/civet.git and cd civet
  2. conda env create -f environment.yml
  3. conda activate civet
  4. python setup.py install

Note: we recommend using civet in the conda environment specified in the environment.yml file as per the instructions above. If you can't use conda for some reason, dependency details can be found in the environment.yml file.

Check the install worked

Type (in the civet environment):

civet

and you should see the help menu of civet printed

Updating civet

Note: Even if you have previously installed civet, as it is being worked on intensively, we recommend you check for updates before running.

To update:

  1. conda activate civet
  2. git pull
    pulls the latest changes from github
  3. python setup.py install
    re-installs civet
  4. conda env update -f environment.yml
    updates the conda environment

Troubleshooting update

  • If you have previously installed civet using pip, you will need to update civet in the same way (pip install .)
  • Try pip uninstall civet and then re-install with python setup.py install

Next: Input options