Merge pull request #129 from miykael/update_ld_library_path_spec

FIX: don't overwrite LD_LIBRARY_PATH

Author: miykael

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.2-dev
-# Timestamp: 2018-10-09 20:48:57 UTC
+# Timestamp: 2018-10-10 04:25:17 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -63,7 +63,7 @@ RUN apt-get update -qq \
 
 RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 
-ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
+ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 
 ENV FORCE_SPMMCR="1" \
     LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
@@ -212,7 +212,7 @@ RUN echo '{ \
     \n    [ \
     \n      "env", \
     \n      { \
-    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
     \n      } \
     \n    ], \
     \n    [ \

Singularity

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.2-dev
-# Timestamp: 2018-10-09 20:48:58 UTC
+# Timestamp: 2018-10-10 04:25:18 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -204,7 +204,7 @@ echo '{
 \n    [
 \n      "env",
 \n      {
-\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib"
+\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 \n      }
 \n    ],
 \n    [
@@ -319,7 +319,7 @@ echo '{
 export LANG="en_US.UTF-8"
 export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
-export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
+export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 export FORCE_SPMMCR="1"
 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"
 export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"

generate.sh

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