diff --git a/Dockerfile b/Dockerfile index a14ec26dfc..d73e1a9791 100644 --- a/Dockerfile +++ b/Dockerfile @@ -56,27 +56,6 @@ COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exc RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \ | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt -# AFNI -FROM downloader as afni -# Bump the date to current to update AFNI -RUN echo "2023.04.04" -RUN mkdir -p /opt/afni-latest \ - && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \ - | tar -xz -C /opt/afni-latest --strip-components 1 \ - --exclude "linux_openmp_64/*.gz" \ - --exclude "linux_openmp_64/funstuff" \ - --exclude "linux_openmp_64/shiny" \ - --exclude "linux_openmp_64/afnipy" \ - --exclude "linux_openmp_64/lib/RetroTS" \ - --exclude "linux_openmp_64/lib_RetroTS" \ - --exclude "linux_openmp_64/meica.libs" \ - # Keep only what we use - && find /opt/afni-latest -type f -not \( \ - -name "3dTshift" -or \ - -name "3dUnifize" -or \ - -name "3dAutomask" -or \ - -name "3dvolreg" \) -delete - # Connectome Workbench 1.5.0 FROM downloader as workbench RUN mkdir /opt/workbench && \ @@ -128,43 +107,8 @@ RUN apt-get update && \ xvfb && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -# Configure PPAs for libpng12 and libxp6 -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 - -# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04) -RUN apt-get update -qq \ - && apt-get install -y -q --no-install-recommends \ - ed \ - gsl-bin \ - libglib2.0-0 \ - libglu1-mesa-dev \ - libglw1-mesa \ - libgomp1 \ - libjpeg62 \ - libpng12-0 \ - libxm4 \ - libxp6 \ - netpbm \ - tcsh \ - xfonts-base \ - xvfb \ - && curl -sSL --retry 5 -o /tmp/multiarch.deb http://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/* \ - && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \ - && if [ -n "$gsl2_path" ]; then \ - ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \ - fi \ - && ldconfig - # Install files from stages COPY --from=freesurfer /opt/freesurfer /opt/freesurfer -COPY --from=afni /opt/afni-latest /opt/afni-latest COPY --from=workbench /opt/workbench /opt/workbench # Simulate SetUpFreeSurfer.sh @@ -184,11 +128,6 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" -# AFNI config -ENV PATH="/opt/afni-latest:$PATH" \ - AFNI_IMSAVE_WARNINGS="NO" \ - AFNI_PLUGINPATH="/opt/afni-latest" - # Workbench config ENV PATH="/opt/workbench/bin_linux64:$PATH" \ LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"