Support for compiling FreeSurfer from source

neurodocker/templates/freesurfer.yaml

@@ -7,6 +7,9 @@
     - version
     optional:
       install_path: /opt/freesurfer-{{ self.version }}
+      license_base64: ""
+      license_path: "/opt"
+      license_file: license.txt
       exclude_paths: |
         average/mult-comp-cor
         lib/cuda
@@ -26,6 +29,10 @@
     "7.3.2": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-centos7_x86_64-7.3.2.tar.gz
     "7.3.1": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.1/freesurfer-linux-centos7_x86_64-7.3.1.tar.gz
     "7.3.0": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.0/freesurfer-linux-centos7_x86_64-7.3.0.tar.gz
+    "7.2.0-centos6": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-CentOS6-7.2.0-1.x86_64.rpm
+    "7.2.0-centos7": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-CentOS7-7.2.0-1.x86_64.rpm
+    "7.2.0-centos8": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-CentOS8-7.2.0-1.x86_64.rpm
+    "7.2.0-deb": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer_7.2.0_amd64.deb 
     "7.2.0": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-centos6_x86_64-7.2.0.tar.gz
     "7.1.1": https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos6_x86_64-7.1.1.tar.gz
     "7.1.1-min": https://dl.dropbox.com/s/c3earkfhhvdyuo4/freesurfer-7.1.1-min.tgz
@@ -69,7 +76,7 @@
     # default freesurfer options
     FS_OVERRIDE: "0"
     FIX_VERTEX_AREA: ""
-    FSF_OUTPUT_FORMAT: "nii.gz# mni env requirements"
+    FSF_OUTPUT_FORMAT: "nii.gz"
     # mni environment requirements
     MINC_BIN_DIR: "{{ self.install_path }}/mni/bin"
     MINC_LIB_DIR: "{{ self.install_path }}/mni/lib"
@@ -79,15 +86,287 @@
     PERL5LIB: "{{ self.install_path }}/mni/share/perl5"
   instructions: |
     {{ self.install_dependencies() }}
-    echo "Downloading FreeSurfer ..."
-    mkdir -p {{ self.install_path }}
-    curl -fL {{ self.urls[self.version] }} \
-    | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --strip-components 1 {% if self.exclude_paths -%}\
-    {%- for exclude_path in self.exclude_paths.split() %}
-      {% if not loop.last -%}
-      --exclude='{{ exclude_path }}' \
+    {%- if self.version in ["6.0.0-min", "6.0.0", "6.0.1", "7.1.0", "7.1.1-min", "7.1.1", "7.2.0"] %}
+      echo "Downloading FreeSurfer ..."
+      mkdir -p {{ self.install_path }}
+      curl -fL {{ self.urls[self.version] }} \
+      | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --strip-components 1 {% if self.exclude_paths -%}\
+      {%- for exclude_path in self.exclude_paths.split() %}
+        {% if not loop.last -%}
+        --exclude='{{ exclude_path }}' \
+        {%- else -%}
+        --exclude='{{ exclude_path }}'
+        {%- endif -%}
+      {%- endfor %}
+      {%- endif %}    
+    {%- else -%}
+      {%- if self.version in ["deb"] %}
+        apt-get update -qq
+        apt-get install --fix-missing -y \
+          apt-file apt-utils apt-transport-https dpkg-dev debhelper devscripts librpm-dev rpm
+        curl -o /stage/freesurfer_amd64.deb {{ self.urls[self.version] }}
+        dpkg -i /stage/freesurfer_amd64.deb
+        DEBIAN_FRONTEND=noninteractive apt-get -f -y install
+        apt-get clean
+        rm -rf /var/lib/apt/lists/*
+        sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/'
       {%- else -%}
-      --exclude='{{ exclude_path }}'
+        # todo: wip
+        yum -y update --exclude=filesystem*
+        yum -y install dnf-plugins-core epel-release
+        yum -y config-manager --set-enabled powertools
+        yum -y update --exclude=filesystem* 
       {%- endif -%}
-    {%- endfor %}
-    {%- endif %}
+      echo "{{ self.pkg_manager }}"
+    {%- endif -%}
+
+source:
+  arguments:
+    optional:
+      repo: https://github.com/freesurfer/freesurfer
+      branch: "dev"
+      commit: ""
+      license_base64: ""
+      license_path: "/opt"
+      license_file: license.txt
+      # The subject dir is not in /opt, like everything else FreeSurfer-related
+      # Because if we want to run `neurodocker minify` we want to operate over the `/opt`
+      # dir and have the subjects dir excluded
+      subjects_dir: "/ext/fs-subjects"
+      infant_model_dir: "/opt/fs-infant-model"
+      infant_model_s3: ""
+      infant_model_s3_region: ""
+      pkg_url: http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/centos7-packages.tar.gz
+      annex: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
+      # set to niftyreg.yaml default
+      niftyreg_path: /opt/niftyreg-master
+      minimal: "ON"
+      build_guis: "OFF"
+      infant_module: "OFF"
+      install_python_deps: "OFF"
+      distribute_fspython: "OFF"
+      martinos_build: "OFF"
+      samseg_atlas_build: "OFF"
+      git_annex_get: "ON"
+      dev_tools: "OFF"
+      fortran_libs: /usr/lib/gcc/x86_64-linux-gnu/5/libgfortran.so
+      # --- Probably don't have to change args below here ---
+      # Were using a source path of `/stage` instead of `/temp` in case we want to 
+      # keep the source dir around for debugging (dev_tools=ON) with singularity containers
+      # (which bind mount the `/tmp` dir by default)   
+      source_path: /stage/freesurfer/freesurfer-{{ self.branch }}
+      pkg_path: /opt/freesurfer-pkg
+      install_path: /opt/freesurfer-{{ self.branch }}
+      cxx_flags: "-msse2 -mfpmath=sse -fPIC -fpermissive"
+      c_flags: "-msse2 -mfpmath=sse -fPIC"
+      cmake_opts: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_GUIS={{ self.build_guis }} -DMINIMAL={{ self.minimal }} -DINFANT_MODULE={{ self.infant_module }} -DFS_PACKAGES_DIR={{ self.pkg_path }} -DGFORTRAN_LIBRARIES={{ self.fortran_libs }} -DINSTALL_PYTHON_DEPENDENCIES={{ self.install_python_deps }} -DDISTRIBUTE_FSPYTHON={{ self.distribute_fspython }} -DMARTINOS_BUILD={{ self.martinos_build }} -DGEMS_BUILD_EXECUTABLES={{ self.samseg_atlas_build }} -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CXX_COMPILER_AR=/usr/bin/ar -DCMAKE_CXX_COMPILER_RANLIB=/usr/bin/ranlib -DCMAKE_CXX_FLAGS="{{ self.cxx_flags }}" -DCMAKE_C_COMPILER=/usr/bin/cc -DCMAKE_C_COMPILER_AR=/usr/bin/ar -DCMAKE_C_COMPILER_RANLIB=/usr/bin/ranlib -DCMAKE_C_FLAGS="{{ self.c_flags }}"
+      make_opts: -j4
+  env:
+    FS_LICENSE: "{{ self.license_path }}/{{ self.license_file }}"
+    SUBJECTS_DIR: "{{ self.subjects_dir }}"
+    FS_INFANT_MODEL: "{{ self.infant_model_dir }}"
+    SSCNN_MODEL_DIR: "{{ self.infant_model_dir }}/sscnn_skullstrip"
+    # From https://github.com/freesurfer/freesurfer/blob/54018f7d6f620d6288b28f50e14a0a4ba421757c/Dockerfile#L20-L42
+    OS: "Linux"
+    PATH: "{{ self.niftyreg_path }}/bin:{{ self.pkg_path }}/mni/current/bin:{{ self.install_path }}/bin:{{ self.install_path }}/fsfast/bin:{{ self.install_path }}/tktools:{{ self.install_path }}/mni/bin:$PATH"
+    FREESURFER_HOME: "{{ self.install_path }}"
+    FREESURFER: "{{ self.install_path }}"
+    PERL5LIB: "{{ self.install_path }}/mni/share/perl5"
+    LOCAL_DIR: "{{ self.install_path }}/local"
+    FSFAST_HOME: "{{ self.install_path }}/fsfast"
+    FMRI_ANALYSIS_DIR: "{{ self.install_path }}/fsfast"
+    FSF_OUTPUT_FORMAT: "nii.gz"
+    FUNCTIONALS_DIR: "{{ self.install_path }}/sessions"
+    PYTHONPATH: "{{ self.install_path }}/python/packages"
+    # default freesurfer options
+    FS_OVERRIDE: "0"
+    FIX_VERTEX_AREA: ""
+    # To supress a `Could not set locale` error when `mri_convert` is run in recon-all
+    FS_DISABLE_LANG: "1"
+    # Just in case: https://github.com/freesurfer/freesurfer/issues/776
+    FS_TIME_ALLOW: "0"
+    # mni environment requirements
+    MINC_BIN_DIR: "{{ self.pkg_path }}/mni/current/bin"
+    MINC_LIB_DIR: "{{ self.pkg_path }}/mni/current/lib"
+    MNI_DIR: "{{ self.pkg_path }}/mni"
+    MNI_DATAPATH: "{{ self.pkg_path }}/mni/current/data"
+    MNI_PERL5LIB: "{{ self.pkg_path }}/mni/current/share/perl5"
+    PERL5LIB: "{{ self.pkg_path }}/mni/current/share/perl5"
+    # infant model setup, see:
+    #   - https://github.com/pwighton/fs-docker/blob/f691232312e97f2ea87b8ae45bfd5c365e2bc91c/baby/dockerfile#L85
+    #   - https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/infant/freesurfer-linux-centos7_x86_64-infant.tar.gz
+    # This temporary and should migrate somewhere else
+    CNYBCH_TEMPLATE_SUBJECTS_DIR: "{{ self.infant_model_dir }}/CNYBCH"
+    CNYBCH_SUBJECTS: "Template1 Template2 Template3 Template4 Template5 Template6 Template7 Template8 Template9 Template10 Template11 Template12 Template13 Template14 Template15 Template16 Template17 Template18 Template19 Template20 Template21 Template22 Template23 Template24 Template25 Template26"
+    # age at MRI scan (mo)
+    CNYBCH_AGES: "9 7 6 5 18 12 0 0 3 8 10 10 18 4 2 14 3 16 0 12 0 15 5 17 16 0"
+    CNYBCH_GMWM_SUBJECTS: "Template5 Template6 Template8 Template10 Template13 Template18 Template20 Template22"
+    # mo
+    CNYBCH_GMWM_AGES: "18 12 0 8 18 16 12 15"
+    CNYBCH_NEONATES: "Template7 Template8 Template19 Template21 Template26"
+    # days (first two computed from weeks)
+    CNYBCH_NEONATEAGES: "3 4 1 2 4"
+    CNYBCH_AROUNDONE: "Template11 Template12 Template6 Template20 Template16"
+    #mo
+    CNYBCH_AROUNDONEAGES: "10 10 12 12 14"
+  dependencies:
+    apt:
+    - ca-certificates
+    - cmake
+    - git
+    - git-annex
+    - make
+    - bc
+    - binutils
+    - bzip2
+    - coreutils
+    - curl
+    - g++-4.8
+    - gcc-4.8-base
+    - gcc-4.8
+    - gfortran-4.8
+    - libbz2-dev
+    - libfreetype6-dev
+    - libgfortran-4.8-dev
+    - libglib2.0-0
+    - libglu1-mesa-dev
+    - libgomp1
+    - libjpeg62-dev
+    - libopenblas-dev
+    - libssl-dev
+    - libsqlite3-dev
+    - libtool
+    - libtool-bin
+    - libx11-dev
+    - libxaw7-dev
+    - libxi-dev
+    - libxml2-utils
+    - libxmu-dev
+    - libxmu-headers
+    - libxmu6
+    - libxt-dev
+    - libxt6
+    - perl
+    - sudo
+    - tar
+    - tcsh
+    - unzip
+    - uuid-dev
+    - vim-common
+    - wget
+    yum:
+    - ca-certificates
+    - cmake
+    - gcc-c++
+    - git
+    - make
+  instructions: |
+    {{ self.install_dependencies() }}
+    {%- if self.license_base64 is defined and self.license_base64|length %}
+    echo "   fs license (base64):      "{{ self.license_base64 }}
+    mkdir -p {{ self.license_path }}
+    echo {{ self.license_base64 }} | base64 -d > {{ self.license_path }}/{{ self.license_file }}
+    {% endif -%}
+    # git config
+    # -------------------------------------------------------------------------
+    git config --global user.email "[email protected]"
+    git config --global user.name "CI"
+    # Switch to gcc 4.8
+    # -------------------------------------------------------------------------
+    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 100
+    update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 100
+    update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.8 100
+    # Make a staging directory, we don't want to use /tmp since it doesn't play nice with singularity
+    # See: https://github.com/ReproNim/neurodocker/issues/246
+    # -------------------------------------------------------------------------    
+    mkdir -p /stage
+    # Python  v3.8.9
+    # -------------------------------------------------------------------------
+    curl -sSL --retry 5 https://www.python.org/ftp/python/3.8.9/Python-3.8.9.tgz | tar -xz -C /stage
+    cd /stage/Python-3.8.9
+    ./configure
+    make
+    make install
+    cd /
+    rm -rf /stage/Python-3.8.9
+    pip3 install -q --no-cache-dir -U pip
+    pip3 install -q --no-cache-dir wheel
+    sync
+    # Cmake v3.19.0 (must be > v3.6.8)
+    # -------------------------------------------------------------------------
+    wget https://github.com/Kitware/CMake/releases/download/v3.19.0/cmake-3.19.0-Linux-x86_64.sh -q -O /stage/cmake-install.sh
+    chmod u+x /stage/cmake-install.sh
+    mkdir -p /usr/share/cmake-3.19.0
+    /stage/cmake-install.sh --skip-license --prefix=/usr/share/cmake-3.19.0
+    CMAKE_BINPATH=`which cmake`
+    rm -rf $CMAKE_BINPATH
+    ln -s /usr/share/cmake-3.19.0/bin/cmake $CMAKE_BINPATH
+    rm /stage/cmake-install.sh
+    # Compile FreeSurfer
+    # ----------------------------------------------------------------
+    mkdir -p {{ self.pkg_path }}
+    mkdir -p {{ self.install_path }}
+    wget -q -c {{ self.pkg_url }} -O - | tar -xz -C {{ self.pkg_path }}
+    mv {{ self.pkg_path }}/packages/* {{ self.pkg_path }}
+    rm -rf {{ self.pkg_path }}/packages
+    echo "Cloning..."
+    echo "   remote:      "{{ self.repo }}
+    echo "   branch:      "{{ self.branch }}
+    echo "   commit:      "{{ self.commit }}
+    echo "   destination: "{{ self.source_path }}
+    git clone --branch {{ self.branch }} {{ self.repo }} {{ self.source_path }} 
+    {%- if self.commit is defined and self.commit|length %}
+    cd {{ self.source_path }}
+    git checkout {{ self.commit }}
+    {% endif -%}
+    cd {{ self.install_path }}
+    cmake {{ self.cmake_opts }} {{ self.source_path }}
+    make {{ self.make_opts }}
+    # Install python reqs
+    # ----------------------------------------------------------------
+    {%- if self.infant_module.lower() in ["on", "true", "1", "y"] %}
+    pip3 install -r {{ self.source_path }}/infant/docker/requirements.txt
+    ln -s {{ self.install_path }}/bin/infant-container-entrypoint.bash /bin/infant-container-entrypoint.bash
+    ln -s {{ self.install_path }}/bin/infant-container-entrypoint-aws.bash /bin/infant-container-entrypoint-aws.bash
+    {% else %}
+    pip3 install -r {{ self.source_path }}/python/requirements.txt
+    {% endif -%}
+    # Setup annex remote
+    # ----------------------------------------------------------------
+    cd {{ self.source_path }}
+    git remote add datasrc {{ self.annex }}
+    git fetch datasrc
+    git annex enableremote datasrc || true      
+    # Pull from annex and install 
+    # (`make install` will fail if `git annex get` isn't run)
+    # ----------------------------------------------------------------
+    {%- if self.git_annex_get.lower() in ["on", "true", "1", "y"] %}
+    cd {{ self.source_path }}
+    git annex get -q .
+    git annex unlock
+    cd {{ self.install_path }}
+    make install
+    {% endif -%}
+    # Setup mount points
+    # ----------------------------------------------------------------
+    mkdir -p {{ self.subjects_dir }}
+    mkdir -p {{ self.infant_model_dir }}
+    # Dev tools
+    #   - jupyter relies on `libsqlite3-dev` being present before python is compiled
+    #   - the /stage dir isn't deleted (to facilitate recompile/install/test)
+    #   - awscli is installed (todo, best place for this?)
+    # ----------------------------------------------------------------
+    {%- if self.dev_tools.lower() in ["on", "true", "1", "y"] %}
+    pip3 install jupyter
+    cd /stage
+    curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+    unzip awscliv2.zip
+    ./aws/install
+    rm -rf /stage/aws
+    rm -rf /stage/awscliv2.zip
+    {%- if self.infant_model_s3 is defined and self.infant_model_s3|length and self.infant_model_s3_region is defined and self.infant_model_s3_region|length %}
+    aws s3 cp --no-sign-request --region={{ self.infant_model_s3_region }} --recursive --include '*' {{ self.infant_model_s3 }} {{ self.infant_model_dir }}/
+    {% endif %}
+    {% else %}
+    rm -rf /stage
+    {% endif -%}