Installation

Protlego can be installed via github, pip, or conda.

PIP installation

To install Protlego via pip, type:

pip install protlego

Graph-tool is not included in Pypi, you will need to install it separately. To do so, please refer to the graph-tool documentation: https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions

CONDA installation

We only support Linux at the moment. To install Protlego via conda, you will first have to install conda. If you are familiar with conda you might already have an environment, otherwise create one as follows:

conda create -n myenv

And then activate it:

conda activate myenv

Later, you might need to add some channels:

conda config --append channels bioconda
conda config --append channels conda-forge
conda config --append channels acellera

And then you are good to install protlego:

conda install -c nferruz protlego

Once the environment installed, you can start designing chimeras with protlego!

Setup

You will need a Fuzzle database. You can download the latest version here: https://fuzzle.uni-bayreuth.de:8443/static/fuzzle2.07.db

Then place it in your protle place it in your protlego folder. If you don’t know where your protlego folder got installed, import protlego in a python terminal and see its path:

$ python
>>> import protlego
>>> protlego.__file__

Installing from environment file

If you have issues installing Protlego, please post an issue in our GitHub repository and we will assist you. Alternatively, you can create a conda environment directly from the requirements.

Download the environment file from our repository: https://github.com/Hoecker-Lab/protlego And then:

conda env create -f environment.yml

Troubleshooting

Post issues in our GitHub repository: https://github.com/Hoecker-Lab/protlego/issues/