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miykaelmiykael
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FIX: changes library for libgcc_s.so.1 import
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‎Dockerfile

Lines changed: 10 additions & 10 deletions
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@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.2-dev
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# Timestamp: 2018-10-10 04:25:17 UTC
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# Generated by Neurodocker version 0.4.1-22-g7c44e01
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# Timestamp: 2018-10-10 17:39:05 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
@@ -63,8 +63,6 @@ RUN apt-get update -qq \
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RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
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ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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ENV FORCE_SPMMCR="1" \
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
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MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
@@ -168,6 +166,8 @@ RUN chown -R neuro /home/neuro/nipype_tutorial
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RUN rm -rf /opt/conda/pkgs/*
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ENV LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
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USER neuro
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RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
@@ -210,12 +210,6 @@ RUN echo '{ \
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\n "source /etc/fsl/fsl.sh" \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
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\n } \
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\n ], \
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\n [ \
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\n "spm12", \
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\n { \
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\n "version": "r7219" \
@@ -309,6 +303,12 @@ RUN echo '{ \
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\n "rm -rf /opt/conda/pkgs/*" \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" \
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\n } \
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\n ], \
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\n [ \
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\n "user", \
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\n "neuro" \
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\n ], \

‎Singularity

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.2-dev
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# Timestamp: 2018-10-10 04:25:18 UTC
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# Generated by Neurodocker version 0.4.1-22-g7c44e01
2+
# Timestamp: 2018-10-10 17:39:06 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
@@ -202,12 +202,6 @@ echo '{
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\n "source /etc/fsl/fsl.sh"
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\n ],
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\n [
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\n "env",
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\n {
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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\n }
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\n ],
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\n [
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\n "spm12",
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\n {
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\n "version": "r7219"
@@ -301,6 +295,12 @@ echo '{
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\n "rm -rf /opt/conda/pkgs/*"
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\n ],
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\n [
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\n "env",
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\n {
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\n "LD_LIBRARY_PATH": "/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
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\n }
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\n ],
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\n [
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\n "user",
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\n "neuro"
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\n ],
@@ -319,12 +319,12 @@ echo '{
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export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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export FORCE_SPMMCR="1"
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export LD_LIBRARY_PATH="$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"
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export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
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%files
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. /home/neuro/nipype_tutorial

‎generate.sh

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Original file line numberDiff line numberDiff line change
@@ -11,7 +11,6 @@ generate_docker() {
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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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--user=root \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run 'rm -rf /opt/conda/pkgs/*' \
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--env LD_LIBRARY_PATH='/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
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--user=neuro \
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--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
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--workdir /home/neuro/nipype_tutorial \
@@ -49,7 +49,6 @@ generate_singularity() {
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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
@@ -72,6 +71,7 @@ generate_singularity() {
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--user=root \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run 'rm -rf /opt/conda/pkgs/*' \
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--env LD_LIBRARY_PATH='/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
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--user=neuro \
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--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
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--workdir /home/neuro/nipype_tutorial

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