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=== Do not change lines below ===
{
"chain": [],
"cmd": "pre-commit run yamlfmt --files neurodocker/templates/afni.yaml neurodocker/templates/spm12.yaml",
"exit": 1,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,198 +1,199 @@ | ||
| --- | ||
| # Instructions to install AFNI. | ||
|
|
||
| # TODO: consider updating the source instructions to use cmake. | ||
|
|
||
| name: afni | ||
| url: https://afni.nimh.nih.gov | ||
| binaries: | ||
| arguments: | ||
| optional: | ||
| install_path: /opt/afni-{{ self.version }} | ||
| version: latest | ||
| install_r_pkgs: "false" | ||
| install_python3: "false" | ||
| urls: | ||
| latest: https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | ||
| env: | ||
| PATH: "{{ self.install_path }}:$PATH" | ||
| AFNI_PLUGINPATH: "{{ self.install_path }}" | ||
| dependencies: | ||
| apt: | ||
| - ca-certificates | ||
| - cmake | ||
| - curl | ||
| - ed | ||
| - gsl-bin | ||
| - libcurl4-openssl-dev | ||
| - libgl1-mesa-dri | ||
| - libjpeg-dev | ||
| - libglu1-mesa-dev | ||
| - libglib2.0-0 | ||
| - libglw1-mesa | ||
| - libgomp1 | ||
| - libpng-dev | ||
| - libssl-dev | ||
| - libudunits2-dev | ||
| - libxm4 | ||
| - netpbm | ||
| - python-is-python3 | ||
| - python3-pip | ||
| - tcsh | ||
| - xfonts-base | ||
| - xvfb | ||
| yum: | ||
| - cmake | ||
| - curl | ||
| - ed | ||
| - gsl | ||
| - libcurl-devel | ||
| - libGLU | ||
| - libgomp | ||
| - libjpeg-turbo-devel | ||
| - libpng12 | ||
| - libXp | ||
| - libXpm | ||
| - mesa-dri-drivers | ||
| - netpbm-progs | ||
| - openmotif | ||
| - openssl-devel | ||
| - python-is-python3 | ||
| - python3-pip | ||
| - R | ||
| - tcsh | ||
| - udunits2-devel | ||
| - which | ||
| - xorg-x11-fonts-misc | ||
| - xorg-x11-server-Xvfb | ||
| - wget | ||
| - mesa-dri-drivers | ||
| - mesa-libGLw | ||
| - which | ||
| - unzip | ||
| - ncurses-compat-libs | ||
| debs: | ||
| - https://snapshot.debian.org/archive/debian-security/20221017T140424Z/pool/updates/main/g/glibc/multiarch-support_2.28-10%2Bdeb10u2_amd64.deb | ||
| - https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb | ||
| instructions: | | ||
| {{ self.install_dependencies() }} | ||
| {% if self.install_python3.lower() in ["true", "1", "y"] -%} | ||
| {{ self.install(["python3"]) }} | ||
| pip3 install matplotlib | ||
| {%- endif %} | ||
| gsl_path="$(find / -name 'libgsl.so.??' || printf '')" | ||
| if [ -n "$gsl_path" ]; then \ | ||
| ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \ | ||
| fi | ||
| ldconfig | ||
| mkdir -p {{ self.install_path }} | ||
| echo "Downloading AFNI ..." | ||
| curl -fL {{ self.urls[self.version] }} \ | ||
| | tar -xz -C {{ self.install_path }} --strip-components 1 | ||
| {%- if self.install_r_pkgs.lower() in ["true", "1", "y"] %} | ||
| {%- if self.pkg_manager == "apt" %} | ||
| {{ self.install(["r-base", "r-base-dev", "libnlopt-dev"]) }} | ||
| {% elif self.pkg_manager == "yum" %} | ||
| {{ self.install(["R-devel"]) }} | ||
| {% endif -%} | ||
| rPkgsInstall -pkgs ALL | ||
| {% endif -%} | ||
| arguments: | ||
| optional: | ||
| install_path: /opt/afni-{{ self.version }} | ||
| version: latest | ||
| install_r_pkgs: 'false' | ||
| install_python3: 'false' | ||
| urls: | ||
| latest: https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | ||
| env: | ||
| PATH: '{{ self.install_path }}:$PATH' | ||
| AFNI_PLUGINPATH: '{{ self.install_path }}' | ||
| dependencies: | ||
| apt: | ||
| - ca-certificates | ||
| - cmake | ||
| - curl | ||
| - ed | ||
| - gsl-bin | ||
| - libcurl4-openssl-dev | ||
| - libgl1-mesa-dri | ||
| - libjpeg-dev | ||
| - libglu1-mesa-dev | ||
| - libglib2.0-0 | ||
| - libglw1-mesa | ||
| - libgomp1 | ||
| - libpng-dev | ||
| - libssl-dev | ||
| - libudunits2-dev | ||
| - libxm4 | ||
| - netpbm | ||
| - python-is-python3 | ||
| - python3-pip | ||
| - tcsh | ||
| - xfonts-base | ||
| - xvfb | ||
| yum: | ||
| - cmake | ||
| - curl | ||
| - ed | ||
| - gsl | ||
| - libcurl-devel | ||
| - libGLU | ||
| - libgomp | ||
| - libjpeg-turbo-devel | ||
| - libpng12 | ||
| - libXp | ||
| - libXpm | ||
| - mesa-dri-drivers | ||
| - netpbm-progs | ||
| - openmotif | ||
| - openssl-devel | ||
| - python-is-python3 | ||
| - python3-pip | ||
| - R | ||
| - tcsh | ||
| - udunits2-devel | ||
| - which | ||
| - xorg-x11-fonts-misc | ||
| - xorg-x11-server-Xvfb | ||
| - wget | ||
| - mesa-dri-drivers | ||
| - mesa-libGLw | ||
| - which | ||
| - unzip | ||
| - ncurses-compat-libs | ||
| debs: | ||
| - https://snapshot.debian.org/archive/debian-security/20221017T140424Z/pool/updates/main/g/glibc/multiarch-support_2.28-10%2Bdeb10u2_amd64.deb | ||
| - https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb | ||
| instructions: | | ||
| {{ self.install_dependencies() }} | ||
| {% if self.install_python3.lower() in ["true", "1", "y"] -%} | ||
| {{ self.install(["python3"]) }} | ||
| pip3 install matplotlib | ||
| {%- endif %} | ||
| gsl_path="$(find / -name 'libgsl.so.??' || printf '')" | ||
| if [ -n "$gsl_path" ]; then \ | ||
| ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \ | ||
| fi | ||
| ldconfig | ||
| mkdir -p {{ self.install_path }} | ||
| echo "Downloading AFNI ..." | ||
| curl -fL {{ self.urls[self.version] }} \ | ||
| | tar -xz -C {{ self.install_path }} --strip-components 1 | ||
| {%- if self.install_r_pkgs.lower() in ["true", "1", "y"] %} | ||
| {%- if self.pkg_manager == "apt" %} | ||
| {{ self.install(["r-base", "r-base-dev", "libnlopt-dev"]) }} | ||
| {% elif self.pkg_manager == "yum" %} | ||
| {{ self.install(["R-devel"]) }} | ||
| {% endif -%} | ||
| rPkgsInstall -pkgs ALL | ||
| {% endif -%} | ||
| source: | ||
| arguments: | ||
| required: | ||
| - version | ||
| optional: | ||
| repo: https://github.com/afni/afni.git | ||
| install_path: /opt/afni-{{ self.version }} | ||
| install_r_pkgs: "false" | ||
| install_python3: "false" | ||
| env: | ||
| PATH: "{{ self.install_path }}:$PATH" | ||
| AFNI_PLUGINPATH: "{{ self.install_path }}" | ||
| dependencies: | ||
| apt: | ||
| - ca-certificates | ||
| - curl | ||
| - ed | ||
| - g++ | ||
| - gcc | ||
| - git | ||
| - libgl1-mesa-dri | ||
| - libglib2.0-dev | ||
| - libglu1-mesa-dev | ||
| - libgsl-dev | ||
| - libmotif-dev | ||
| - libnetpbm10-dev | ||
| - libpng-dev | ||
| - libxext-dev | ||
| - libxi-dev | ||
| - libxmu-headers | ||
| - libxpm-dev | ||
| - libxt-dev | ||
| - m4 | ||
| - make | ||
| - mesa-common-dev | ||
| - tcsh | ||
| - zlib1g-dev | ||
| yum: | ||
| - compat-gcc-34 | ||
| - curl | ||
| - expat-devel | ||
| - gcc | ||
| - gcc-c++ | ||
| - gcc-gfortran | ||
| - git | ||
| - glib2-devel | ||
| - gsl-devel | ||
| - libXext-devel | ||
| - libXi-devel | ||
| - libXmu-devel | ||
| - libXpm-devel | ||
| - libXt-devel | ||
| - m4 | ||
| - make | ||
| - mesa-dri-drivers | ||
| - mesa-libGL-devel | ||
| - mesa-libGLU-devel | ||
| - netpbm-devel | ||
| - openmotif-devel | ||
| - R | ||
| - tcsh | ||
| - which | ||
| - zlib-devel | ||
| debs: | ||
| - https://snapshot.debian.org/archive/debian-security/20221017T140424Z/pool/updates/main/g/glibc/multiarch-support_2.28-10%2Bdeb10u2_amd64.deb | ||
| - https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb | ||
| instructions: | | ||
| {{ self.install_dependencies() }} | ||
| {%- if self.install_python3.lower() in ["true", "1", "y"] %} | ||
| {{ self.install(["python3"]) }}{% endif %} | ||
| git clone {{ self.repo }} {{ self.install_path }} | ||
| cd {{ self.install_path }} | ||
| {% if self.version != "master" and self.version != "latest" -%} | ||
| git fetch --tags | ||
| git checkout {{ self.version }} | ||
| {% endif -%} | ||
| cd src | ||
| cp Makefile.linux_openmp_64 Makefile | ||
| perl -p -i -e 's/^LGIFTI.*/LGIFTI = -lexpat/' Makefile | ||
| perl -p -i -e 's/^USE_LOCAL_X_TREE/#USE_LOCAL_X_TREE/' Makefile | ||
| perl -p -i -e 's/XLIBS = \$\(XROOT\)\/lib64\/libXm.a -lXt/XLIBS = \$\(XROOT\)\/lib64\/libXm.a \$\(XROOT\)\/lib\/x86_64-linux-gnu\/libXm.a -lXt/' Makefile | ||
| perl -p -i -e 's/^# XLIBS =/XLIBS =/' Makefile | ||
| perl -p -i -e 's/^CCOLD.*/CCOLD = \$\(CC\)/' Makefile | ||
| perl -p -i -e 's/(^LFLAGS.*)/$1 -L\/usr\/lib\/x86_64-linux-gnu/' Makefile | ||
| perl -p -i -e 's/(^PLFLAGS.*)/$1 -L\/usr\/lib -L\/usr\/lib\/x86_64-linux-gnu/' Makefile | ||
| perl -p -i -e 's/-lXpm -lXext/-lXpm -lfontconfig -lXext/' Makefile | ||
| perl -p -i -e 's/(^SUMA_INCLUDE_PATH.*)/$1 -I\/usr\/lib\/x86_64-linux-gnu\/glib-2.0\/include/' Makefile | ||
| # If we do not symlink, gcc complains that it cannot find these libraries. | ||
| ln -s /usr/lib/x86_64-linux-gnu/libXmu.so.6 /usr/lib/x86_64-linux-gnu/libXmu.so | ||
| ln -s /usr/lib/x86_64-linux-gnu/libXp.so.6 /usr/lib/x86_64-linux-gnu/libXp.so | ||
| make INSTALLDIR="{{ self.install_path }}" vastness | ||
| {%- if self.install_r_pkgs.lower() in ["true", "1", "y"] %} | ||
| {%- if self.pkg_manager == "apt" %} | ||
| {{ self.install(["r-base", "r-base-dev", "libnlopt-dev"]) }} | ||
| {% elif self.pkg_manager == "yum" %} | ||
| {{ self.install(["R-devel"]) }} | ||
| {% endif -%} | ||
| rPkgsInstall -pkgs ALL | ||
| {% endif -%} | ||
| arguments: | ||
| required: | ||
| - version | ||
| optional: | ||
| repo: https://github.com/afni/afni.git | ||
| install_path: /opt/afni-{{ self.version }} | ||
| install_r_pkgs: 'false' | ||
| install_python3: 'false' | ||
| env: | ||
| PATH: '{{ self.install_path }}:$PATH' | ||
| AFNI_PLUGINPATH: '{{ self.install_path }}' | ||
| dependencies: | ||
| apt: | ||
| - ca-certificates | ||
| - curl | ||
| - ed | ||
| - g++ | ||
| - gcc | ||
| - git | ||
| - libgl1-mesa-dri | ||
| - libglib2.0-dev | ||
| - libglu1-mesa-dev | ||
| - libgsl-dev | ||
| - libmotif-dev | ||
| - libnetpbm10-dev | ||
| - libpng-dev | ||
| - libxext-dev | ||
| - libxi-dev | ||
| - libxmu-headers | ||
| - libxpm-dev | ||
| - libxt-dev | ||
| - m4 | ||
| - make | ||
| - mesa-common-dev | ||
| - tcsh | ||
| - zlib1g-dev | ||
| yum: | ||
| - compat-gcc-34 | ||
| - curl | ||
| - expat-devel | ||
| - gcc | ||
| - gcc-c++ | ||
| - gcc-gfortran | ||
| - git | ||
| - glib2-devel | ||
| - gsl-devel | ||
| - libXext-devel | ||
| - libXi-devel | ||
| - libXmu-devel | ||
| - libXpm-devel | ||
| - libXt-devel | ||
| - m4 | ||
| - make | ||
| - mesa-dri-drivers | ||
| - mesa-libGL-devel | ||
| - mesa-libGLU-devel | ||
| - netpbm-devel | ||
| - openmotif-devel | ||
| - R | ||
| - tcsh | ||
| - which | ||
| - zlib-devel | ||
| debs: | ||
| - https://snapshot.debian.org/archive/debian-security/20221017T140424Z/pool/updates/main/g/glibc/multiarch-support_2.28-10%2Bdeb10u2_amd64.deb | ||
| - https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb | ||
| instructions: | | ||
| {{ self.install_dependencies() }} | ||
| {%- if self.install_python3.lower() in ["true", "1", "y"] %} | ||
| {{ self.install(["python3"]) }}{% endif %} | ||
| git clone {{ self.repo }} {{ self.install_path }} | ||
| cd {{ self.install_path }} | ||
| {% if self.version != "master" and self.version != "latest" -%} | ||
| git fetch --tags | ||
| git checkout {{ self.version }} | ||
| {% endif -%} | ||
| cd src | ||
| cp Makefile.linux_openmp_64 Makefile | ||
| perl -p -i -e 's/^LGIFTI.*/LGIFTI = -lexpat/' Makefile | ||
| perl -p -i -e 's/^USE_LOCAL_X_TREE/#USE_LOCAL_X_TREE/' Makefile | ||
| perl -p -i -e 's/XLIBS = \$\(XROOT\)\/lib64\/libXm.a -lXt/XLIBS = \$\(XROOT\)\/lib64\/libXm.a \$\(XROOT\)\/lib\/x86_64-linux-gnu\/libXm.a -lXt/' Makefile | ||
| perl -p -i -e 's/^# XLIBS =/XLIBS =/' Makefile | ||
| perl -p -i -e 's/^CCOLD.*/CCOLD = \$\(CC\)/' Makefile | ||
| perl -p -i -e 's/(^LFLAGS.*)/$1 -L\/usr\/lib\/x86_64-linux-gnu/' Makefile | ||
| perl -p -i -e 's/(^PLFLAGS.*)/$1 -L\/usr\/lib -L\/usr\/lib\/x86_64-linux-gnu/' Makefile | ||
| perl -p -i -e 's/-lXpm -lXext/-lXpm -lfontconfig -lXext/' Makefile | ||
| perl -p -i -e 's/(^SUMA_INCLUDE_PATH.*)/$1 -I\/usr\/lib\/x86_64-linux-gnu\/glib-2.0\/include/' Makefile | ||
| # If we do not symlink, gcc complains that it cannot find these libraries. | ||
| ln -s /usr/lib/x86_64-linux-gnu/libXmu.so.6 /usr/lib/x86_64-linux-gnu/libXmu.so | ||
| ln -s /usr/lib/x86_64-linux-gnu/libXp.so.6 /usr/lib/x86_64-linux-gnu/libXp.so | ||
| make INSTALLDIR="{{ self.install_path }}" vastness | ||
| {%- if self.install_r_pkgs.lower() in ["true", "1", "y"] %} | ||
| {%- if self.pkg_manager == "apt" %} | ||
| {{ self.install(["r-base", "r-base-dev", "libnlopt-dev"]) }} | ||
| {% elif self.pkg_manager == "yum" %} | ||
| {{ self.install(["R-devel"]) }} | ||
| {% endif -%} | ||
| rPkgsInstall -pkgs ALL | ||
| {% endif -%} |
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