Dockerfile.base

# XCP-D Docker base image
#
# Runtime environment with non-Python/non-conda dependencies.

# Ubuntu 22.04 LTS - Jammy
ARG BASE_IMAGE=ubuntu:jammy-20250730

#
# Download stages
#

# Utilities for downloading packages
FROM ${BASE_IMAGE} AS downloader
ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    HOME="/home/xcp_d"

# Bump the date to refresh curl/certificates/etc
RUN echo "2025.02.25"
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    binutils \
                    bzip2 \
                    ca-certificates \
                    curl \
                    unzip && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

#
# Main stage
#
FROM ${BASE_IMAGE} AS base

# Configure apt
ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8"

# Install AFNI subset directly from AFNI Docker image
COPY --link --from=afni/afni_make_build:AFNI_25.2.09 \
    /opt/afni/install/libf2c.so \
    /usr/lib/x86_64-linux-gnu/libgsl.so \
    /usr/lib/x86_64-linux-gnu/libgsl.so.23 \
    /usr/lib/x86_64-linux-gnu/libgslcblas.so \
    /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 \
    /opt/afni/install/libmri.so \
    /usr/local/lib/
COPY --link --from=afni/afni_make_build:AFNI_25.2.09 \
    /opt/afni/install/3dReHo \
    /opt/afni/install/3dDespike \
    /opt/afni/install/3dFWHMx \
    /opt/afni-bin/
RUN chmod +x /opt/afni-bin/3dReHo /opt/afni-bin/3dDespike /opt/afni-bin/3dFWHMx

# Baseline system packages (libs for Workbench/FSL/AFNI)
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    ca-certificates \
                    curl \
                    git \
                    gnupg \
                    libgomp1 \
                    libopenblas0-openmp \
                    lsb-release \
                    netbase \
                    pandoc \
                    xvfb && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# PPAs and packages for FreeSurfer/Workbench (libpng12, libxp, netpbm, etc.)
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
    && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
    && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
    && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           connectome-workbench=1.5.0-2 \
           ed \
           gsl-bin \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libjpeg62 \
           libpng12-0 \
           libxm4 \
           libxp6 \
           netpbm \
           tcsh \
           xfonts-base \
    && curl -sSL --retry 5 -o /tmp/multiarch.deb https://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
    && dpkg -i /tmp/multiarch.deb \
    && rm /tmp/multiarch.deb \
    && apt-get install -f \
    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && gsl_path="$(ldconfig -p | awk '/libgsl\.so\.[0-9]+/{print $NF; exit}')" \
    && if [ -n "$gsl_path" ] && [ "$(basename "$gsl_path")" != "libgsl.so.0" ]; then ln -sfv "$gsl_path" "$(dirname "$gsl_path")/libgsl.so.0"; fi \
    && gslcblas_path="$(ldconfig -p | awk '/libgslcblas\.so\.[0-9]+/{print $NF; exit}')" \
    && if [ -n "$gslcblas_path" ] && [ "$(basename "$gslcblas_path")" != "libgslcblas.so.0" ]; then ln -sfv "$gslcblas_path" "$(dirname "$gslcblas_path")/libgslcblas.so.0"; fi \
    && ldconfig

# Download atlases from AtlasPack (stored in tar.gz file on Box)
RUN mkdir -p "/home/xcp_d/.cache/xcp_d" && \
    curl -o AtlasPack.tar.gz -sSL "https://upenn.box.com/shared/static/0gxdoe77tuih5p9ainn4utdqj3kcq7p1.tar.gz" && \
    tar -xzf AtlasPack.tar.gz && \
    mv AtlasPack "/home/xcp_d/.cache/xcp_d/AtlasPack" && \
    rm AtlasPack.tar.gz

# Download XCP-D atlases (stored in tar.gz file on Box)
RUN mkdir -p "/home/xcp_d/.cache/xcp_d" && \
    curl -o XCPDAtlases.tar.gz -sSL "https://upenn.box.com/shared/static/4amxp72grenmp1up689k5oyn1i6nhunq.tar.gz" && \
    tar -xzf XCPDAtlases.tar.gz && \
    mv XCPDAtlases "/home/xcp_d/.cache/xcp_d/XCPDAtlases" && \
    rm XCPDAtlases.tar.gz && \
    find "/home/xcp_d/.cache/xcp_d" -type d -exec chmod go=u {} + && \
    find "/home/xcp_d/.cache/xcp_d" -type f -exec chmod go=u {} +

# AFNI
ENV PATH="/opt/afni-bin:$PATH" \
    AFNI_IMSAVE_WARNINGS="NO" \
    AFNI_PLUGINPATH="/opt/afni-bin"

# FSL / runtime (FSLDIR is set in the main Dockerfile, pointing to the pixi env)
ENV LANG="C.UTF-8" \
    LC_ALL="C.UTF-8" \
    PYTHONNOUSERSITE=1 \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"

RUN ldconfig
WORKDIR /tmp

LABEL org.label-schema.name="xcp_d-base" \
      org.label-schema.description="XCP-D base image - runtime dependencies without the xcp_d package" \
      org.label-schema.url="https://xcp-d.readthedocs.io/" \
      org.label-schema.vcs-url="https://github.com/PennLINC/xcp_d" \
      org.label-schema.schema-version="1.0"