Installation

Instructions for installing polecat locally

Requirements

polecat runs on MacOS and Linux. The conda environment recipe may not build on Windows (and is not supported) but polecat 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 polecat

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

Note: we recommend using polecat 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 polecat environment):

polecat

and you should see the help menu of polecat printed

Updating polecat

To update:

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

Troubleshooting update

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

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