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Get the code

First, download and checkout the latest release

# from a directory of your choice
git clone https://github.com/weberlab-hhu/Helixer.git
cd Helixer
# git checkout dev # v0.2.0

System dependencies

Python 3.10

Python development libraries

Ubuntu (& co.)

sudo apt install python3-dev

Fedora (& co.)

sudo dnf install python3-devel

Virtualenv (optional)

We recommend installing all the python packages in a virtual environment: https://docs.python-guide.org/dev/virtualenvs/

For example, create and activate an environment called 'env':

python3 -m venv env
source env/bin/activate

The steps below assume you are working in the same environment.

GPU requirements (optional, but highly recommended for realistically sized datasets)

And to run on a GPU (highly recommended for realistically sized datasets), everything for tensorflow-gpu is required, see: https://www.tensorflow.org/install/gpu

# Linux instructions from the tensorflow GPU install
pip install tensorflow[and-cuda]  # inside a virtual environment, otherwise use: python3 -m pip install tensorflow[and-cuda]
# Verify the installation:
python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"

# sometimes the following error will pop up: Unable to register cuDNN factory... (and other factories)
# sometimes the following warning will pop up: tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
# usually those can be ignored and will not impair Helixer's performance

The following has been most recently tested.

system packages:

  • cuda-12-2
  • libcudnn8
  • libcudnn8-dev
  • nvidia-driver-555

A GPU with 11GB Memory (e.g. GTX 1080 Ti) can run the largest configurations described below, for smaller GPUs you might have to reduce the network or batch size.

Post processor

https://github.com/TonyBolger/HelixerPost

Setup according to included instructions and further add the compiled helixer_post_bin to your system PATH.

Most python dependencies of Helixer

You may need to run pip install --upgrade pip and pip install wheel first before continuing with installing Helixer and it's requirements. So when in doubt, just run these commands first.

# from the Helixer directory
pip install -r requirements.3.10.txt

Helixer itself

# from the Helixer directory
pip install .  # or `pip install -e .`, if you will be changing the code

Test Helixer

Helixer comes with test data and unit tests.

# switch to the Helixer code subdirectory
cd Helixer/helixer
# run the unit tests
pytest --verbose tests/test_helixer.py