From e72aec3cc50dacdfa0f9e04c87a55ad3ab8a7e4a Mon Sep 17 00:00:00 2001
From: Daniel Asay <danielasay@fas.harvard.edu>
Date: Wed, 4 Dec 2024 13:12:28 -0500
Subject: [PATCH] updated dockerfile with python 3.13

---
 Dockerfile | 70 +++++++++++++++++++++++++-----------------------------
 1 file changed, 32 insertions(+), 38 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3f510ea..ec41acd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,37 +1,28 @@
-FROM rockylinux:8
+FROM rockylinux:9
 
-# Install necessary packages
-RUN dnf install -y git vim tcsh libpng15 motif make curl clang zlib-devel \
-    libXt-devel libXext-devel expat-devel motif-devel f2c unzip cmake gcc-c++ \
-    epel-release && \
-    dnf --enablerepo=powertools install -y libstdc++-static
+# install some base necessities
+RUN dnf install -y git vim
+RUN dnf install -y epel-release
+RUN dnf install -y conda
+RUN conda create -y -n python3.13t --override-channels -c conda-forge python-freethreading
+RUN conda env config vars set PYTHON_GIL=0 -n python3.13t
+RUN conda run -n python3.13t --no-capture-output python3 -m pip install git+https://github.com/harvard-nrg/scanbuddy.git
+RUN conda run -n python3.13t start.py --help # ENTRYPOINT ["conda", "run", "-n", "python3.13t", "start.py"]
+#RUN dnf install -y git vim python3.13 && \
+#    alternatives --set python /usr/bin/python3
 
-# Install Mambaforge
-WORKDIR /tmp
-RUN curl -L https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Mambaforge-24.9.2-0-Linux-x86_64.sh -o Mambaforge-24.9.2-0.sh && \
-    chmod 755 Mambaforge-24.9.2-0.sh && \
-    ./Mambaforge-24.9.2-0.sh -b -p /opt/conda && \
-    rm Mambaforge-24.9.2-0.sh
-ENV PATH=/opt/conda/bin:$PATH
-
-# Create a Conda environment with Python 3.13
-RUN conda create -n py313 python=3.13 python-freethreading -c conda-forge/label/python_rc -c conda-forge && \
-    echo "conda activate py313" >> ~/.bashrc
-ENV CONDA_DEFAULT_ENV=py313
-ENV PATH /opt/conda/envs/py313/bin:$PATH
-
-# Verify Python version
-RUN python --version
-
-# Create a home directory
+# create a home directory
 RUN mkdir -p /home/scanbuddy
 ENV HOME=/home/scanbuddy
 
-# Compile and install 3dvolreg from AFNI (linux/amd64 and linux/arm64/v8)
+# compile and install 3dvolreg from AFNI (linux/amd64 and linux/arm64/v8)
 ARG AFNI_PREFIX="/sw/apps/afni"
 ARG AFNI_URI="https://github.com/afni/afni"
 WORKDIR /tmp
-RUN git clone "${AFNI_URI}"
+RUN dnf install -y epel-release && \
+    dnf install -y --allowerasing curl tcsh libpng15 motif && \
+    dnf install -y make clang zlib-devel libXt-devel libXext-devel expat-devel motif-devel f2c && \
+    git clone "${AFNI_URI}"
 WORKDIR afni/src
 RUN cp other_builds/Makefile.linux_ubuntu_22_64 Makefile && \
     make libmri.a 3dvolreg && \
@@ -39,12 +30,15 @@ RUN cp other_builds/Makefile.linux_ubuntu_22_64 Makefile && \
     mv 3dvolreg "${AFNI_PREFIX}" && \
     rm -r /tmp/afni
 
-# Compile and install dcm2niix (linux/amd64 and linux/arm64/v8)
+# compile and install dcm2niix (linux/amd64 and linux/arm64/v8)
 ARG D2N_PREFIX="/sw/apps/dcm2niix"
 ARG D2N_VERSION="1.0.20220720"
 ARG D2N_URI="https://github.com/rordenlab/dcm2niix/archive/refs/tags/v${D2N_VERSION}.zip"
-WORKDIR /tmp
-RUN curl -sL "${D2N_URI}" -o "dcm2niix_src.zip" && \
+WORKDIR "/tmp"
+RUN dnf install -y unzip cmake gcc-c++ && \
+    dnf config-manager --set-enabled crb && \
+    dnf install -y libstdc++-static && \
+    curl -sL "${D2N_URI}" -o "dcm2niix_src.zip" && \
     unzip "dcm2niix_src.zip" && \
     rm "dcm2niix_src.zip" && \
     mkdir "dcm2niix-${D2N_VERSION}/build"
@@ -55,23 +49,23 @@ RUN cmake .. && \
     cp bin/dcm2niix "${D2N_PREFIX}" && \
     rm -r "/tmp/dcm2niix-${D2N_VERSION}"
 
-# Install scanbuddy
+# install scanbuddy
 ARG SB_PREFIX="/sw/apps/scanbuddy"
-ARG SB_VERSION="v0.1.7"
-RUN python -m venv "${SB_PREFIX}" && \
-    dnf install -y gcc zlib-devel libjpeg-devel python39-tkinter && \
+ARG SB_VERSION="v0.1.10"
+RUN python3 -m venv "${SB_PREFIX}" && \
+    dnf install -y gcc zlib-devel libjpeg-devel python3-tkinter && \
     "${SB_PREFIX}/bin/pip" install "git+https://github.com/harvard-nrg/scanbuddy.git@${SB_VERSION}"
 
-# Set up AFNI environment
+# set up afni environment
 ENV PATH="${AFNI_PREFIX}:${PATH}"
 
-# Set up dcm2niix environment
+# set up dcm2niix environment f
 ENV PATH="${D2N_PREFIX}:${PATH}"
 
-# Set up scanbuddy
+# set up scanbuddy
 ENV TERM="xterm-256color"
 
-# Expose port
+# expose port
 EXPOSE 11112
 
-ENTRYPOINT ["/sw/apps/scanbuddy/bin/start.py"]
\ No newline at end of file
+ENTRYPOINT ["/sw/apps/scanbuddy/bin/start.py"]