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Dockerfile
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FROM centos:6.8
ENV LD_LIBRARY_PATH /Downloads/BROCCOLI/code/BROCCOLI_LIB/clBLASLinux
ENV BROCCOLI_DIR /Downloads/BROCCOLI/
ENV PATH $PATH:/Downloads/BROCCOLI/compiled/Bash/Linux/Release/
ENV SHELL /bin/bash
ENV FSLDIR /usr/local/fsl
ENV PATH $PATH:/usr/local/fsl/bin
ENV FSLOUTPUTTYPE NIFTI_GZ
ENV PATH $PATH:/Downloads/BROCCOLI/code/bids
RUN rm /bin/sh && \
ln -s /bin/bash /bin/sh && \
yum -y install wget && \
yum -y install git && \
yum -y install zlib-devel && \
yum -y install cifs-utils && \
yum -y install emacs && \
yum -y install libgomp.x86_64 && \
yum -y install numactl.x86_64 && \
yum -y install libXp.x86_64 && \
yum -y install gcc-c++ && \
yum -y install libXmu.x86_64 && \
yum -y install bc-1.06.95-1.el6.x86_64 && \
yum -y update
RUN mkdir Downloads && \
cd Downloads && \
wget https://dl.dropboxusercontent.com/u/4494604/opencl_runtime_15.1_x64_5.0.0.57.tar && \
tar -xf opencl_runtime_15.1_x64_5.0.0.57.tar && \
cd opencl_runtime_15.1_x64_5.0.0.57 && \
chmod +x install.sh && \
sed -i 's/decline/accept/g' silent.cfg && \
./install.sh -s silent.cfg && \
cd .. && \
rm opencl_runtime_15.1_x64_5.0.0.57.tar && \
rm -rf opencl_runtime_15.1_x64_5.0.0.57
RUN wget https://dl.dropboxusercontent.com/u/4494604/intel_code_builder_for_opencl_2015_5.0.0.62_x64.tar && \
tar -xf intel_code_builder_for_opencl_2015_5.0.0.62_x64.tar && \
cd intel_code_builder_for_opencl_2015_5.0.0.62_x64 && \
sed -i 's/decline/accept/g' silent.cfg && \
chmod +x install.sh && \
./install.sh -s silent.cfg && \
cd .. && \
rm intel_code_builder_for_opencl_2015_5.0.0.62_x64.tar && \
rm -rf intel_code_builder_for_opencl_2015_5.0.0.62_x64
RUN cd /Downloads && \
mkdir BROCCOLI && \
cd BROCCOLI && \
git clone --depth 1 https://github.com/wanderine/BROCCOLI.git . && \
cd code && \
cd BROCCOLI_LIB && \
./compile_broccoli_library.sh && \
cd .. && \
cd Bash_Wrapper && \
./compile_wrappers.sh && \
cd .. && \
cd .. && \
cd compiled/Bash/Linux/Release/ && \
./GetOpenCLInfo && \
cp /Downloads/BROCCOLI/test_data/fcon1000/classic/Beijing/sub00440/func/rest.nii.gz . && \
./Smoothing rest.nii.gz -verbose && \
rm rest.nii.gz && \
rm rest_sm.nii.gz && \
cd /Downloads/BROCCOLI/code/bids && \
chmod +x broccolipipeline.sh && \
chmod +x BIDSto3col.sh
RUN cd /Downloads/BROCCOLI/code/bids && \
chmod +x fslinstaller.py && \
python2.6 fslinstaller.py -q -d /usr/local && \
. /usr/local/fsl/etc/fslconf/fsl.sh
RUN curl --silent --location https://rpm.nodesource.com/setup_6.x | bash - && \
yum install -y nodejs
RUN npm install -g bids-validator@0.21.1
COPY version /version
ENTRYPOINT ["/Downloads/BROCCOLI/code/bids/broccolipipeline.sh"]