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Installation

We recommend using SeqDesign with a GPU that supports CUDA, especially for training. If a GPU is available, install the TensorFlow GPU dependencies, then install the SeqDesign dependencies with:

pip install -r requirements_gpu.txt

Using the linux_setup.sh script, installation on a fresh Ubuntu 18.04 LTS machine took 5 minutes.

If no GPU is available, use:

pip install -r requirements.txt

Then install SeqDesign:

python setup.py install

Used software and versions tested:

  • python - 3.7
  • tensorflow - 1.15
  • numpy - 1.15
  • scipy - 0.19
  • sklearn - 0.18

Tested on Ubuntu 18.04 LTS