FIX: specify LD_LIBRARY_PATH for miniconda after creation of miniconda

Author: miykael

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-10 18:42:03 UTC
+# Timestamp: 2018-10-10 18:57:39 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -97,8 +97,6 @@ RUN apt-get update -qq \
     && /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
     && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
 
-ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
-
 RUN useradd --no-user-group --create-home --shell /bin/bash neuro
 USER neuro
 
@@ -144,6 +142,8 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     && sync \
     && sed -i '$isource activate neuro' $ND_ENTRYPOINT
 
+ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
+
 RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'
 
 USER root
@@ -216,12 +216,6 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
-    \n      "env", \
-    \n      { \
-    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
-    \n      } \
-    \n    ], \
-    \n    [ \
     \n      "user", \
     \n      "neuro" \
     \n    ], \
@@ -258,6 +252,12 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
+    \n      "env", \
+    \n      { \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
+    \n      } \
+    \n    ], \
+    \n    [ \
     \n      "run_bash", \
     \n      "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
     \n    ], \

Singularity

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

generate.sh

@@ -12,7 +12,6 @@ generate_docker() {
                      tig git-annex-remote-rclone octave netbase \
            --add-to-entrypoint "source /etc/fsl/fsl.sh" \
            --spm12 version=r7219 \
-           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --user=neuro \
            --miniconda miniconda_version="4.3.31" \
              conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -22,6 +21,7 @@ generate_docker() {
                           nilearn datalad[full] nipy duecredit nbval" \
              create_env="neuro" \
              activate=True \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
            --user=root \
            --run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
@@ -50,7 +50,6 @@ generate_singularity() {
                      tig git-annex-remote-rclone octave netbase \
            --add-to-entrypoint "source /etc/fsl/fsl.sh" \
            --spm12 version=r7219 \
-           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --user=neuro \
            --miniconda miniconda_version="4.3.31" \
              conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -60,6 +59,7 @@ generate_singularity() {
                           nilearn datalad[full] nipy duecredit nbval" \
              create_env="neuro" \
              activate=True \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
            --user=root \
            --run 'mkdir /data && chmod 777 /data && chmod a+s /data' \