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| # requirement: anaconda | |
| conda install virtualenv | |
| python3 -m venv ~/deepG_env | |
| source ~/deepG_env/bin/activate | |
| # deepG is tested with tensorflow 1.14 | |
| pip3 install https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.14.0-cp37-cp37m-linux_x86_64.whl | |
| pip3 install keras | |
| # setup cuda, required is cuda10 and cudnn 7.4 | |
| conda install -c anaconda cudatoolkit | |
| conda install -c fragcolor cuda10.0 | |
| conda install pytorch | |
| export LD_LIBRARY_PATH=LD_LIBRARY_PATH:/usr/local/cuda-9.0/lib64/ |
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| # requirement: devtools, reticulate_1.12 | |
| # cave: previous version of reticulate cannot make use of the pip3 environment and will lead to an error when executing line 7 | |
| # python3 is not supported on reticulate_1.10 !!! So you may want to update packages using update.packages(ask=F) | |
| devtools::install_github("rstudio/tensorflow") | |
| library(tensorflow) | |
| library(keras) | |
| use_virtualenv("~/deepG_env/", required = TRUE) | |
| use_condaenv(condaenv = "myenv", required=TRUE) | |
| keras::load_model_hdf5("example_files/GenomeNet_v1.hdf5") |
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