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Merge pull request miykael#86 from miykael/move_pages_to_docs
Make gh-pages more beautiful and move them into /docs
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‎Dockerfile

Lines changed: 21 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
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# pull request on our GitHub repository:
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# https://github.com/kaczmarj/neurodocker
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#
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# Timestamp: 2018-05-07 20:43:57
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# Timestamp: 2018-05-14 11:52:36
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FROM neurodebian:stretch-non-free
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@@ -129,16 +129,16 @@ RUN conda create -y -q --name neuro python=3.6 \
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# User-defined BASH instruction
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RUN bash -c "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main"
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# User-defined instruction
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RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
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# User-defined BASH instruction
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RUN bash -c "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\"0.0.0.0\\" > ~/.jupyter/jupyter_notebook_config.py"
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USER root
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# User-defined instruction
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RUN mkdir /data && chmod 777 /data && chmod a+s /data
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# User-defined BASH instruction
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RUN bash -c "mkdir /data && chmod 777 /data && chmod a+s /data"
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# User-defined instruction
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RUN mkdir /output && chmod 777 /output && chmod a+s /output
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# User-defined BASH instruction
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RUN bash -c "mkdir /output && chmod 777 /output && chmod a+s /output"
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USER neuro
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@@ -150,10 +150,13 @@ RUN bash -c "curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorag
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COPY [".", "/home/neuro/nipype_tutorial"]
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# User-defined BASH instruction
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RUN bash -c "printf \"[user]\n\tname = miykael\n\temail = michaelnotter@hotmail.com\n\" > ~/.gitconfig"
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USER root
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# User-defined instruction
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RUN chown -R neuro /home/neuro/nipype_tutorial
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# User-defined BASH instruction
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RUN bash -c "chown -R neuro /home/neuro/nipype_tutorial"
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# User-defined BASH instruction
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RUN bash -c "rm -rf /opt/conda/pkgs/*"
@@ -228,19 +231,19 @@ RUN echo '{ \
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\n "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
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\n ], \
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\n [ \
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\n "run", \
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\n "run_bash", \
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\n "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
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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 "run_bash", \
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\n "mkdir /data && chmod 777 /data && chmod a+s /data" \
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\n ], \
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\n [ \
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\n "run", \
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\n "run_bash", \
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\n "mkdir /output && chmod 777 /output && chmod a+s /output" \
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\n ], \
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\n [ \
@@ -263,11 +266,15 @@ RUN echo '{ \
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\n ] \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "printf \"[user]\\\n\\tname = miykael\\\n\\temail = michaelnotter@hotmail.com\\\n\" > ~/.gitconfig" \
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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 "run_bash", \
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\n "chown -R neuro /home/neuro/nipype_tutorial" \
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\n ], \
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\n [ \
@@ -289,6 +296,6 @@ RUN echo '{ \
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\n ] \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2018-05-07 20:43:57", \
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\n "generation_timestamp": "2018-05-14 11:52:36", \
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\n "neurodocker_version": "0.3.2" \
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\n}' > /neurodocker/neurodocker_specs.json

‎create_dockerfile.sh

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -16,16 +16,17 @@ docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b neurodebian:stretch-non-
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env_name="neuro" \
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activate=True \
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--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
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--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
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--run-bash 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
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--user=root \
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--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
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--run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
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--run-bash 'mkdir /data && chmod 777 /data && chmod a+s /data' \
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--run-bash 'mkdir /output && chmod 777 /output && chmod a+s /output' \
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--user=neuro \
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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-bash '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-bash 'printf "[user]\n\tname = miykael\n\temail = michaelnotter@hotmail.com\n" > ~/.gitconfig' \
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--user=root \
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--run 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run-bash 'chown -R neuro /home/neuro/nipype_tutorial' \
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--run-bash 'rm -rf /opt/conda/pkgs/*' \
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--user=neuro \
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--workdir /home/neuro/nipype_tutorial \

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