Merge pull request #1 from khanlab/nomatlab

no matlab, add greedy

Dockerfile

@@ -4,17 +4,9 @@ MAINTAINER alik@robarts.ca
 
 #dependencies for hippocampal autotop
 # note: this installs minified versions of fsl and ants to save space.. 
-# note 2: niftynet and snakemake/snakebids are installed in two separate conda environments
 
-ENV PATH /opt/conda/bin:$PATH
-#needed to create /usr/share/man/man1 folder to avoid error when installing jre
-#python dependencies
-
-#install linux deps
-RUN apt-get update && mkdir -p /usr/share/man/man1  &&  apt-get install -y curl tree unzip bc default-jre libgomp1 cmake cmake-curses-gui libpng-dev zlib1g-dev build-essential wget bzip2 ca-certificates gnupg2 squashfs-tools git graphviz-dev
-
-#install niftyreg
-RUN mkdir -p /opt/niftyreg-1.3.9/src && \
+RUN apt-get update && mkdir -p /usr/share/man/man1  &&  apt-get install -y curl tree unzip bc default-jre libgomp1 cmake cmake-curses-gui libpng-dev zlib1g-dev build-essential wget bzip2 ca-certificates gnupg2 squashfs-tools git graphviz-dev && \
+mkdir -p /opt/niftyreg-1.3.9/src && \
   echo "Downloading http://sourceforge.net/projects/niftyreg/files/nifty_reg-${NIFTY_VER}/nifty_reg-${NIFTY_VER}.tar.gz/download" && \
   curl -L http://sourceforge.net/projects/niftyreg/files/nifty_reg-1.3.9/nifty_reg-1.3.9.tar.gz/download \
     | tar xz -C /opt/niftyreg-1.3.9/src --strip-components 1 && \
@@ -25,45 +17,27 @@ cmake /opt/niftyreg-1.3.9/src \
     -DBUILD_TESTING=OFF \
     -DCMAKE_INSTALL_PREFIX=/opt/niftyreg-1.3.9  && \
   make && \
-  make install && rm -rf /opt/niftyreg-1.3.9/src 
-ENV LD_LIBRARY_PATH /opt/niftyreg-1.3.9/lib:$LD_LIBRARY_PATH 
-ENV PATH /opt/niftyreg-1.3.9/bin:$PATH
-
-#install workbench
-RUN mkdir -p /opt && cd /opt && wget -q https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && unzip workbench-linux64-v1.5.0.zip && rm workbench-linux64-v1.5.0.zip && cd /
-ENV PATH "/opt/workbench/bin_linux64:$PATH"
-ENV LD_LIBRARY_PATH "/opt/workbench/libs_linux64:/opt/workbench/libs_linux64_software_opengl:$LD_LIBRARY_PATH"
-
-
-#install ants
-#we only need antsRegistration N4BiasFieldCorrection ComposeMultiTransform and antsApplyTransforms , can remove everything else
-RUN mkdir -p /opt/ants-2.3.1 && curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
+  make install && rm -rf /opt/niftyreg-1.3.9/src && \
+mkdir -p /opt && cd /opt && wget -q https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && unzip workbench-linux64-v1.5.0.zip && rm workbench-linux64-v1.5.0.zip && cd /  && \
+mkdir -p /opt/ants-2.3.1 && curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
 | tar -xz -C /opt/ants-2.3.1 --strip-components 1 && \
 mkdir /opt/ants-2.3.1-minify && for bin in antsRegistration antsApplyTransforms N4BiasFieldCorrection ComposeMultiTransform; do mv /opt/ants-2.3.1/${bin} /opt/ants-2.3.1-minify; done  && \
-rm -rf /opt/ants-2.3.1
-ENV PATH "/opt/ants-2.3.1-minify:$PATH"
-
-#install fsl
-#we only need {flirt,fslmaths,fslreorient2std,fslroi,fslstats} from fsl, can remove everything else from bin
-# we also remove {data,extras,lib,src,doc} to save space
-RUN mkdir -p /opt/fsl-5.0.11 && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
+rm -rf /opt/ants-2.3.1  && \
+mkdir -p /opt/fsl-5.0.11 && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
 | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 && \
 mkdir /opt/fsl-5.0.11/bin-minify && for bin in flirt fslmaths fslreorient2std fslroi fslstats; do mv /opt/fsl-5.0.11/bin/${bin} /opt/fsl-5.0.11/bin-minify; done && \
-rm -rf /opt/fsl-5.0.11/bin && rm -rf /opt/fsl-5.0.11/data /opt/fsl-5.0.11/extras /opt/fsl-5.0.11/lib /opt/fsl-5.0.11/src /opt/fsl-5.0.11/doc
+rm -rf /opt/fsl-5.0.11/bin && rm -rf /opt/fsl-5.0.11/data /opt/fsl-5.0.11/extras /opt/fsl-5.0.11/lib /opt/fsl-5.0.11/src /opt/fsl-5.0.11/doc && \
+wget -O itksnap.tar.gz 'https://sourceforge.net/projects/itk-snap/files/itk-snap/Nightly/itksnap-nightly-master-Linux-gcc64-qt4.tar.gz/download' \
+\
+&& tar -zxf itksnap.tar.gz -C /opt/ \
+&& mv /opt/itksnap-*/ /opt/itksnap/ \
+&& rm itksnap.tar.gz
+
+ENV LD_LIBRARY_PATH=/opt/itksnap/lib/:/opt/niftyreg-1.3.9/lib:/opt/workbench/libs_linux64:/opt/workbench/libs_linux64_software_opengl:${LD_LIBRARY_PATH}
+ENV PATH /opt/conda/bin:/opt/itksnap/bin/:/opt/niftyreg-1.3.9/bin:/opt/workbench/bin_linux64:/opt/ants-2.3.1-minify:/opt/fsl-5.0.11/bin-minify:$PATH
+
 ENV FSLDIR "/opt/fsl-5.0.11"
-ENV PATH "/opt/fsl-5.0.11/bin-minify:$PATH"
 ENV FSLOUTPUTTYPE NIFTI_GZ
 ENV FSLMULTIFILEQUIT TRUE
 
-#install c3d
-RUN mkdir -p /opt/c3d && curl -s -L --retry 6 https://www.dropbox.com/s/bkw5mfp8r4mczsx/c3d-1.1.0-Linux-gcc64.tar.gz | tar zx -C /opt/c3d --strip-components=1
-ENV PATH "/opt/c3d/bin:$PATH"
-
-
-#install mcr
-RUN mkdir -p /opt/mcr-install && curl -L --retry 5 https://ssd.mathworks.com/supportfiles/downloads/R2019b/Release/5/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2019b_Update_5_glnxa64.zip > /opt/mcr-install/install.zip && \
-unzip /opt/mcr-install/install.zip -d /opt/mcr-install && \
-/opt/mcr-install/install -mode silent -agreeToLicense yes -destinationFolder /opt/mcr && \
-rm -rf /opt/mcr-install
-