FIX: move old LD_LIBRARY specs at the end of container creation

Author: miykael

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-10 17:39:05 UTC
+# Timestamp: 2018-10-10 18:29:21 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -166,7 +166,7 @@ RUN chown -R neuro /home/neuro/nipype_tutorial
 
 RUN rm -rf /opt/conda/pkgs/*
 
-ENV LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 
 USER neuro
 
@@ -305,7 +305,7 @@ RUN echo '{ \
     \n    [ \
     \n      "env", \
     \n      { \
-    \n        "LD_LIBRARY_PATH": "/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
     \n      } \
     \n    ], \
     \n    [ \

Singularity

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-10 17:39:06 UTC
+# Timestamp: 2018-10-10 18:29:22 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -297,7 +297,7 @@ echo '{
 \n    [
 \n      "env",
 \n      {
-\n        "LD_LIBRARY_PATH": "/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 \n      }
 \n    ],
 \n    [
@@ -324,7 +324,7 @@ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmc
 export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
 export CONDA_DIR="/opt/miniconda-latest"
 export PATH="/opt/miniconda-latest/bin:$PATH"
-export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 
 %files
 . /home/neuro/nipype_tutorial

generate.sh

@@ -33,7 +33,7 @@ generate_docker() {
            --user=root \
            --run 'chown -R neuro /home/neuro/nipype_tutorial' \
            --run 'rm -rf /opt/conda/pkgs/*' \
-           --env LD_LIBRARY_PATH='/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --user=neuro \
            --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
            --workdir /home/neuro/nipype_tutorial \
@@ -71,7 +71,7 @@ generate_singularity() {
            --user=root \
            --run 'chown -R neuro /home/neuro/nipype_tutorial' \
            --run 'rm -rf /opt/conda/pkgs/*' \
-           --env LD_LIBRARY_PATH='/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --user=neuro \
            --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
            --workdir /home/neuro/nipype_tutorial