biota is written in Python and was developped on a Linux platform. Provided you can use Python and can install modules on your computer, it should be possible to run on most OS or a Linux server.
On this page, we explain how to set up your Linux or Windows machine to use biota.
We recommend running
biota in Anaconda.
If you are using a Linux machine, open a terminal window, change directory to the location you downloaded Anaconda Python, and run the following commands:
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh bash Anaconda3-2020.11-Linux-x86_64.sh
Once complete, you’ll need to add this version of Python to your .bashrc file as follows (replacing
~/ with your installation directory):
# Substitute root for the path to your system's installation and .bashrc file. echo 'export PATH="~/anaconda3/bin:$PATH"' >> ~/.bashrc exec -l $SHELL
If this has functioned, on executing
python in a terminal window, you should see the following:
Python 2.7.12 |Anaconda custom (64-bit)| (default, Jul 2 2016, 17:42:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org >>>
For Windows users, go to the Anaconda website ) and download the installer for your version of Windows (64-bit or 32-bit). Once the download is finished, run the installer. This may take a while, but when it is done you will be able to open the Anaconda Prompt.
Setting up your Anaconda environment¶
To ensure you are working with the appropriate version of Python as well as the correct modules, we recommend that you create an Anaconda virtual environment set up for running
biota. This is done by running the following commands in your terminal or the Anaconda prompt (recommended procedure):
conda create -n biota -c conda-forge python=3.7 tqdm scikit-image pillow pyshp gdal
the GDAL package is notoriously temperamental. If this step fails, try again and add ` openssl=1.0` at the end of the line
biota environment whenever opening a new terminal window by running this command:
conda activate biota
Remember to activate the
biota environment whenever you want to use
If you are SURE you won’t use anything else than biota, you can do without virtual environments. In this case, just type:
conda install -c conda-forge python=3.7 tqdm scikit-image pillow pyshp gdal
If you want to use the biota graphical interface, you need an extra package called PyQt5. To install it, type:
pip install pyqt5
Navigate to the folder where you want to install biota. To do this in both Linuw and Windows, type the following:
If you don’t want to type the full path (and really, you souldn’t), copy it from your file explorer into the terminal after the `cd ` command.
biota, you will need to use the version control software
git (if you don’t have
git, follow the instructions here ). You can collect the
biota source code with the command:
git clone https://github.com/smfm-project/biota.git
biota, run the following command:
python setup.py install
Congratulations, you are now ready to use biota.