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Merged
merged 2 commits into from
Jul 14, 2019
Merged

Update generation file #144

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1359b0b
Update generation file
miykael Jul 14, 2019
3c2fda2
Merge branch 'master' into debug_permission
miykael Jul 14, 2019
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63 changes: 36 additions & 27 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Generated by Neurodocker version 0.4.2-dev
# Timestamp: 2018-10-15 12:01:29 UTC
# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-07-14 08:54:07 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
Expand All @@ -24,7 +24,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
locales \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& rm -rf /var/lib/apt/lists/* \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
Expand All @@ -33,6 +33,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
Expand All @@ -59,14 +60,15 @@ RUN apt-get update -qq \
octave \
netbase \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
&& rm -rf /var/lib/apt/lists/*

RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT

ENV FORCE_SPMMCR="1" \
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
RUN apt-get update -qq \
RUN export TMPDIR="$(mktemp -d)" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
libncurses5 \
Expand All @@ -75,18 +77,19 @@ RUN apt-get update -qq \
libxpm-dev \
libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/toinstall.deb \
&& rm /tmp/toinstall.deb \
&& apt-get install -f \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
&& chmod +x /tmp/MCRInstaller.bin \
&& /tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a" \
&& rm -rf /tmp/* \
&& rm -rf /var/lib/apt/lists/* \
&& curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
&& chmod +x "$TMPDIR/MCRInstaller.bin" \
&& "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
&& rm -rf "$TMPDIR" \
&& unset TMPDIR \
&& echo "Downloading standalone SPM ..." \
&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
&& unzip -q /tmp/spm12.zip -d /tmp \
Expand All @@ -97,9 +100,11 @@ RUN apt-get update -qq \
&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

RUN useradd --no-user-group --create-home --shell /bin/bash neuro
RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

WORKDIR /home/neuro

ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
Expand All @@ -112,23 +117,23 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& sync && conda clean -tipsy && sync \
&& sync && conda clean --all && sync \
&& conda create -y -q --name neuro \
&& conda install -y -q --name neuro \
python=3.6 \
pytest \
jupyter \
jupyterlab \
jupyter_contrib_nbextensions \
traits \
pandas \
matplotlib \
scikit-learn \
scikit-image \
seaborn \
nbformat \
nb_conda \
&& sync && conda clean -tipsy && sync \
'python=3.6' \
'pytest' \
'jupyter' \
'jupyterlab' \
'jupyter_contrib_nbextensions' \
'traits' \
'pandas' \
'matplotlib' \
'scikit-learn' \
'scikit-image' \
'seaborn' \
'nbformat' \
'nb_conda' \
&& sync && conda clean --all && sync \
&& bash -c "source activate neuro \
&& pip install --no-cache-dir \
https://github.com/nipy/nipype/tarball/master \
Expand Down Expand Up @@ -220,6 +225,10 @@ RUN echo '{ \
\n "neuro" \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "miniconda_version": "4.3.31", \
Expand Down
61 changes: 35 additions & 26 deletions Singularity
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Generated by Neurodocker version 0.4.2-dev
# Timestamp: 2018-10-15 12:01:30 UTC
# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-07-14 08:54:09 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
Expand All @@ -21,7 +21,7 @@ apt-get install -y -q --no-install-recommends \
locales \
unzip
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
rm -rf /var/lib/apt/lists/*
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
dpkg-reconfigure --frontend=noninteractive locales
update-locale LANG="en_US.UTF-8"
Expand All @@ -30,6 +30,7 @@ mkdir -p /neurodocker
if [ ! -f "$ND_ENTRYPOINT" ]; then
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
echo 'set -e' >> "$ND_ENTRYPOINT"
echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker
Expand All @@ -54,10 +55,11 @@ apt-get install -y -q --no-install-recommends \
octave \
netbase
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
rm -rf /var/lib/apt/lists/*

sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT

export TMPDIR="$(mktemp -d)"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
bc \
Expand All @@ -67,18 +69,19 @@ apt-get install -y -q --no-install-recommends \
libxpm-dev \
libxt6
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
rm -rf /var/lib/apt/lists/*
echo "Downloading MATLAB Compiler Runtime ..."
curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
dpkg -i /tmp/toinstall.deb
rm /tmp/toinstall.deb
apt-get install -f
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
chmod +x /tmp/MCRInstaller.bin
/tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a"
rm -rf /tmp/*
rm -rf /var/lib/apt/lists/*
curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
chmod +x "$TMPDIR/MCRInstaller.bin"
"$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a"
rm -rf "$TMPDIR"
unset TMPDIR
echo "Downloading standalone SPM ..."
curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
unzip -q /tmp/spm12.zip -d /tmp
Expand All @@ -89,9 +92,11 @@ rm -rf /tmp/*
/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

useradd --no-user-group --create-home --shell /bin/bash neuro
test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
su - neuro

cd /home/neuro

export PATH="/opt/miniconda-latest/bin:$PATH"
echo "Downloading Miniconda installer ..."
conda_installer="/tmp/miniconda.sh"
Expand All @@ -102,23 +107,23 @@ conda update -yq -nbase conda
conda config --system --prepend channels conda-forge
conda config --system --set auto_update_conda false
conda config --system --set show_channel_urls true
sync && conda clean -tipsy && sync
sync && conda clean --all && sync
conda create -y -q --name neuro
conda install -y -q --name neuro \
python=3.6 \
pytest \
jupyter \
jupyterlab \
jupyter_contrib_nbextensions \
traits \
pandas \
matplotlib \
scikit-learn \
scikit-image \
seaborn \
nbformat \
nb_conda
sync && conda clean -tipsy && sync
'python=3.6' \
'pytest' \
'jupyter' \
'jupyterlab' \
'jupyter_contrib_nbextensions' \
'traits' \
'pandas' \
'matplotlib' \
'scikit-learn' \
'scikit-image' \
'seaborn' \
'nbformat' \
'nb_conda'
sync && conda clean --all && sync
bash -c "source activate neuro
pip install --no-cache-dir \
https://github.com/nipy/nipype/tarball/master \
Expand Down Expand Up @@ -212,6 +217,10 @@ echo '{
\n "neuro"
\n ],
\n [
\n "workdir",
\n "/home/neuro"
\n ],
\n [
\n "miniconda",
\n {
\n "miniconda_version": "4.3.31",
Expand Down
2 changes: 2 additions & 0 deletions generate.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ generate_docker() {
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
--spm12 version=r7219 \
--user=neuro \
--workdir /home/neuro \
--miniconda miniconda_version="4.3.31" \
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
Expand Down Expand Up @@ -51,6 +52,7 @@ generate_singularity() {
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
--spm12 version=r7219 \
--user=neuro \
--workdir /home/neuro \
--miniconda miniconda_version="4.3.31" \
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
Expand Down