Merge pull request #509 from NeuroDesk/minc_install_from_deb_and_rpm

Minc install from deb and rpm
ReproNim · Feb 8, 2023 · 3731b0e · 3731b0e
2 parents dc3112f + 6f06168
commit 3731b0e
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diff --git a/.DS_Store b/.DS_Store
diff --git a/neurodocker/templates/minc.yaml b/neurodocker/templates/minc.yaml
@@ -2,9 +2,8 @@
 #
 # Repository: https://github.com/BIC-MNI/minc-toolkit-v2
 #
-# Binaries are compiled in a CentOS 6.9 Docker container, based on this
-# Dockerfile:
-# https://github.com/BIC-MNI/build_packages/blob/master/build_centos_6.9_x64/Dockerfile
+# Instructions: http://bic-mni.github.io/#on-debianubuntu
+# The Debian packages are unpacked for yum based distributions as well
 
 name: minc
 binaries:
@@ -14,7 +13,10 @@ binaries:
     optional:
       install_path: /opt/minc-{{ self.version }}
   urls:
-    "1.9.15": https://dl.dropbox.com/s/40hjzizaqi91373/minc-toolkit-1.9.15-20170529-CentOS_6.9-x86_64.tar.gz
+      "1.9.15": https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_16.04-x86_64.deb
+      "1.9.16": https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.16-20180117-Ubuntu_18.04-x86_64.deb
+      "1.9.17": https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.17-20190313-Ubuntu_18.04-x86_64.deb
+      "1.9.18": https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.18-20200813-Ubuntu_18.04-x86_64.deb
   dependencies:
     apt:
     - ca-certificates
@@ -29,6 +31,18 @@ binaries:
     - libgomp1
     - libjpeg62
     - unzip
+    - octave 
+    - libglu1-mesa 
+    - libgl1-mesa-glx 
+    - perl 
+    - imagemagick 
+    - bc 
+    - ed 
+    - libc6 
+    - libstdc++6 
+    - gdebi-core 
+    - binutils 
+    - git
     yum:
     - curl
     - libICE
@@ -41,9 +55,19 @@ binaries:
     - libjpeg-turbo
     - mesa-libGL-devel
     - unzip
+    - octave
+    - mesa-dri-drivers
+    - epel-release 
+    - glibc 
+    - libstdc++ 
+    - ImageMagick 
+    - perl 
+    - binutils 
+    - git
   env:
     MINC_TOOLKIT: "{{ self.install_path }}"
-    PATH: "$PATH:{{ self.install_path }}/bin:{{ self.install_path }}/pipeline"
+    MINC_TOOLKIT_VERSION: "{{ self.install_path }}"
+    PATH: "{{ self.install_path }}/bin:{{ self.install_path }}/volgenmodel-nipype/extra-scripts:{{ self.install_path }}/pipeline:$PATH"
     PERL5LIB: "{{ self.install_path }}/perl:{{ self.install_path }}/pipeline:${PERL5LIB}"
     LD_LIBRARY_PATH: "{{ self.install_path }}/lib:{{ self.install_path }}/lib/InsightToolkit:${LD_LIBRARY_PATH}"
     MNI_DATAPATH: "{{ self.install_path }}/share"
@@ -54,14 +78,15 @@ binaries:
   instructions: |
     {{ self.install_dependencies() }}
     echo "Downloading MINC, BEASTLIB, and MODELS..."
-    mkdir -p {{ self.install_path }}
-    curl -fL {{ self.urls[self.version] }} \
-    | tar -xz -C {{ self.install_path }} --strip-components 1
+    cd /
+    # ar allows to extract the debian package so we can also install this in centos based OSs.
+    curl {{ self.urls[self.version] }} -o minc.deb && ar p minc.deb data.tar.gz | tar zx && rm minc.deb
+    ln -s /opt/minc/{{ self.version }} {{ self.install_path }} 
+    git clone https://github.com/CAIsr/volgenmodel-nipype.git {{ self.install_path }}/volgenmodel-nipype/
     curl -fL http://packages.bic.mni.mcgill.ca/tgz/beast-library-1.1.tar.gz \
     | tar -xz -C {{ self.install_path }}/share
     curl -fL -o /tmp/mni_90a.zip http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_minc2.zip
     unzip /tmp/mni_90a.zip -d {{ self.install_path }}/share/icbm152_model_09a
     curl -fL -o /tmp/mni_90c.zip http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_minc2.zip
     unzip /tmp/mni_90c.zip -d {{ self.install_path }}/share/icbm152_model_09c
-    sed -i 's+MINC_TOOLKIT=/opt/minc+MINC_TOOLKIT={{ self.install_path }}+g' {{ self.install_path }}/minc-toolkit-config.sh
     rm -rf /tmp/mni*