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FIX move sed to root block
1 parent ea7b469 commit 148cc05

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-16
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3 files changed

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‎Dockerfile

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Generated by Neurodocker version 0.4.1-22-g7c44e01
2-
# Timestamp: 2018-10-09 20:32:51 UTC
2+
# Timestamp: 2018-10-09 22:00:07 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
55
# 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
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COPY [".", "/home/neuro/nipype_tutorial"]
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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' {} +
158-
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USER root
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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' {} +
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RUN chown -R neuro /home/neuro/nipype_tutorial
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RUN rm -rf /opt/conda/pkgs/*
@@ -285,15 +285,15 @@ RUN echo '{ \
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\n ] \
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\n ], \
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\n [ \
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\n "run", \
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\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'"'"' {} +" \
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\n ], \
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\n [ \
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\n "user", \
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\n "root" \
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\n ], \
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\n [ \
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\n "run", \
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\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'"'"' {} +" \
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\n ], \
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\n [ \
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\n "run", \
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\n "chown -R neuro /home/neuro/nipype_tutorial" \
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\n ], \
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\n [ \

‎Singularity

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.1-22-g7c44e01
2-
# Timestamp: 2018-10-09 20:32:53 UTC
2+
# Timestamp: 2018-10-09 22:00:09 UTC
33
#
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# Thank you for using Neurodocker. If you discover any issues
55
# 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
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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
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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' {} +
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su - root
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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' {} +
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chown -R neuro /home/neuro/nipype_tutorial
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rm -rf /opt/conda/pkgs/*
@@ -279,15 +279,15 @@ echo '{
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\n ]
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\n ],
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\n [
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\n "run",
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\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'"'"' {} +"
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\n ],
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\n [
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\n "user",
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\n "root"
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\n ],
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\n [
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\n "run",
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\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'"'"' {} +"
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\n ],
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\n [
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\n "run",
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\n "chown -R neuro /home/neuro/nipype_tutorial"
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\n ],
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\n [

‎generate.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,8 @@ generate_docker() {
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--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*' \
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--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' \
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--copy . "/home/neuro/nipype_tutorial" \
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--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'\'' {} +' \
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--user=root \
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--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'\'' {} +' \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run 'rm -rf /opt/conda/pkgs/*' \
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--user=neuro \
@@ -68,8 +68,8 @@ generate_singularity() {
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--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*' \
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--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' \
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--copy . "/home/neuro/nipype_tutorial" \
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--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'\'' {} +' \
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--user=root \
72+
--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'\'' {} +' \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run 'rm -rf /opt/conda/pkgs/*' \
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--user=neuro \

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