FIX update Dockerfile and Singularity

Author: Shotgunosine

Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.0
-# Timestamp: 2018-07-14 20:29:37 UTC
+# Generated by Neurodocker version 0.4.2-dev
+# Timestamp: 2018-10-09 20:28:32 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -64,30 +64,32 @@ RUN apt-get update -qq \
 RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 
 ENV FORCE_SPMMCR="1" \
-    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018a/v94/runtime/glnxa64:/opt/matlabmcr-2018a/v94/bin/glnxa64:/opt/matlabmcr-2018a/v94/sys/os/glnxa64:/opt/matlabmcr-2018a/v94/extern/bin/glnxa64" \
-    MATLABCMD="/opt/matlabmcr-2018a/v94/toolbox/matlab"
+    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64" \
+    MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            bc \
+           libncurses5 \
            libxext6 \
+           libxmu6 \
            libxpm-dev \
            libxt6 \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && echo "Downloading MATLAB Compiler Runtime ..." \
-    && curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018a/deployment_files/R2018a/installers/glnxa64/MCR_R2018a_glnxa64_installer.zip \
+    && curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018b/deployment_files/R2018b/installers/glnxa64/MCR_R2018b_glnxa64_installer.zip \
     && unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
-    && /tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018a -mode silent -agreeToLicense yes \
+    && /tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes \
     && rm -rf /tmp/* \
     && echo "Downloading standalone SPM ..." \
-    && curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018a.zip \
+    && curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip \
     && unzip -q /tmp/spm12.zip -d /tmp \
     && mkdir -p /opt/spm12-dev \
     && mv /tmp/spm12/* /opt/spm12-dev/ \
     && chmod -R 777 /opt/spm12-dev \
     && rm -rf /tmp/* \
-    && /opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 quit \
-    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 script\"' $ND_ENTRYPOINT
+    && /opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit \
+    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
 
 RUN useradd --no-user-group --create-home --shell /bin/bash neuro
 USER neuro
@@ -122,7 +124,7 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
            nb_conda \
     && sync && conda clean -tipsy && sync \
     && bash -c "source activate neuro \
-    &&   pip install  --no-cache-dir \
+    &&   pip install --no-cache-dir  \
              https://github.com/nipy/nipype/tarball/master \
              https://github.com/INCF/pybids/tarball/master \
              nilearn \
@@ -152,6 +154,8 @@ RUN curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5807050
 
 COPY [".", "/home/neuro/nipype_tutorial"]
 
+RUN find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
+
 USER root
 
 RUN chown -R neuro /home/neuro/nipype_tutorial
@@ -281,6 +285,10 @@ RUN echo '{ \
     \n      ] \
     \n    ], \
     \n    [ \
+    \n      "run", \
+    \n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +" \
+    \n    ], \
+    \n    [ \
     \n      "user", \
     \n      "root" \
     \n    ], \

Singularity

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1-dev
-# Timestamp: 2018-09-27 11:07:19 UTC
+# Generated by Neurodocker version 0.4.2-dev
+# Timestamp: 2018-10-09 20:28:34 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -61,25 +61,27 @@ sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 apt-get update -qq
 apt-get install -y -q --no-install-recommends \
     bc \
+    libncurses5 \
     libxext6 \
+    libxmu6 \
     libxpm-dev \
     libxt6
 apt-get clean
 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 echo "Downloading MATLAB Compiler Runtime ..."
-curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018a/deployment_files/R2018a/installers/glnxa64/MCR_R2018a_glnxa64_installer.zip
+curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018b/deployment_files/R2018b/installers/glnxa64/MCR_R2018b_glnxa64_installer.zip
 unzip -q /tmp/mcr.zip -d /tmp/mcrtmp
-/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018a -mode silent -agreeToLicense yes
+/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes
 rm -rf /tmp/*
 echo "Downloading standalone SPM ..."
-curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018a.zip
+curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip
 unzip -q /tmp/spm12.zip -d /tmp
 mkdir -p /opt/spm12-dev
 mv /tmp/spm12/* /opt/spm12-dev/
 chmod -R 777 /opt/spm12-dev
 rm -rf /tmp/*
-/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 quit
-sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 script\"' $ND_ENTRYPOINT
+/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit
+sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
 
 useradd --no-user-group --create-home --shell /bin/bash neuro
 su - neuro
@@ -112,7 +114,7 @@ conda install -y -q --name neuro \
     nb_conda
 sync && conda clean -tipsy && sync
 bash -c "source activate neuro
-  pip install  --no-cache-dir \
+  pip install --no-cache-dir  \
       https://github.com/nipy/nipype/tarball/master \
       https://github.com/INCF/pybids/tarball/master \
       nilearn \
@@ -141,6 +143,8 @@ bash -c 'source activate neuro && cd /data && datalad install -r ///workshops/ni
 
 curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete
 
+find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
+
 su - root
 
 chown -R neuro /home/neuro/nipype_tutorial
@@ -275,6 +279,10 @@ echo '{
 \n      ]
 \n    ],
 \n    [
+\n      "run",
+\n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +"
+\n    ],
+\n    [
 \n      "user",
 \n      "root"
 \n    ],
@@ -306,8 +314,8 @@ export LANG="en_US.UTF-8"
 export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
 export FORCE_SPMMCR="1"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018a/v94/runtime/glnxa64:/opt/matlabmcr-2018a/v94/bin/glnxa64:/opt/matlabmcr-2018a/v94/sys/os/glnxa64:/opt/matlabmcr-2018a/v94/extern/bin/glnxa64"
-export MATLABCMD="/opt/matlabmcr-2018a/v94/toolbox/matlab"
+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64"
+export MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
 export CONDA_DIR="/opt/miniconda-latest"
 export PATH="/opt/miniconda-latest/bin:$PATH"