Use system version of cmake instead of python version

docker/Dockerfile

@@ -45,7 +45,6 @@ RUN wget -q https://bootstrap.pypa.io/get-pip.py && \
 
 # Install required Python packages
 RUN python3 -m pip install --no-cache-dir \
-    cmake \
     numpy \
     nodejs-wheel \
     toil[cwl]