This project has submodules. To get their content there are multiple options:

• Clone the repository with the --recurse-submodules option
• Initialize submodules after cloning with: git submodule update --init --recursive

For the snakemake conda environment use:

conda env create --prefix snakemake --file env.yaml

Also you need to configure the keras backend file ~/.keras/keras.json:

• change "backend": "tensorflow"to "backend": "theano"

• I changed DeepBind so it takes variables from snakemake for running
• I changed iDeepS to save the file structure.gz in model_dir instead of ./ (by default methods/iDeepS). This makes parallel execution more easy!
• Also I change the environment (THEANO_FLAGS) so that every job running iDeepS has a different base_compiledir to avoid locking the theanos compile directory