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removed empty line continuation [skip ci]
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Ali Khan
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Jul 24, 2020
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@@ -7,24 +7,24 @@ MAINTAINER [email protected] | |
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ENV PATH /opt/conda/bin:$PATH | ||
#needed to create /usr/share/man/man1 folder to avoid error when installing jre | ||
RUN apt-get update && mkdir -p /usr/share/man/man1 && apt-get install -y curl tree unzip default-jre && pip install --upgrade pip && \ | ||
#python dependencies | ||
RUN apt-get update && mkdir -p /usr/share/man/man1 && apt-get install -y curl tree unzip default-jre && pip install --upgrade pip && \ | ||
conda install tensorflow-gpu==1.14 && conda install -c anaconda opencv scikit-learn pyyaml && conda install -c simpleitk simpleitk && \ | ||
pip install niftynet==0.6.0 niwidgets==0.1.3 | ||
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#install ants | ||
#we only need antsRegistration and antsApplyTransforms, can remove everything else | ||
RUN mkdir -p /opt/ants-2.3.1 && curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \ | ||
| tar -xz -C /opt/ants-2.3.1 --strip-components 1 && \ | ||
#we only need antsRegistration and antsApplyTransforms, can remove everything else | ||
mkdir /opt/ants-2.3.1-minify && for bin in antsRegistration antsApplyTransforms; do mv /opt/ants-2.3.1/${bin} /opt/ants-2.3.1-minify; done && \ | ||
rm -rf /opt/ants-2.3.1 | ||
ENV PATH "/opt/ants-2.3.1-minify:$PATH" | ||
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#install fsl | ||
RUN mkdir -p /opt/fsl-5.0.11 && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \ | ||
| tar -xz -C /opt/fsl-5.0.11 --strip-components 1 && \ | ||
#we only need {flirt,fslmaths,fslreorient2std,fslroi,fslstats} from fsl, can remove everything else from bin | ||
# we also remove {data,extras,lib,src,doc} to save space | ||
RUN mkdir -p /opt/fsl-5.0.11 && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \ | ||
| tar -xz -C /opt/fsl-5.0.11 --strip-components 1 && \ | ||
mkdir /opt/fsl-5.0.11/bin-minify && for bin in flirt fslmaths fslreorient2std fslroi fslstats; do mv /opt/fsl-5.0.11/bin/${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 | ||
ENV FSLDIR "/opt/fsl-5.0.11" | ||
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