Install

Requirements

This package requires Python 3.7 or later. It is tested on Linux, but should also run on MacOS and Windows, with some limitations regarding parallelization.

Dependencies

This package relies on the tools morpheus and pyABC.

To install morpheus, checkout https://morpheus.gitlab.io/#download.
To install pyabc, checkout https://pyabc.readthedocs.io/en/latest/installation.html.

Install from PIP

The package can be installedd from the Python Package Index PyPI via pip:

pip3 install fitmulticell

Install from GIT

If you want the bleeding edge version, install directly from gitlab:

pip3 install git+https://gitlab.com/fitmulticell/fit

If you need to have access to the source code, you can instead download it via:

git clone https://gitlab.com/fitmulticell/fit

and then install from the local repository via:

cd fit
pip3 install -e .

Install as user into your home directory (recommended)

Installing fitmulticell into your system’s Python distribution can be problematic as you might not want to change your system’s Python installation or you don’t have root rights. The recommended alternative is to install fitmulticell into your home directory with:

pip3 install --user fitmulticell

Install on AWS

Here is a link to a video that explains how to install the FitMultiCell pipeline in the AWS Amazon cloud:

https://cloudstore.zih.tu-dresden.de/index.php/s/NMiLZmpktaGGgWp

Moreover, here is the list of commands used in the video:

sudo apt update
sudo apt install --yes libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 \
libxcomposite1 libasound2 libxi6 libxtst6 gnuplot-nox joe
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
bash Anaconda3-2020.11-Linux-x86_64.sh
source ~/.bashrc
pip install jupyter
pip install pyabc
pip install fitmulticell
openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout mykey.key -out mycert.pem
jupyter notebook password
jupyter notebook --generate-config
jupyter notebook &

Upgrade

If you want to upgrade an installation, replace install by install --upgrade in the above pip commands.