Merge pull request #391 from NIEHS/dev

Dev
NIEHS · Feb 26, 2025 · ee2cb89 · ee2cb89
2 parents 6a7a40e + e4f98d2
commit ee2cb89
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diff --git a/Docker/Dockerfile-base b/Docker/Dockerfile-base
@@ -1,22 +1,20 @@
-FROM nvidia/cuda:12.1.0-base-ubuntu20.04
+FROM ubuntu:24.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && apt-get install -y \
-	python3-dev default-libmysqlclient-dev build-essential wget libglib2.0-0 ffmpeg libsm6 libxext6 curl mariadb-server git && \
+	python3-dev default-libmysqlclient-dev build-essential wget libglib2.0-0 ffmpeg libsm6 libxext6 curl mariadb-server git pkg-config && \
 	apt-get clean && rm -rf /var/cache/apt/lists
 
 # RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
 # 	bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 && \
 # 	rm Miniconda3-latest-Linux-x86_64.sh
 
-RUN wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.11.24_RHEL7-64_CUDA10.1.sh && ls && \
-	yes | bash imod_4.11.24_RHEL7-64_CUDA10.1.sh -name IMOD && \
-	rm imod_4.11.24_RHEL7-64_CUDA10.1.sh
+COPY --link IMOD /usr/local/IMOD
 
-ADD config/singularity/ctffind /usr/local/
-
-ENV PATH=$PATH:/opt/miniconda3/bin
+ENV IMOD_DIR=/usr/local/IMOD
+ENV PATH=$PATH:/opt/miniforge3/bin:/usr/local/IMOD/bin
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/IMOD/lib
 
 # RUN conda update -y conda && \
 # 	yes | conda install python=3.9 && \

diff --git a/Docker/Dockerfile-smartscope b/Docker/Dockerfile-smartscope
@@ -1,4 +1,4 @@
-FROM smartscope-base-test
+FROM 20241029-base
 
 ARG VERSION='0.8-rc.2'
 ARG BRANCH='stable'
@@ -47,7 +47,7 @@ ENV PATH=$PATH:/opt/smartscope/Smartscope/bin:/usr/local/IMOD/bin
 
 COPY --link Template_files/ /opt/Template_files/
 COPY --link ctffind /opt/
-COPY --link miniconda3/ /opt/miniconda3/
+COPY --link miniforge3/ /opt/miniforge3/
 COPY smartscope/ /opt/smartscope/
 COPY external_plugins/ /opt/external_plugins/
 COPY Smartscope-connector /opt/Smartscope-connector/

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diff --git a/SerialEM-python/.hg/store/data/_py_s_e_m_socket.cpp.i b/SerialEM-python/.hg/store/data/_py_s_e_m_socket.cpp.i
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diff --git a/SerialEM-python/.hg/store/data/buildall.bat.i b/SerialEM-python/.hg/store/data/buildall.bat.i
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diff --git a/SerialEM-python/.hg/store/data/stdafx.cpp.i b/SerialEM-python/.hg/store/data/stdafx.cpp.i
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diff --git a/SerialEM-python/MacroMasterList.h b/SerialEM-python/MacroMasterList.h