Build/install the thing with pip.

docker/Dockerfile

@@ -8,27 +8,19 @@ ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update && apt-get install --assume-yes apt-transport-https \
 	ca-certificates gnupg software-properties-common gcc git wget numactl cmake
 
-# Anaconda
-RUN cd /opt && wget -P /tmp https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh \
-    && bash /tmp/Anaconda3-2020.02-Linux-x86_64.sh -b -p /opt/anaconda \
-    && rm -rf /tmp/Anaconda3-2020.02-Linux-x86_64.sh \
-    && eval "$(/opt/anaconda/bin/conda shell.bash hook)"
+RUN wget -P /tmp https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh
+RUN bash /tmp/Anaconda3-2022.10-Linux-x86_64.sh -b -p /opt/anaconda
+RUN rm -rf /tmp/Anaconda3-2022.10-Linux-x86_64.sh
+RUN cd /opt && eval "$(/opt/anaconda/bin/conda shell.bash hook)"
 ENV PATH /opt/anaconda/bin:${PATH}
 ENV LD_LIBRARY_PATH /opt/anaconda/lib:${LD_LIBRARY_PATH}
 
 # python prereqs
 RUN pip install numpy scipy cython nibabel dipy tqdm
 
 # copy stuff
-COPY CMakeLists.txt /opt/GPUStreamlines/CMakeLists.txt
-COPY run_dipy_gpu.py /opt/GPUStreamlines/run_dipy_gpu.py
-COPY run_dipy_cpu.py /opt/GPUStreamlines/run_dipy_cpu.py
-COPY run_dipy_gpu_hardi.py /opt/GPUStreamlines/run_dipy_gpu_hardi.py
-COPY run_dipy_cpu_hardi.py /opt/GPUStreamlines/run_dipy_cpu_hardi.py
-COPY merge_trk.sh /opt/exec/merge_trk.sh
-COPY cuslines /opt/GPUStreamlines/cuslines
-COPY external /opt/GPUStreamlines/external
-RUN mkdir -p /opt/exec/output
+COPY . /opt/GPUStreamlines
+RUN /opt/GPUStreamlines && pip install .
 
 # compile
 RUN cd /opt/GPUStreamlines && mkdir build && cd build \