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FIX: specify LD_LIBRARY_PATH for miniconda after creation of miniconda
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-19
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‎Dockerfile

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 0.4.1-22-g7c44e01
2-
# Timestamp: 2018-10-10 18:42:03 UTC
2+
# Timestamp: 2018-10-10 18:57:39 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
@@ -97,8 +97,6 @@ RUN apt-get update -qq \
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&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
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&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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RUN useradd --no-user-group --create-home --shell /bin/bash neuro
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USER neuro
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@@ -144,6 +142,8 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
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&& sync \
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&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
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145+
ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'
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USER root
@@ -216,12 +216,6 @@ RUN echo '{ \
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\n } \
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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:$LD_LIBRARY_PATH" \
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\n } \
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\n ], \
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\n [ \
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\n "user", \
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\n "neuro" \
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\n ], \
@@ -258,6 +252,12 @@ RUN echo '{ \
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\n } \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
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\n } \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
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\n ], \

‎Singularity

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Generated by Neurodocker version 0.4.1-22-g7c44e01
2-
# Timestamp: 2018-10-10 18:42:04 UTC
2+
# Timestamp: 2018-10-10 18:57:40 UTC
33
#
44
# Thank you for using Neurodocker. If you discover any issues
55
# or ways to improve this software, please submit an issue or
@@ -208,12 +208,6 @@ echo '{
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\n }
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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:$LD_LIBRARY_PATH"
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\n }
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\n ],
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\n [
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\n "user",
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\n "neuro"
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\n ],
@@ -250,6 +244,12 @@ echo '{
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\n }
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\n ],
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\n [
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\n "env",
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\n {
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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\n }
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\n ],
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\n [
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\n "run_bash",
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\n "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main"
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\n ],
@@ -322,9 +322,9 @@ export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export FORCE_SPMMCR="1"
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export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
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export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
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%files
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. /home/neuro/nipype_tutorial

‎generate.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,6 @@ generate_docker() {
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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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--spm12 version=r7219 \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -22,6 +21,7 @@ generate_docker() {
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nilearn datalad[full] nipy duecredit nbval" \
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create_env="neuro" \
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activate=True \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
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--user=root \
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--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
@@ -50,7 +50,6 @@ generate_singularity() {
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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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--spm12 version=r7219 \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -60,6 +59,7 @@ generate_singularity() {
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nilearn datalad[full] nipy duecredit nbval" \
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create_env="neuro" \
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activate=True \
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--env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
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--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
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--user=root \
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--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \

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