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Merge pull request #193 from PeerHerholz/add-singularity
Add singularity
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‎colors_script/calc_colormap.py

100755100644
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‎colors_script/convert_to_mipav_lut.py

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‎install/Singularity

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# Generated by Neurodocker version 0.4.2-3-gf7055a1
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# Timestamp: 2019-11-04 21:05:10 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/kaczmarj/neurodocker
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Bootstrap: docker
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From: neurodebian:stretch
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%post
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
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dpkg-reconfigure --frontend=noninteractive locales
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update-locale LANG="en_US.UTF-8"
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chmod 777 /opt && chmod a+s /opt
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mkdir -p /neurodocker
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if [ ! -f "$ND_ENTRYPOINT" ]; then
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
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echo 'set -e' >> "$ND_ENTRYPOINT"
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echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
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fi
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chmod -R 777 /neurodocker && chmod a+s /neurodocker
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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graphviz \
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tree \
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git-annex-standalone \
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vim \
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emacs-nox \
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nano \
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less \
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ncdu \
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tig \
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sed \
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build-essential \
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libsm-dev \
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libx11-dev \
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libxt-dev \
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libxext-dev \
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libglu1-mesa
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
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export PATH="/opt/miniconda-latest/bin:$PATH"
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echo "Downloading Miniconda installer ..."
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conda_installer="/tmp/miniconda.sh"
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curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash "$conda_installer" -b -p /opt/miniconda-latest
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rm -f "$conda_installer"
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conda update -yq -nbase conda
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conda config --system --prepend channels conda-forge
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conda config --system --set auto_update_conda false
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conda config --system --set show_channel_urls true
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sync && conda clean -tipsy && sync
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conda create -y -q --name mb
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conda install -y -q --name mb \
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'python=3.6' \
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'pip' \
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'jupyter' \
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'cmake' \
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'mesalib' \
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'vtk=8.2.0=py36ha8e561a_201' \
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'pandas' \
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'matplotlib' \
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'colormath' \
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'nipype>=1.1.4' \
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'nilearn' \
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'tbb-devel' \
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'nose' \
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'etelemetry'
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sync && conda clean -tipsy && sync
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bash -c "source activate mb
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pip install --no-cache-dir \
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'datalad[full]' \
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'duecredit'"
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rm -rf ~/.cache/pip/*
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sync
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sed -i '$isource activate mb' $ND_ENTRYPOINT
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cd /opt
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mkdir -p /opt/data && cd /opt/data && \
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curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
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unzip templates.zip && \
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rm -f /opt/data/templates.zip && \
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curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \
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mkdir OASIS-TRT-20_brains && \
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cd OASIS-TRT-20_brains && \
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unzip ../OASIS-TRT-20_brains.zip && \
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cd .. && \
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rm OASIS-TRT-20_brains.zip && \
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curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \
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mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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unzip ../cmalabels.zip && \
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cd .. && \
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rm cmalabels.zip && \
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curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
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rm -rf __MACOSX
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bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
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conda activate mb && \
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git clone https://github.com/nipy/mindboggle.git && \
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cd /opt/mindboggle && \
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python setup.py install && \
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mkdir /opt/vtk_cpp_tools && \
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cd /opt/vtk_cpp_tools && \
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cmake /opt/mindboggle/vtk_cpp_tools && \
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make'
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bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
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conda activate mb && \
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conda install -y flask && \
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git clone https://github.com/akeshavan/roygbiv && \
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cd /opt/roygbiv && \
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git checkout fbbf31c29952d0ea22ed05d98e0a5a7e7d0827f9 && \
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python setup.py install && \
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cd /opt && \
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rm -rf /opt/roygbiv'
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mkdir -p /.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > /.jupyter/jupyter_notebook_config.py
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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cmake \
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g++ \
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gcc \
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git \
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make \
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zlib1g-dev
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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mkdir -p /tmp/ants/build
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git clone https://github.com/ANTsX/ANTs.git /tmp/ants/source
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cd /tmp/ants/source
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git fetch --tags
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git checkout b43df4bfc8
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cd /tmp/ants/build
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cmake -DBUILD_SHARED_LIBS=ON /tmp/ants/source
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make -j 4
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mkdir -p /opt/ants-b43df4bfc8
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mv bin lib /opt/ants-b43df4bfc8/
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mv /tmp/ants/source/Scripts/* /opt/ants-b43df4bfc8/bin
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rm -rf /tmp/ants
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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bc \
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libgomp1 \
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libxmu6 \
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libxt6 \
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perl \
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tcsh
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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echo "Downloading FreeSurfer ..."
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mkdir -p /opt/freesurfer-6.0.0-min
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curl -fsSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz \
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| tar -xz -C /opt/freesurfer-6.0.0-min --strip-components 1
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sed -i '$isource "/opt/freesurfer-6.0.0-min/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
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curl -sSL https://osf.io/download/n3ud2/?revision=1 -o /opt/freesurfer-6.0.0-min/license.txt
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echo '{
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\n "pkg_manager": "apt",
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\n "instructions": [
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\n [
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\n "base",
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\n "neurodebian:stretch"
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\n ],
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\n [
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\n "_header",
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\n {
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\n "version": "generic",
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\n "method": "custom"
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\n }
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\n ],
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\n [
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\n "install",
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\n [
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\n "graphviz",
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\n "tree",
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\n "git-annex-standalone",
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\n "vim",
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\n "emacs-nox",
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\n "nano",
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\n "less",
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\n "ncdu",
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\n "tig",
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\n "sed",
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\n "build-essential",
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\n "libsm-dev",
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\n "libx11-dev",
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\n "libxt-dev",
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\n "libxext-dev",
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\n "libglu1-mesa"
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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 "ln -s /usr/lib/x86_64-linux-gnu /usr/lib64"
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\n ],
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\n [
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\n "miniconda",
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\n {
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\n "conda_install": [
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\n "python=3.6",
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\n "pip",
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\n "jupyter",
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\n "cmake",
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\n "mesalib",
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\n "vtk=8.2.0=py36ha8e561a_201",
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\n "pandas",
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\n "matplotlib",
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\n "colormath",
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\n "nipype>=1.1.4",
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\n "nilearn",
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\n "tbb-devel",
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\n "nose",
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\n "etelemetry"
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\n ],
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\n "pip_install": [
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\n "datalad[full]",
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\n "duecredit"
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\n ],
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\n "create_env": "mb",
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\n "activate": true
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\n }
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\n ],
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\n [
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\n "workdir",
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\n "/opt"
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\n ],
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\n [
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\n "run",
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\n "mkdir -p /opt/data && cd /opt/data && \\\\n curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n unzip templates.zip && \\\\n rm -f /opt/data/templates.zip && \\\\n curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \\\\n mkdir OASIS-TRT-20_brains && \\\\n cd OASIS-TRT-20_brains && \\\\n unzip ../OASIS-TRT-20_brains.zip && \\\\n cd .. && \\\\n rm OASIS-TRT-20_brains.zip && \\\\n curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \\\\n mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n unzip ../cmalabels.zip && \\\\n cd .. && \\\\n rm cmalabels.zip && \\\\n curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n rm -rf __MACOSX"
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\n ],
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\n [
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\n "run_bash",
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\n "source /opt/miniconda-latest/etc/profile.d/conda.sh && \\\\n conda activate mb && \\\\n git clone https://github.com/nipy/mindboggle.git && \\\\n cd /opt/mindboggle && \\\\n python setup.py install && \\\\n mkdir /opt/vtk_cpp_tools && \\\\n cd /opt/vtk_cpp_tools && \\\\n cmake /opt/mindboggle/vtk_cpp_tools && \\\\n make"
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\n ],
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\n [
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\n "env",
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\n {
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\n "vtk_cpp_tools": "/opt/vtk_cpp_tools"
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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 "source /opt/miniconda-latest/etc/profile.d/conda.sh && \\\\n conda activate mb && \\\\n conda install -y flask && \\\\n git clone https://github.com/akeshavan/roygbiv && \\\\n cd /opt/roygbiv && \\\\n git checkout fbbf31c29952d0ea22ed05d98e0a5a7e7d0827f9 && \\\\n python setup.py install && \\\\n cd /opt && \\\\n rm -rf /opt/roygbiv"
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\n ],
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\n [
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\n "run",
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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 "ants",
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\n {
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\n "version": "b43df4bfc8",
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\n "method": "source",
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\n "cmake_opts": "-DBUILD_SHARED_LIBS=ON",
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\n "make_opts": "-j 4"
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\n }
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\n ],
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\n [
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\n "freesurfer",
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\n {
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\n "version": "6.0.0-min"
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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 "curl -sSL https://osf.io/download/n3ud2/?revision=1 -o /opt/freesurfer-6.0.0-min/license.txt"
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\n ]
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\n ]
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\n}' > /neurodocker/neurodocker_specs.json
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%environment
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export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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export vtk_cpp_tools="/opt/vtk_cpp_tools"
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export ANTSPATH="/opt/ants-b43df4bfc8/bin"
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export PATH="/opt/ants-b43df4bfc8/bin:$PATH"
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export LD_LIBRARY_PATH="/opt/ants-b43df4bfc8/lib:$LD_LIBRARY_PATH"
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export FREESURFER_HOME="/opt/freesurfer-6.0.0-min"
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export PATH="/opt/freesurfer-6.0.0-min/bin:$PATH"
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%runscript
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/neurodocker/startup.sh "$@"

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