From f6de3a448cb6950722edf99319a138385a47cf10 Mon Sep 17 00:00:00 2001
From: Daniel Asay <danielasay@fas.harvard.edu>
Date: Fri, 3 Jan 2025 12:04:28 -0500
Subject: [PATCH] add Dockerfile for building on debian

---
 debian/Dockerfile | 64 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 debian/Dockerfile

diff --git a/debian/Dockerfile b/debian/Dockerfile
new file mode 100644
index 0000000..995c9b4
--- /dev/null
+++ b/debian/Dockerfile
@@ -0,0 +1,64 @@
+FROM ubuntu:focal
+
+# create a home directory
+RUN mkdir -p /home/scanbuddy
+ENV HOME=/home/scanbuddy
+
+RUN apt-get update
+
+RUN apt-get install -y git
+
+# 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 "${AFNI_URI}"
+WORKDIR afni/src
+ARG DEBIAN_FRONTEND=noninteractive
+ARG TZ="America/New_York"
+RUN apt-get install -y make cmake
+RUN apt-get install -y zlib1g-dev libxt-dev libxtst-dev libexpat1-dev libmotif-dev
+RUN cp other_builds/Makefile.linux_ubuntu_22_64 Makefile && \
+    make libmri.a 3dvolreg && \
+    mkdir -p "${AFNI_PREFIX}" && \
+    mv 3dvolreg "${AFNI_PREFIX}" && \
+    rm -r /tmp/afni
+ENV PATH="${AFNI_PREFIX}:${PATH}"
+
+# compile and install dcm2niix (linux/amd64 and linux/arm64/v8)
+ARG D2N_PREFIX="/sw/apps/dcm2niix"
+#ARG D2N_VERSION="1.0.20220720"
+ARG D2N_VERSION="1.0.20241211"
+ARG D2N_URI="https://github.com/rordenlab/dcm2niix/archive/refs/tags/v${D2N_VERSION}.zip"
+WORKDIR "/tmp"
+RUN apt-get install -y curl unzip g++ vim-nox
+RUN curl -sL "${D2N_URI}" -o "dcm2niix_src.zip" && \
+    unzip "dcm2niix_src.zip" && \
+    rm "dcm2niix_src.zip" && \
+    mkdir "dcm2niix-${D2N_VERSION}/build"
+WORKDIR "/tmp/dcm2niix-${D2N_VERSION}/build"
+RUN cmake .. && \
+    make && \
+    mkdir -p "${D2N_PREFIX}" && \
+    cp bin/dcm2niix "${D2N_PREFIX}" && \
+    rm -r "/tmp/dcm2niix-${D2N_VERSION}"
+ENV PATH="${D2N_PREFIX}:${PATH}"
+
+# install miniforge
+ARG MFG_PREFIX="/sw/miniforge"
+WORKDIR "/tmp"
+RUN curl -sL "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -o "miniforge.sh"
+RUN bash "miniforge.sh" -b -p "${MFG_PREFIX}"
+RUN rm "miniforge.sh"
+ENV PATH="${MFG_PREFIX}/bin:${PATH}"
+
+# install scanbuddy
+RUN mamba create -y -n python3.13t --override-channels -c conda-forge python-freethreading
+RUN mamba env config vars set PYTHON_GIL=0 -n python3.13t
+ARG SB_VERSION="main"
+COPY requirements.txt /tmp/requirements.txt
+RUN apt-get install -y libjpeg-dev libf2c2-dev
+RUN mamba run -n python3.13t --no-capture-output python3 -m pip install -r /tmp/requirements.txt
+RUN mamba run -n python3.13t --no-capture-output python3 -m pip install "git+https://github.com/harvard-nrg/scanbuddy.git@${SB_VERSION}"
+
+ENTRYPOINT ["mamba", "run", "-n", "python3.13t", "--no-capture-output", "start.py"]