mrtrix.def

BootStrap: docker
From: debian:buster-slim

%post
   
   # install dependencies
   apt-get -y update
   apt-get install -y curl wget nano bzip2 less git
   apt-get install -y libgl1-mesa-glx libgl1-mesa-dev freeglut3 libx11-dev libxtst6 libfontconfig libdbus-1-3 mesa-utils
   

   # install Qt
   cd / && mkdir Qt
   wget http://download.qt.io/official_releases/qt/5.9/5.9.0/qt-opensource-linux-x64-5.9.0.run
   git clone https://github.com/benlau/qtci
   qtci/bin/extract-qt-installer qt-opensource-linux-x64-5.9.0.run /Qt
   rm -rf qtci qt-opensource-linux-x64-5.9.0.run

   # install mrtrix
   mkdir -p /opt
   wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   bash Miniconda3-latest-Linux-x86_64.sh -f -b -p /opt/conda
   . /opt/conda/etc/profile.d/conda.sh
   conda activate base
   conda update --yes --all
   conda create -n mrtrix
   conda activate mrtrix
   conda install --yes -c mrtrix3 mrtrix3=3.0.1

   # create bind points for NIH HPC environment
   mkdir -p /vf /gpfs /spin1 /data /scratch /fdb /lscratch
   for i in $(seq 1 30); do ln -s /gpfs/gsfs${i} /gs${i}; done

   # clean up
   apt-get clean
   conda clean --yes --all

%environment
   export LC_ALL=C
   export PATH=/opt/conda/envs/mrtrix/bin:${PATH}
   export LD_LIBRARY_PATH=/lib64:${LD_LIBRARY_PATH}