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Datalad oldver #14

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2550ef5
testing new datalad
djarecka Mar 19, 2018
d20d59c
testing datalad
djarecka Mar 19, 2018
fad654f
testing datalad
djarecka Mar 19, 2018
e17317d
testing datalad
djarecka Mar 19, 2018
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44 changes: 6 additions & 38 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
# pull request on our GitHub repository:
# https://github.com/kaczmarj/neurodocker
#
# Timestamp: 2018-03-07 15:33:37
# Timestamp: 2018-03-19 18:16:33

FROM neurodebian:stretch-non-free

Expand Down Expand Up @@ -54,31 +54,6 @@ RUN apt-get update -qq \
# Add command(s) to entrypoint
RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT

#----------------------
# Install MCR and SPM12
#----------------------
# Install MATLAB Compiler Runtime
RUN apt-get update -qq && apt-get install -yq --no-install-recommends libxext6 libxt6 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -sSL --retry 5 -o /tmp/mcr.zip https://www.mathworks.com/supportfiles/downloads/R2017a/deployment_files/R2017a/installers/glnxa64/MCR_R2017a_glnxa64_installer.zip \
&& unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
&& /tmp/mcrtmp/install -destinationFolder /opt/mcr -mode silent -agreeToLicense yes \
&& rm -rf /tmp/*

# Install standalone SPM
RUN echo "Downloading standalone SPM ..." \
&& curl -sSL --retry 5 -o spm.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2017a.zip \
&& unzip -q spm.zip -d /opt \
&& chmod -R 777 /opt/spm* \
&& rm -rf spm.zip \
&& /opt/spm12/run_spm12.sh /opt/mcr/v92/ quit \
&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12/run_spm12.sh /opt/mcr/v92/ script\"' $ND_ENTRYPOINT
ENV MATLABCMD=/opt/mcr/v92/toolbox/matlab \
FORCE_SPMMCR=1 \
LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:$LD_LIBRARY_PATH

# Create new user: neuro
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro
Expand Down Expand Up @@ -117,7 +92,7 @@ RUN conda create -y -q --name neuro python=3.6 \
&& pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master \
https://github.com/INCF/pybids/tarball/master \
nilearn \
datalad[full]==0.9.1 \
datalad[full] \
nipy \
duecredit" \
&& sync \
Expand All @@ -140,7 +115,7 @@ RUN mkdir /output && chmod 777 /output && chmod a+s /output
USER neuro

# User-defined BASH instruction
RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\" || datalad --report-status=failure get -r \"$paths\""
RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\""

# User-defined BASH instruction
RUN bash -c "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"
Expand Down Expand Up @@ -196,13 +171,6 @@ RUN echo '{ \
\n ] \
\n ], \
\n [ \
\n "spm", \
\n { \
\n "version": "12", \
\n "matlab_version": "R2017a" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
Expand All @@ -211,7 +179,7 @@ RUN echo '{ \
\n { \
\n "miniconda_version": "4.3.31", \
\n "conda_install": "python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat", \
\n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full]==0.9.1 nipy duecredit", \
\n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full] nipy duecredit", \
\n "env_name": "neuro", \
\n "activate": true \
\n } \
Expand Down Expand Up @@ -242,7 +210,7 @@ RUN echo '{ \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate neuro && cd\t/data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\" || datalad --report-status=failure get -r \"$paths\"" \
\n "source activate neuro && cd\t/data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\"" \
\n ], \
\n [ \
\n "run_bash", \
Expand Down Expand Up @@ -278,6 +246,6 @@ RUN echo '{ \
\n ] \
\n ] \
\n ], \
\n "generation_timestamp": "2018-03-07 15:33:37", \
\n "generation_timestamp": "2018-03-19 18:16:33", \
\n "neurodocker_version": "0.3.2" \
\n}' > /neurodocker/neurodocker_specs.json
8 changes: 3 additions & 5 deletions create_dockerfile.sh
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,12 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
git-annex-standalone vim emacs-nox nano less ncdu \
tig git-annex-remote-rclone \
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
--spm version=12 matlab_version=R2017a \
--user=neuro \
--miniconda miniconda_version="4.3.31" \
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat" \
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat" \
pip_install="https://github.com/nipy/nipype/tarball/master
https://github.com/INCF/pybids/tarball/master
nilearn datalad[full]==0.9.1 nipy duecredit" \
nilearn datalad[full] nipy duecredit" \
env_name="neuro" \
activate=True \
--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
Expand All @@ -21,7 +19,7 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
--run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
--user=neuro \
--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths="///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01" && datalad --report-status=failure get -r -J4 "$paths" || datalad --report-status=failure get -r "$paths"' \
--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths="sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01" && datalad --report-status=failure get -r -J4 "$paths"' \
--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' \
--copy . "/home/neuro/nipype_tutorial" \
--user=root \
Expand Down