Dockerfile.centos7

FROM centos:7.5.1804

MAINTAINER Tashrif Billah <tbillah@bwh.harvard.edu>

# set up user and working directory
WORKDIR /
ENV USER="root"

COPY startup.sh /

## primary image for deployment ##
# libraries and commands for FSL
RUN yum -y update > /dev/null 2>&1 && \
    yum -y install epel-release wget which file bzip2 openblas-devel libquadmath && \
    yum clean all && \
# install FSL
    echo "Downloading FSL installer" && \
    wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -O fslinstaller.py > /dev/null 2>&1 && \
    echo "Installing FSL" && \
    python fslinstaller.py -V 5.0.11 -d `pwd`/fsl-5.0.11-centos7 -p > /dev/null 2>&1 && \
# setup FSL environment
    export FSLDIR="$PWD/fsl-5.0.11-centos7" && \
    echo "export FSLDIR=$PWD/fsl-5.0.11-centos7" >> ~/.bashrc && \
    export PATH="$FSLDIR/bin/:$PATH" && \
    echo "export PATH=\$FSLDIR/bin/:\$PATH" >> ~/.bashrc && \
    source $FSLDIR/etc/fslconf/fsl.sh && \
    echo "source $FSLDIR/etc/fslconf/fsl.sh" >> ~/.bashrc && \
# apply patch
    echo "Installing FSL patch" && \
    $FSLDIR/fslpython/bin/conda install -y -n fslpython -c conda-forge deprecation==1.* > /dev/null 2>&1 && \
    $FSLDIR/fslpython/bin/conda clean --all && \
    rm -f fslinstaller.py && \
# install python
    echo "Downloading miniconda3 installer" && \
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3-latest-Linux-x86_64.sh > /dev/null 2>&1 && \
    /bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3/ && \
    rm -f Miniconda3-latest-Linux-x86_64.sh && \
    source miniconda3/bin/activate && \
    echo "source $PWD/miniconda3/bin/activate" >> ~/.bashrc && \
# install ANTs=2.3.0
    conda install -y -c pnlbwh ants && \
    export ANTSPATH="$PWD/miniconda3/bin/" && \
    echo "export ANTSPATH=$PWD/miniconda3/bin/" >> ~/.bashrc && \
# libraries and commands for TBSS
    yum -y install git bc unzip gcc && \
    yum clean all && \
    rm -rf /var/yum/cache/ && \
# clone TBSS
    git clone --single-branch --branch master https://github.com/pnlbwh/tbss.git && \
# install TBSS
    /bin/bash tbss/install.sh setup && \
# clear cache
    conda clean -y --all && rm -rf ~/.cache/pip/* && \
# define alias
    echo "alias ls=\"ls --color\"" >> ~/.bashrc && \
# clean up redundant files
    cd $FSLDIR/ && rm -rf doc/ refdoc/ src/ extras/ data/first data/mist data/possum bin/FSLeyes && \
    chmod +x /startup.sh

## secondary image for testing ##
# disable unittest within install.sh script, run pipeline, and remove redundant test files
RUN source ~/.bashrc && sed -i "s/pytest -v/# pytest -v/g" tbss/install.sh && tbss/install.sh test && cd tbss/lib/tests/ && for i in `find . -type f \( ! -iname "*combined_roi_avg.csv" -a ! -iname "*py" \)`; do rm $i; done
    

ENTRYPOINT ["/startup.sh"]