diff --git a/Dockerfile b/Dockerfile index 9110fff..a029189 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 @@ -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 @@ -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 \ @@ -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 \"$paths\"" # User-defined BASH instruction RUN bash -c "curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz" @@ -196,13 +171,6 @@ RUN echo '{ \ \n ] \ \n ], \ \n [ \ - \n "spm", \ - \n { \ - \n "version": "12", \ - \n "matlab_version": "R2017a" \ - \n } \ - \n ], \ - \n [ \ \n "user", \ \n "neuro" \ \n ], \ @@ -211,7 +179,7 @@ RUN echo '{ \ \n { \ \n "miniconda_version": "4.3.31", \ \n "conda_install": "python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat", \ - \n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full]==0.9.1 nipy duecredit", \ + \n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full] nipy duecredit", \ \n "env_name": "neuro", \ \n "activate": true \ \n } \ @@ -242,7 +210,7 @@ RUN echo '{ \ \n ], \ \n [ \ \n "run_bash", \ - \n "source activate neuro && cd\t/data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$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", \ @@ -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 diff --git a/create_dockerfile.sh b/create_dockerfile.sh index 6cb58e8..4d9a237 100755 --- a/create_dockerfile.sh +++ b/create_dockerfile.sh @@ -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" \ @@ -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 \