Created
May 31, 2017 17:33
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| 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"] |
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