Merge pull request #32 from CoBrALab/updates

BIDS data structure available, single shot commonspace resampling, more specific datasink outputs, introduction of logs

Dockerfile

@@ -94,12 +94,9 @@ RUN wget afni.nimh.nih.gov/pub/dist/tgz/linux_ubuntu_16_64.tgz \
     && tar -xzf linux_ubuntu_16_64.tgz -C $HOME/afni \
     && rm -rf linux_ubuntu_16_64.tgz
 
-ENV AFNIPATH="$HOME/ants-v2.3.1/bin" \
+ENV AFNIPATH="$HOME/afni/linux_ubuntu_16_64/" \
     PATH="$HOME/afni/linux_ubuntu_16_64:$PATH"
 
-
-### Local CIC VM from https://github.com/CobraLab/MINC-VM/blob/master/provision.sh
-
 RUN apt-get update && \
   apt-get install -y --no-install-recommends htop nano wget imagemagick parallel zram-config debconf
 
@@ -111,6 +108,8 @@ RUN echo ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula selec
     zenity libcurl4-openssl-dev bc gawk libxkbcommon-x11-0 \
     ttf-mscorefonts-installer bc
 
+#Install python environment
+
 ENV CONDA_DIR="$HOME/miniconda-latest" \
     PATH="$HOME/miniconda-latest/bin:$PATH" \
     ND_ENTRYPOINT="$HOME/startup.sh"
@@ -131,111 +130,6 @@ RUN export PATH="$HOME/miniconda-latest/bin:$PATH" \
     && rm -rf ~/.cache/pip/* \
     && sync
 
-# set paths
-ENV minc_toolkit_v2=https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.17-20190313-Ubuntu_18.04-x86_64.deb \
-  minc_toolkit_v1=https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.0.09-20170529-Ubuntu_18.04-x86_64.deb \
-  bic_mni_models=http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/bic-mni-models-0.1.1-20120421.deb \
-  beast_library=http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/beast-library-1.1.0-20121212.deb \
-  pyminc=https://github.com/Mouse-Imaging-Centre/pyminc/archive/v0.52.tar.gz \
-  minc_stuffs=https://github.com/Mouse-Imaging-Centre/minc-stuffs/archive/v0.1.24.tar.gz \
-  pyezminc=https://github.com/BIC-MNI/pyezminc/archive/release-1.2.01.tar.gz \
-  quarter=https://github.com/Alexpux/Quarter/archive/master.tar.gz \
-  bicinventor=https://github.com/BIC-MNI/bicInventor/archive/master.tar.gz \
-  brain_view2=https://github.com/Mouse-Imaging-Centre/brain-view2/archive/master.tar.gz \
-  itksnap_minc=http://www.bic.mni.mcgill.ca/~vfonov/temp/itksnap-3.4.0-20151130-Linux-x86_64-qt4.tar.gz \
-  mni_cortical_statistics=https://github.com/BIC-MNI/mni.cortical.statistics/archive/ver-0_9_5.tar.gz \
-  generate_deformation_fields=https://github.com/Mouse-Imaging-Centre/generate_deformation_fields/archive/1.0.1.tar.gz \
-  pydpiper=https://github.com/Mouse-Imaging-Centre/pydpiper/archive/v2.0.13.tar.gz \
-  bpipe=https://github.com/ssadedin/bpipe/releases/download/0.9.9.6/bpipe-0.9.9.6.tar.gz
-
-
-#Download and install external debs
-RUN wget --progress=dot:mega $minc_toolkit_v2 && \
-  wget --progress=dot:mega $minc_toolkit_v1 && \
-  wget --progress=dot:mega $bic_mni_models && \
-  wget --progress=dot:mega $beast_library && \
-  for file in *.deb; do gdebi --n $file; done && \
-  rm -f *.deb
-
-
-RUN echo '. /opt/minc/1.9.17/minc-toolkit-config.sh' >> $HOME/.bashrc && \
-  echo 'export LD_LIBRARY_PATH=/opt/minc/1.9.17/lib' >> $HOME/.bashrc && \
-  echo 'export PATH=/opt/minc-toolkit-extras/:$PATH' >> $HOME/.bashrc
-
-#Enable minc-toolkit in this script, need to escape error checking
-RUN set +u && \
-  . /opt/minc/1.9.17/minc-toolkit-config.sh && \
-  set -u
-
-#Download other packages
-RUN wget --progress=dot:mega $pyminc -O pyminc.tar.gz && \
-  wget --progress=dot:mega $minc_stuffs -O minc-stuffs.tar.gz && \
-  wget --progress=dot:mega $pyezminc -O pyezminc.tar.gz && \
-  wget --progress=dot:mega $generate_deformation_fields -O generate_deformation_fields.tar.gz && \
-  wget --progress=dot:mega $pydpiper -O pydpiper.tar.gz && \
-  wget --progress=dot:mega $bpipe -O bpipe.tar.gz && \
-  wget https://raw.githubusercontent.com/andrewjanke/volgenmodel/master/volgenmodel -O /usr/local/bin/volgenmodel && \
-  git clone https://github.com/CobraLab/minc-toolkit-extras.git /opt/minc-toolkit-extras
-
-
-#Do this so that we don't need to keep track of version numbers for build
-RUN mkdir -p pyminc && tar xzvf pyminc.tar.gz -C pyminc --strip-components 1 && \
-  mkdir -p minc-stuffs && tar xzvf minc-stuffs.tar.gz -C minc-stuffs --strip-components 1 && \
-  mkdir -p generate_deformation_fields && tar xzvf generate_deformation_fields.tar.gz -C generate_deformation_fields --strip-components 1 && \
-  mkdir -p pyezminc && tar xzvf pyezminc.tar.gz -C pyezminc --strip-components 1 && \
-  mkdir -p pydpiper && tar xzvf pydpiper.tar.gz -C pydpiper --strip-components 1 && \
-  mkdir -p /opt/bpipe && tar xzvf bpipe.tar.gz -C /opt/bpipe --strip-components 1 && ln -s /opt/bpipe/bin/bpipe /usr/local/bin/bpipe
-
-
-#Build and install packages
-RUN ( cd pyezminc && python setup.py install --mincdir /opt/minc/1.9.17 ) && \
-  ( cd pyminc && python setup.py install ) && \
-  ( cd minc-stuffs && ./autogen.sh && ./configure --with-build-path=/opt/minc/1.9.17 && make && make install && python setup.py install ) && \
-  ( cd generate_deformation_fields && ./autogen.sh && ./configure --with-minc2 --with-build-path=/opt/minc/1.9.17 && make && make install) && \
-  ( cd generate_deformation_fields/scripts && python setup.py build_ext --inplace && python setup.py install) && \
-  ( cd pydpiper && python setup.py install)
-
-RUN pip install -U qbatch==2.1.5 && \
-  rm -rf pyezminc* pyminc* minc-stuffs* generate_deformation_fields* pydpiper* bpipe*
-
-#Installing brain-view2
-RUN apt install -y --no-install-recommends libcoin80-dev libpcre++-dev qt4-default libqt4-opengl-dev libtool && \
-  wget $quarter -O quarter.tar.gz && \
-  wget $bicinventor -O bicinventor.tar.gz && \
-  wget $brain_view2 -O brain-view2.tar.gz && \
-  mkdir quarter && tar xzvf quarter.tar.gz -C quarter --strip-components 1 && \
-  mkdir bicinventor && tar xzvf bicinventor.tar.gz -C bicinventor --strip-components 1 && \
-  mkdir brain-view2 && tar xzvf brain-view2.tar.gz -C brain-view2 --strip-components 1 && \
-  ( cd quarter && cmake . && make && make install ) && \
-  ( cd bicinventor && ./autogen.sh && ./configure --with-build-path=/opt/minc/1.9.17 --prefix=/opt/minc/1.9.17 --with-minc2 && make && make install ) && \
-  ( cd brain-view2 && /usr/bin/qmake-qt4 MINCDIR=/opt/minc/1.9.17 HDF5DIR=/opt/minc/1.9.17 INVENTORDIR=/opt/minc/1.9.17 && make && cp brain-view2 /opt/minc/1.9.17/bin ) && \
-  rm -rf quarter* bicinventor* brain-view2*
-
-#Install itksnap-MINC
-RUN wget $itksnap_minc -O itksnap_minc.tar.gz && \
-  tar xzvf itksnap_minc.tar.gz -C /usr/local --strip-components 1 && \
-  rm -f itksnap_minc.tar.gz
-
-ENV export MINC_PATH=/opt/minc/1.9.17 \
-  export PATH=${OLDPATH}
-
-#Purge unneeded packages
-RUN apt-get purge $(dpkg -l | tr -s ' ' | cut -d" " -f2 | sed 's/:amd64//g' | grep -e -E '(-dev|-doc)$')
-
-#Remove a hunk of useless packages which seem to be safe to remove
-RUN apt-get -y purge printer-driver.* xserver-xorg-video.* xscreensaver.* wpasupplicant wireless-tools .*vdpau.* \
-  bluez-cups cups-browsed cups-bsd cups-client cups-common cups-core-drivers cups-daemon cups-filters \
-  cups-filters-core-drivers cups-ppdc cups-server-common linux-headers.* snapd bluez linux-firmware .*sane.* .*ppds.* && \
-  apt-get -y clean && \
-  apt-get -y --purge autoremove
-
-#Cleanup to ensure extra files aren't packed into VM
-RUN cd ~ && \
-  rm -rf /tmp/provision && \
-  rm -f /var/cache/apt/archives/*.deb && \
-  rm -rf /var/lib/apt/lists/*
-
-
 #### install RABIES
 
 ENV export LD_LIBRARY_PATH=/opt/minc/1.9.17/lib \