ENH: adds singularity file and script

Author: miykael

Singularity

@@ -0,0 +1,318 @@
+# Generated by Neurodocker version 0.4.1-dev
+# Timestamp: 2018-09-27 11:07:19 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/kaczmarj/neurodocker
+
+Bootstrap: docker
+From: neurodebian:stretch-non-free
+
+%post
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    apt-utils \
+    bzip2 \
+    ca-certificates \
+    curl \
+    locales \
+    unzip
+apt-get clean
+rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
+dpkg-reconfigure --frontend=noninteractive locales
+update-locale LANG="en_US.UTF-8"
+chmod 777 /opt && chmod a+s /opt
+mkdir -p /neurodocker
+if [ ! -f "$ND_ENTRYPOINT" ]; then
+  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
+  echo 'set -e' >> "$ND_ENTRYPOINT"
+  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
+fi
+chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    convert3d \
+    ants \
+    fsl \
+    gcc \
+    g++ \
+    graphviz \
+    tree \
+    git-annex-standalone \
+    vim \
+    emacs-nox \
+    nano \
+    less \
+    ncdu \
+    tig \
+    git-annex-remote-rclone \
+    octave \
+    netbase
+apt-get clean
+rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
+
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    bc \
+    libxext6 \
+    libxpm-dev \
+    libxt6
+apt-get clean
+rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+echo "Downloading MATLAB Compiler Runtime ..."
+curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018a/deployment_files/R2018a/installers/glnxa64/MCR_R2018a_glnxa64_installer.zip
+unzip -q /tmp/mcr.zip -d /tmp/mcrtmp
+/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018a -mode silent -agreeToLicense yes
+rm -rf /tmp/*
+echo "Downloading standalone SPM ..."
+curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018a.zip
+unzip -q /tmp/spm12.zip -d /tmp
+mkdir -p /opt/spm12-dev
+mv /tmp/spm12/* /opt/spm12-dev/
+chmod -R 777 /opt/spm12-dev
+rm -rf /tmp/*
+/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 quit
+sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94 script\"' $ND_ENTRYPOINT
+
+useradd --no-user-group --create-home --shell /bin/bash neuro
+su - neuro
+
+export PATH="/opt/miniconda-latest/bin:$PATH"
+echo "Downloading Miniconda installer ..."
+conda_installer="/tmp/miniconda.sh"
+curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash "$conda_installer" -b -p /opt/miniconda-latest
+rm -f "$conda_installer"
+conda update -yq -nbase conda
+conda config --system --prepend channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+sync && conda clean -tipsy && sync
+conda create -y -q --name neuro
+conda install -y -q --name neuro \
+    python=3.6 \
+    pytest \
+    jupyter \
+    jupyterlab \
+    jupyter_contrib_nbextensions \
+    traits \
+    pandas \
+    matplotlib \
+    scikit-learn \
+    scikit-image \
+    seaborn \
+    nbformat \
+    nb_conda
+sync && conda clean -tipsy && sync
+bash -c "source activate neuro
+  pip install  --no-cache-dir \
+      https://github.com/nipy/nipype/tarball/master \
+      https://github.com/INCF/pybids/tarball/master \
+      nilearn \
+      datalad[full] \
+      nipy \
+      duecredit \
+      nbval"
+rm -rf ~/.cache/pip/*
+sync
+sed -i '$isource activate neuro' $ND_ENTRYPOINT
+
+
+bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'
+
+su - root
+
+mkdir /data && chmod 777 /data && chmod a+s /data
+
+mkdir /output && chmod 777 /output && chmod a+s /output
+
+su - neuro
+
+printf "[user]\n\tname = miykael\n\temail = [email protected]\n" > ~/.gitconfig
+
+bash -c '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*'
+
+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
+
+su - root
+
+chown -R neuro /home/neuro/nipype_tutorial
+
+rm -rf /opt/conda/pkgs/*
+
+su - neuro
+
+mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+cd /home/neuro/nipype_tutorial
+
+echo '{
+\n  "pkg_manager": "apt",
+\n  "instructions": [
+\n    [
+\n      "base",
+\n      "neurodebian:stretch-non-free"
+\n    ],
+\n    [
+\n      "_header",
+\n      {
+\n        "version": "generic",
+\n        "method": "custom"
+\n      }
+\n    ],
+\n    [
+\n      "install",
+\n      [
+\n        "convert3d",
+\n        "ants",
+\n        "fsl",
+\n        "gcc",
+\n        "g++",
+\n        "graphviz",
+\n        "tree",
+\n        "git-annex-standalone",
+\n        "vim",
+\n        "emacs-nox",
+\n        "nano",
+\n        "less",
+\n        "ncdu",
+\n        "tig",
+\n        "git-annex-remote-rclone",
+\n        "octave",
+\n        "netbase"
+\n      ]
+\n    ],
+\n    [
+\n      "add_to_entrypoint",
+\n      "source /etc/fsl/fsl.sh"
+\n    ],
+\n    [
+\n      "spm12",
+\n      {
+\n        "version": "dev"
+\n      }
+\n    ],
+\n    [
+\n      "user",
+\n      "neuro"
+\n    ],
+\n    [
+\n      "miniconda",
+\n      {
+\n        "miniconda_version": "4.3.31",
+\n        "conda_install": [
+\n          "python=3.6",
+\n          "pytest",
+\n          "jupyter",
+\n          "jupyterlab",
+\n          "jupyter_contrib_nbextensions",
+\n          "traits",
+\n          "pandas",
+\n          "matplotlib",
+\n          "scikit-learn",
+\n          "scikit-image",
+\n          "seaborn",
+\n          "nbformat",
+\n          "nb_conda"
+\n        ],
+\n        "pip_install": [
+\n          "https://github.com/nipy/nipype/tarball/master",
+\n          "https://github.com/INCF/pybids/tarball/master",
+\n          "nilearn",
+\n          "datalad[full]",
+\n          "nipy",
+\n          "duecredit",
+\n          "nbval"
+\n        ],
+\n        "create_env": "neuro",
+\n        "activate": true
+\n      }
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main"
+\n    ],
+\n    [
+\n      "user",
+\n      "root"
+\n    ],
+\n    [
+\n      "run",
+\n      "mkdir /data && chmod 777 /data && chmod a+s /data"
+\n    ],
+\n    [
+\n      "run",
+\n      "mkdir /output && chmod 777 /output && chmod a+s /output"
+\n    ],
+\n    [
+\n      "user",
+\n      "neuro"
+\n    ],
+\n    [
+\n      "run",
+\n      "printf \"[user]\\\n\\tname = miykael\\\n\\temail = [email protected]\\\n\" > ~/.gitconfig"
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "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*"
+\n    ],
+\n    [
+\n      "run",
+\n      "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"
+\n    ],
+\n    [
+\n      "copy",
+\n      [
+\n        ".",
+\n        "/home/neuro/nipype_tutorial"
+\n      ]
+\n    ],
+\n    [
+\n      "user",
+\n      "root"
+\n    ],
+\n    [
+\n      "run",
+\n      "chown -R neuro /home/neuro/nipype_tutorial"
+\n    ],
+\n    [
+\n      "run",
+\n      "rm -rf /opt/conda/pkgs/*"
+\n    ],
+\n    [
+\n      "user",
+\n      "neuro"
+\n    ],
+\n    [
+\n      "run",
+\n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py"
+\n    ],
+\n    [
+\n      "workdir",
+\n      "/home/neuro/nipype_tutorial"
+\n    ]
+\n  ]
+\n}' > /neurodocker/neurodocker_specs.json
+
+%environment
+export LANG="en_US.UTF-8"
+export LC_ALL="en_US.UTF-8"
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+export FORCE_SPMMCR="1"
+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018a/v94/runtime/glnxa64:/opt/matlabmcr-2018a/v94/bin/glnxa64:/opt/matlabmcr-2018a/v94/sys/os/glnxa64:/opt/matlabmcr-2018a/v94/extern/bin/glnxa64"
+export MATLABCMD="/opt/matlabmcr-2018a/v94/toolbox/matlab"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
+
+%files
+. /home/neuro/nipype_tutorial
+
+%runscript
+/neurodocker/startup.sh "$@"