dockerfile--fs6-build

FROM amazonlinux:latest

# root does everything for now
# ---------------------------------------------------------------------
USER root

# For freesurfer
# ---------------------------------------------------------------------
# So that we can run `yum -y install git-lfs`
RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | bash
RUN \
  yum -y update && \
  yum -y groupinstall "Development Tools"  && \
  yum -y install epel-release && \
  yum -y install mesa-libGLU-devel \
                 freetype-devel \
                 libuuid-devel \
                 uuid-c++-devel \
                 libXmu-devel \
                 libXi-devel \
                 lapack-devel \
                 lapack-static \
                 blas-static \
                 liblapack-devel \
                 libXaw-devel \
                 libpng-devel \
                 tar \
                 tcsh \
                 vim-common \
                 curl \
                 nano \
                 sudo \
                 which \
                 bc \
                 libgomp \
                 git-lfs \
				         psmisc \
                 aws-cli

# For modern version of git-annex
# ---------------------------------------------------------------------
RUN curl -o /root/git-annex-standalone-amd64.tar.gz https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz && \
    tar -zxvf /root/git-annex-standalone-amd64.tar.gz -C /root/ 
ENV PATH /root/git-annex.linux:$PATH

# Configure environment
# ---------------------------------------------------------------------
ENV FREESURFER_HOME /fs/bin
VOLUME /fs/bin

ENV SUBJECTS_DIR /subjects
VOLUME /subjects

VOLUME /fs/code
VOLUME /fs/pkg

ENV OS Linux
ENV FS_OVERRIDE 0
ENV FIX_VERTEX_AREA=
ENV FSF_OUTPUT_FORMAT nii.gz
ENV MNI_DIR $FREESURFER_HOME/mni
ENV LOCAL_DIR $FREESURFER_HOME/local
ENV FSFAST_HOME $FREESURFER_HOME/fsfast
ENV MINC_BIN_DIR $FREESURFER_HOME/mni/bin
ENV MINC_LIB_DIR $FREESURFER_HOME/mni/lib
ENV MNI_DATAPATH $FREESURFER_HOME/mni/data
ENV FMRI_ANALYSIS_DIR $FREESURFER_HOME/fsfast
ENV PERL5LIB $FREESURFER_HOME/mni/lib/perl5/5.8.5
ENV MNI_PERL5LIB $FREESURFER_HOME/mni/lib/perl5/5.8.5
ENV PATH $FREESURFER_HOME/bin:$FREESURFER_HOME/fsfast/bin:$FREESURFER_HOME/tktools:$FREESURFER_HOME/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

ADD entrypoint-aws.bash /usr/local/bin/entrypoint-aws.bash
ENTRYPOINT ["/usr/local/bin/entrypoint-aws.bash"]