rm older dockrfiles

.github/workflows/docker.yml

@@ -13,10 +13,6 @@ concurrency:
 jobs:
 
     build:
-        strategy:
-            matrix:
-                image: [Dockerfile_1]
-            fail-fast: false
         runs-on: ubuntu-latest
         steps:
         -   uses: actions/checkout@v4
@@ -26,7 +22,7 @@ jobs:
             run: make tests/data/MoAEpilot
         -   name: Build the Docker image
             run: |
-                docker build . --file ${{ matrix.image }} --tag cat12
+                docker build . --tag cat12
                 docker images
         -   name: help
             run: docker run --rm cat12 view cat_standalone_segment.m

CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [Unreleased]

Dockerfile

@@ -1,58 +1,72 @@
-FROM debian:bookworm-slim@sha256:5f7d5664eae4a192c2d2d6cb67fc3f3c7891a8722cd2903cc35aa649a12b0c8d
+FROM ubuntu:22.04@sha256:340d9b015b194dc6e2a13938944e0d016e57b9679963fdeb9ce021daac430221
 
-LABEL org.opencontainers.image.authors="[email protected], Malgorzata Wierzba ([email protected]), Felix Hoffstaedter ([email protected])"
+LABEL org.opencontainers.image.authors="[email protected], Malgorzata Wierzba ([email protected]), Felix Hoffstaedter ([email protected]), Remi Gau ([email protected])"
 LABEL org.opencontainers.image.source="https://gin.g-node.org/felixh/cat12-container"
-LABEL org.opencontainers.image.version="v1.1"
-
-ARG DEBIAN_FRONTEND="noninteractive"
-
-ENV CATversion="r2560"
-ENV STANDALONE="/opt/spm12/toolbox/cat12/standalone"
-
-RUN apt-get update -qq && \
-    apt-get -qq -y --no-install-recommends install \
-        build-essential \
-        ca-certificates \
-        curl \
-        unzip \
-        liboctave-dev \
-        libxext6 \
-        libxt6 \
-        moreutils \
-        octave \
-        wget \
-    && apt-get clean \
-    && rm -rf \
-        /tmp/hsperfdata* \
-        /var/*/apt/*/partial \
-        /var/lib/apt/lists/* \
-        /var/log/apt/term*
-
-#  install SPM12
-RUN mkdir /opt/spm12 \
-    && curl -fsSL --retry 5 https://github.com/spm/spm12/archive/r7771.tar.gz | tar -xzC /opt/spm12 --strip-components 1 \
-    && curl -fsSL --retry 5  https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch | patch -p0 \
-    && make -C /opt/spm12/src PLATFORM=octave distclean \
-    && make -C /opt/spm12/src PLATFORM=octave \
-    && make -C /opt/spm12/src PLATFORM=octave install \
-    && ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
+LABEL org.opencontainers.image.version="v1.1dev"
+LABEL org.opencontainers.image.licenses="MIT"
+LABEL org.opencontainers.image.title="cat12-container"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    FORCE_SPMMCR="1" \
+    SPM_HTML_BROWSER="0" \
+    MCR_INHIBIT_CTF_LOCK="1" \
+    MCR_VERSION="2017b"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-${MCR_VERSION}/v93/runtime/glnxa64:/opt/MCR-${MCR_VERSION}/v93/bin/glnxa64:/opt/MCR-${MCR_VERSION}/v93/sys/os/glnxa64:/opt/MCR-${MCR_VERSION}/v93/extern/bin/glnxa64" \
+    MATLABCMD="/opt/MCR-${MCR_VERSION}/v93/toolbox/matlab" \
+    XAPPLRESDIR="/opt//opt/MCR-${MCR_VERSION}/v93/x11/app-defaults" \
+    MCRROOT="/opt/MCR-${MCR_VERSION}/v93" \
+    CAT_VERSION=".8.1_r2042_R${MCR_VERSION}"
+ENV SPMROOT="/opt/CAT12${CAT_VERSION}" \
+    PATH="/opt/CAT12${CAT_VERSION}:$PATH" \
+    STANDALONE="/opt/CAT12${CAT_VERSION}/standalone"
+
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bc \
+           bzip2 \
+           ca-certificates \
+           curl \
+           dbus-x11 \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+           locales \
+           openjdk-8-jre \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt
+
+RUN echo "Downloading MATLAB Compiler Runtime ..." \
+    && export TMPDIR="$(mktemp -d)" \
+    && curl  -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R${MCR_VERSION}/deployment_files/R${MCR_VERSION}/installers/glnxa64/MCR_R${MCR_VERSION}_glnxa64_installer.zip \
+    && unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
+    && "$TMPDIR/mcrtmp/install" -destinationFolder /opt/MCR-${MCR_VERSION} -mode silent -agreeToLicense yes \
+    && rm -rf "$TMPDIR" \
+    && unset TMPDIR
+
+RUN echo "Downloading standalone CAT12 ..." \
+    && curl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12${CAT_VERSION}_MCR_Linux.zip \
+    && unzip -q /tmp/cat12.zip -d /tmp \
+    && rm -rf /tmp/cat12.zip \
+    && mkdir -p /opt/CAT12${CAT_VERSION} \
+    && mv /tmp/*${CAT_VERSION}*/* /opt/CAT12${CAT_VERSION}/ \
+    && chmod -R 777 /opt/CAT12${CAT_VERSION} \
+    # Test
+    && /opt/CAT12${CAT_VERSION}/spm12 function exit
 
 # transfer code and set permission
 RUN mkdir -p /code
 COPY ./code /code
 RUN ls /code && find /code -type f -print0 | xargs -0 chmod +r
 
-# install CAT12
-RUN mkdir -p /batch \
-    && mkdir -p /downloads \
-    && cd /downloads \
-    && wget http://www.neuro.uni-jena.de/cat12/cat12_${CATversion}.zip && unzip -d /opt/spm12/toolbox/ cat12_${CATversion}.zip \
-    && rm -fr /downloads \
-    && cd ${STANDALONE} && chmod +rx *.sh \
-    && cd /code && ln -s ${STANDALONE}/*.sh . \
-    && cd /batch && ln -s ${STANDALONE}/*.m .
-
-# clean
-RUN rm -f /opt/spm12/src/*.{mex,o,a}
+WORKDIR ${STANDALONE}
 
-ENTRYPOINT ['/code/main "$@"']
+ENTRYPOINT ["/code/main"]