FIX move sed to root block

Author: Shotgunosine

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-09 20:32:51 UTC
+# Timestamp: 2018-10-09 22:00:07 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -154,10 +154,10 @@ RUN curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5807050
 
 COPY [".", "/home/neuro/nipype_tutorial"]
 
-RUN find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
-
 USER root
 
+RUN find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
+
 RUN chown -R neuro /home/neuro/nipype_tutorial
 
 RUN rm -rf /opt/conda/pkgs/*
@@ -285,15 +285,15 @@ RUN echo '{ \
     \n      ] \
     \n    ], \
     \n    [ \
-    \n      "run", \
-    \n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +" \
-    \n    ], \
-    \n    [ \
     \n      "user", \
     \n      "root" \
     \n    ], \
     \n    [ \
     \n      "run", \
+    \n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
     \n      "chown -R neuro /home/neuro/nipype_tutorial" \
     \n    ], \
     \n    [ \

Singularity

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.1-22-g7c44e01
-# Timestamp: 2018-10-09 20:32:53 UTC
+# Timestamp: 2018-10-09 22:00:09 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -143,10 +143,10 @@ bash -c 'source activate neuro && cd /data && datalad install -r ///workshops/ni
 
 curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete
 
-find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
-
 su - root
 
+find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e 's/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g' -e 's/"name": "python3"/"name": "conda-env-neuro-py"/g' {} +
+
 chown -R neuro /home/neuro/nipype_tutorial
 
 rm -rf /opt/conda/pkgs/*
@@ -279,15 +279,15 @@ echo '{
 \n      ]
 \n    ],
 \n    [
-\n      "run",
-\n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +"
-\n    ],
-\n    [
 \n      "user",
 \n      "root"
 \n    ],
 \n    [
 \n      "run",
+\n      "find /home/neuro/nipype_tutorial -maxdepth 2 -name \"*.ipynb\" -exec sed -i -e '"'"'s/\"display_name\": \"Python \\[default\\]\"/\"display_name\": \"Python \\[conda env:neuro\\]\"/g'"'"' -e '"'"'s/\"name\": \"python3\"/\"name\": \"conda-env-neuro-py\"/g'"'"' {} +"
+\n    ],
+\n    [
+\n      "run",
 \n      "chown -R neuro /home/neuro/nipype_tutorial"
 \n    ],
 \n    [

generate.sh

@@ -30,8 +30,8 @@ generate_docker() {
            --run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad update -r && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*' \
            --run 'curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete' \
            --copy . "/home/neuro/nipype_tutorial" \
-           --run 'find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e '\''s/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g'\'' -e '\''s/"name": "python3"/"name": "conda-env-neuro-py"/g'\'' {} +' \
            --user=root \
+           --run 'find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e '\''s/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g'\'' -e '\''s/"name": "python3"/"name": "conda-env-neuro-py"/g'\'' {} +' \
            --run 'chown -R neuro /home/neuro/nipype_tutorial' \
            --run 'rm -rf /opt/conda/pkgs/*' \
            --user=neuro \
@@ -68,8 +68,8 @@ generate_singularity() {
            --run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && datalad update -r && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/*fingerfootlips*' \
            --run 'curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && find /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c -type f -not -name ?mm_T1.nii.gz -not -name ?mm_brainmask.nii.gz -not -name ?mm_tpm*.nii.gz -delete' \
            --copy . "/home/neuro/nipype_tutorial" \
-           --run 'find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e '\''s/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g'\'' -e '\''s/"name": "python3"/"name": "conda-env-neuro-py"/g'\'' {} +' \
            --user=root \
+           --run 'find /home/neuro/nipype_tutorial -maxdepth 2 -name "*.ipynb" -exec sed -i -e '\''s/"display_name": "Python \[default\]"/"display_name": "Python \[conda env:neuro\]"/g'\'' -e '\''s/"name": "python3"/"name": "conda-env-neuro-py"/g'\'' {} +' \
            --run 'chown -R neuro /home/neuro/nipype_tutorial' \
            --run 'rm -rf /opt/conda/pkgs/*' \
            --user=neuro \