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FIX: don't overwrite LD_LIBRARY_PATH
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‎Dockerfile

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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: 2018-10-09 20:48:57 UTC
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# Timestamp: 2018-10-10 04:25:17 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
@@ -63,7 +63,7 @@ RUN apt-get update -qq \
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RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
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ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
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ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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ENV FORCE_SPMMCR="1" \
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
@@ -212,7 +212,7 @@ RUN echo '{ \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
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\n } \
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\n ], \
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\n [ \

‎Singularity

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# Generated by Neurodocker version 0.4.2-dev
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# Timestamp: 2018-10-09 20:48:58 UTC
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# Timestamp: 2018-10-10 04:25:18 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
@@ -204,7 +204,7 @@ echo '{
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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"
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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\n }
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\n ],
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\n [
@@ -319,7 +319,7 @@ echo '{
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export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$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"

‎generate.sh

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@@ -11,7 +11,7 @@ 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" \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
@@ -49,7 +49,7 @@ generate_singularity() {
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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
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--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$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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