ENH: add miniconda's neuro env library path

Author: miykael

Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-11 22:11:11 UTC
+# Generated by Neurodocker version 0.4.2-dev
+# Timestamp: 2018-10-15 12:01:29 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -142,6 +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:/usr/lib/fsl/5.0"
+
 RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'
 
 USER root
@@ -250,6 +252,12 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
+    \n      "env", \
+    \n      { \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0" \
+    \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: 2018-10-11 22:11:12 UTC
+# Generated by Neurodocker version 0.4.2-dev
+# Timestamp: 2018-10-15 12:01:30 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -244,6 +244,12 @@ echo '{
 \n      }
 \n    ],
 \n    [
+\n      "env",
+\n      {
+\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0"
+\n      }
+\n    ],
+\n    [
 \n      "run_bash",
 \n      "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main"
 \n    ],
@@ -318,6 +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="/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0"
 
 %files
 . /home/neuro/nipype_tutorial

generate.sh

@@ -21,6 +21,7 @@ generate_docker() {
                           nilearn datalad[full] nipy duecredit nbval" \
              create_env="neuro" \
              activate=True \
+           --env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:$LD_LIBRARY_PATH" \
            --run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
            --user=root \
            --run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
@@ -58,6 +59,7 @@ generate_singularity() {
                           nilearn datalad[full] nipy duecredit nbval" \
              create_env="neuro" \
              activate=True \
+           --env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:$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' \