From 4ea4958e673ca0fcafd88fdd172e5c98660777b1 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Mon, 25 Sep 2023 15:52:41 -0400 Subject: [PATCH] remove fsl as dependency --- Dockerfile | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index e4ee2ba..75dcfe2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ FROM continuumio/miniconda3:4.10.3 MAINTAINER alik@robarts.ca #dependencies for hippunfold -# note: this installs minified versions of fsl and ants to save space.. +# note: this installs minified versions of ants to save space.. RUN apt-get --allow-releaseinfo-change 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 && \ @@ -23,10 +23,6 @@ mkdir -p /opt/ants-2.3.1 && curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhyd | 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 antsRegistrationSyNQuick.sh PrintHeader; do mv /opt/ants-2.3.1/${bin} /opt/ants-2.3.1-minify; done && \ rm -rf /opt/ants-2.3.1 && \ -mkdir -p /opt/fsl-5.0.11 && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \ -| tar -xz -C /opt/fsl-5.0.11 --strip-components 1 && \ -mkdir /opt/fsl-5.0.11/bin-minify && for bin in flirt fslmaths fslreorient2std fslroi fslstats; do mv /opt/fsl-5.0.11/bin/${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 && \ 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/ \ @@ -56,11 +52,8 @@ RUN pip install --no-cache-dir /src && \ mv magick /usr/bin && chmod a+x /usr/bin/magick 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 PATH /opt/conda/bin:/opt/itksnap/bin/:/opt/niftyreg-1.3.9/bin:/opt/workbench/bin_linux64:/opt/ants-2.3.1-minify:$PATH -ENV FSLDIR "/opt/fsl-5.0.11" -ENV FSLOUTPUTTYPE NIFTI_GZ -ENV FSLMULTIFILEQUIT TRUE ENV _JAVA_OPTIONS= ENV ANTSPATH /opt/ants-2.3.1-minify/