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[DATALAD RUNCMD] ./generate_container.sh
=== Do not change lines below === { "chain": [], "cmd": "./generate_container.sh", "exit": 0, "inputs": [], "outputs": [ "Singularity*", "Dockerfile" ], "pwd": "." } ^^^ Do not change lines above ^^^
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‎Dockerfile

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# Generated by Neurodocker version 0.4.1
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# Timestamp: 2019-01-05 04:54:54 UTC
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# Generated by Neurodocker version 0.4.3-2-g01cdd22
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# Timestamp: 2019-01-05 06:19:25 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
@@ -11,6 +11,13 @@ FROM neurodebian:stretch
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ARG DEBIAN_FRONTEND="noninteractive"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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neurodebian-freeze \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& nd_freeze 20190105
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ENV LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
@@ -119,6 +126,12 @@ RUN echo '{ \
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\n "neurodebian:stretch" \
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\n ], \
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\n [ \
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\n "ndfreeze", \
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\n { \
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\n "date": "20190105" \
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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 "vim", \

‎Singularity

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# Generated by Neurodocker version 0.4.1
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# Timestamp: 2019-01-05 04:54:55 UTC
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# Generated by Neurodocker version 0.4.3-2-g01cdd22
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# Timestamp: 2019-01-05 06:19:26 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
@@ -11,6 +11,13 @@ Bootstrap: docker
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From: neurodebian:stretch
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%post
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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neurodebian-freeze
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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nd_freeze 20190105
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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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\n "neurodebian:stretch"
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\n ],
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\n [
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\n "ndfreeze",
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\n {
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\n "date": "20190105"
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\n }
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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",

‎Singularity.0.5.2

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# Generated by Neurodocker version 0.4.3-2-g01cdd22
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# Timestamp: 2019-01-05 06:19:26 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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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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neurodebian-freeze
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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nd_freeze 20190105
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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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vim \
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wget \
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strace \
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time \
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ncdu \
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gnupg \
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curl \
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procps \
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datalad \
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pigz \
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git-annex-standalone \
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python-nipype \
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virtualenv \
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python-dcmstack \
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python-configparser \
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python-funcsigs \
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python-pytest \
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dcmtk \
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python-pip \
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python-wheel \
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python-setuptools \
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python-datalad
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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curl -sL https://deb.nodesource.com/setup_6.x | bash -
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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nodejs \
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npm
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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npm install -g [email protected]
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mkdir /afs /inbox
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pip install heudiconv
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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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pigz \
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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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git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix
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cd /tmp/dcm2niix
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git fetch --tags
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git checkout v1.0.20181125
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mkdir /tmp/dcm2niix/build
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cd /tmp/dcm2niix/build
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cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20181125 ..
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make
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make install
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rm -rf /tmp/dcm2niix
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echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
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useradd --no-user-group --create-home --shell /bin/bash reproin
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su - reproin
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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 "ndfreeze",
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\n {
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\n "date": "20190105"
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\n }
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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 "vim",
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\n "wget",
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\n "strace",
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\n "time",
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\n "ncdu",
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\n "gnupg",
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\n "curl",
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\n "procps",
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\n "datalad",
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\n "pigz",
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\n "git-annex-standalone",
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\n "python-nipype",
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\n "virtualenv",
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\n "python-dcmstack",
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\n "python-configparser",
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\n "python-funcsigs",
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\n "python-pytest",
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\n "dcmtk",
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\n "python-pip",
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\n "python-wheel",
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\n "python-setuptools",
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\n "python-datalad"
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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 -sL https://deb.nodesource.com/setup_6.x | bash - "
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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 "nodejs",
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\n "npm"
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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 "npm install -g [email protected]"
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\n ],
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\n [
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\n "run",
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\n "mkdir /afs /inbox"
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\n ],
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\n [
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\n "run",
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\n "pip install heudiconv"
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\n ],
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\n [
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\n "dcm2niix",
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\n {
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\n "version": "v1.0.20181125",
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\n "method": "source"
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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 "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
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\n ],
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\n [
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\n "user",
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\n "reproin"
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\n ],
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\n [
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\n "entrypoint",
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\n "/neurodocker/heudiconv.sh"
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\n ]
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\n ]
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\n}' > /neurodocker/neurodocker_specs.json
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%environment
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export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export PATH="/opt/dcm2niix-v1.0.20181125/bin:$PATH"
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%runscript
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/neurodocker/heudiconv.sh

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