1- # Generated by Neurodocker v0.3.2.
2- #
1+ # Generated by Neurodocker version 0.4.2-3-gf7055a1
2+ # Timestamp: 2018-11-13 22:04:04 UTC
3+ #
34# Thank you for using Neurodocker. If you discover any issues
45# or ways to improve this software, please submit an issue or
56# pull request on our GitHub repository:
7+ #
68# https://github.com/kaczmarj/neurodocker
7- #
8- # Timestamp: 2018-06-29 18:14:08
99
10- FROM debian :stretch
10+ FROM neurodebian :stretch
1111
12- ARG DEBIAN_FRONTEND=noninteractive
12+ ARG DEBIAN_FRONTEND=" noninteractive"
1313
14- # ----------------------------------------------------------
15- # Install common dependencies and create default entrypoint
16- # ----------------------------------------------------------
1714ENV LANG="en_US.UTF-8" \
18- LC_ALL="C .UTF-8" \
15+ LC_ALL="en_US .UTF-8" \
1916 ND_ENTRYPOINT="/neurodocker/startup.sh"
20- RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
21- apt-utils bzip2 ca-certificates curl locales unzip \
17+ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
18+ && apt-get update -qq \
19+ && apt-get install -y -q --no-install-recommends \
20+ apt-utils \
21+ bzip2 \
22+ ca-certificates \
23+ curl \
24+ locales \
25+ unzip \
2226 && apt-get clean \
2327 && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
24- && localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
28+ && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
29+ && dpkg-reconfigure --frontend=noninteractive locales \
30+ && update-locale LANG="en_US.UTF-8" \
2531 && chmod 777 /opt && chmod a+s /opt \
2632 && mkdir -p /neurodocker \
2733 && if [ ! -f "$ND_ENTRYPOINT" ]; then \
28- echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
29- && echo 'set +x ' >> $ND_ENTRYPOINT \
30- && echo 'if [ -z "$* " ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
31- fi \
34+ echo '#!/usr/bin/env bash' >> " $ND_ENTRYPOINT"
35+ && echo 'set -e ' >> " $ND_ENTRYPOINT"
36+ && echo 'if [ -n "$1 " ]; then "$@"; else /usr/bin/env bash; fi' >> " $ND_ENTRYPOINT"
37+ fi \
3238 && chmod -R 777 /neurodocker && chmod a+s /neurodocker
39+
3340ENTRYPOINT ["/neurodocker/startup.sh" ]
3441
35- # ------------------------
36- # Install dcm2niix v1.0.20180622
37- # ------------------------
38- WORKDIR /tmp
39- RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
40- && apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
42+ ENV PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
43+ RUN apt-get update -qq \
44+ && apt-get install -y -q --no-install-recommends \
45+ cmake \
46+ g++ \
47+ gcc \
48+ git \
49+ make \
50+ pigz \
51+ zlib1g-dev \
4152 && apt-get clean \
4253 && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
43- && mkdir dcm2niix \
44- && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180622 | tar xz -C dcm2niix --strip-components 1 \
45- && mkdir dcm2niix/build && cd dcm2niix/build \
46- && cmake .. && make \
54+ && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
55+ && cd /tmp/dcm2niix \
56+ && git fetch --tags \
57+ && git checkout v1.0.20180622 \
58+ && mkdir /tmp/dcm2niix/build \
59+ && cd /tmp/dcm2niix/build \
60+ && cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 .. \
61+ && make \
4762 && make install \
48- && rm -rf /tmp/* \
49- && apt-get purge -y --auto-remove $deps
50-
51- # --------------------------------------------------
52- # Add NeuroDebian repository
53- # Please note that some packages downloaded through
54- # NeuroDebian may have restrictive licenses.
55- # --------------------------------------------------
56- RUN apt-get update -qq && apt-get install -yq --no-install-recommends dirmngr gnupg \
57- && apt-get clean \
58- && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
59- && curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
60- > /etc/apt/sources.list.d/neurodebian.sources.list \
61- && curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
62- | apt-key add - \
63- && (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
64- && apt-get update
65-
66- # Install NeuroDebian packages
67- RUN apt-get update -qq && apt-get install -yq --no-install-recommends git-annex-standalone \
68- && apt-get clean \
69- && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
63+ && rm -rf /tmp/dcm2niix
7064
7165RUN apt-get update -qq \
72- && apt-get install -y -q --no-install-recommends git \
73- gcc \
74- pigz \
66+ && apt-get install -y -q --no-install-recommends \
67+ git \
68+ gcc \
69+ pigz \
70+ liblzma-dev \
71+ libc-dev \
72+ git-annex-standalone \
73+ netbase \
7574 && apt-get clean \
7675 && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
7776
7877COPY ["." , "/src/heudiconv" ]
7978
80- # ------------------
81- # Install Miniconda
82- # ------------------
83- ENV CONDA_DIR=/opt/conda \
84- PATH=/opt/conda/bin:$PATH
85- RUN echo "Downloading Miniconda installer ..." \
86- && miniconda_installer=/tmp/miniconda.sh \
87- && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
88- && /bin/bash $miniconda_installer -b -p $CONDA_DIR \
89- && rm -f $miniconda_installer \
79+ ENV CONDA_DIR="/opt/miniconda-latest" \
80+ PATH="/opt/miniconda-latest/bin:$PATH"
81+ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
82+ && echo "Downloading Miniconda installer ..." \
83+ && conda_installer="/tmp/miniconda.sh" \
84+ && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
85+ && bash "$conda_installer" -b -p /opt/miniconda-latest \
86+ && rm -f "$conda_installer" \
87+ && conda update -yq -nbase conda \
9088 && conda config --system --prepend channels conda-forge \
9189 && conda config --system --set auto_update_conda false \
9290 && conda config --system --set show_channel_urls true \
93- && conda clean -tipsy && sync
94-
95- # -------------------------
96- # Create conda environment
97- # -------------------------
98- RUN conda create -y -q --name neuro python=2 \
99- traits=4.6.0 \
10091 && sync && conda clean -tipsy && sync \
101- && /bin/bash -c "source activate neuro \
102- && pip install -q --no-cache-dir https://github.com/moloney/dcmstack/tarball/master \
103- /src/heudiconv[all]" \
104- && sync \
105- && sed -i '$isource activate neuro' $ND_ENTRYPOINT
92+ && conda install -y -q --name base \
93+ 'python=3.6' \
94+ 'traits>=4.6.0' \
95+ 'scipy' \
96+ 'numpy' \
97+ 'pandas' \
98+ 'nomkl' \
99+ && sync && conda clean -tipsy && sync \
100+ && bash -c "source activate base \
101+ && pip install --no-cache-dir --editable \
102+ '/src/heudiconv[all]'" \
103+ && rm -rf ~/.cache/pip/* \
104+ && sync
106105
107- ENTRYPOINT ["/neurodocker/startup.sh" , " heudiconv"
106+ ENTRYPOINT ["heudiconv" ]
108107
109- # --------------------------------------
110- # Save container specifications to JSON
111- # --------------------------------------
112108RUN echo '{ \
113109 \n "pkg_manager": "apt", \
114- \n "check_urls": true, \
115110 \n "instructions": [ \
116111 \n [ \
117112 \n "base", \
118- \n "debian :stretch" \
113+ \n "neurodebian :stretch" \
119114 \n ], \
120115 \n [ \
121116 \n "dcm2niix", \
122117 \n { \
123- \n "version": "v1.0.20180622" \
124- \n } \
125- \n ], \
126- \n [ \
127- \n "neurodebian", \
128- \n { \
129- \n "os_codename": "stretch", \
130- \n "download_server": "usa-nh", \
131- \n "pkgs": "git-annex-standalone" \
118+ \n "version": "v1.0.20180622", \
119+ \n "method": "source" \
132120 \n } \
133121 \n ], \
134122 \n [ \
135123 \n "install", \
136124 \n [ \
137125 \n "git", \
138126 \n "gcc", \
139- \n "pigz" \
127+ \n "pigz", \
128+ \n "liblzma-dev", \
129+ \n "libc-dev", \
130+ \n "git-annex-standalone", \
131+ \n "netbase" \
140132 \n ] \
141133 \n ], \
142134 \n [ \
@@ -149,17 +141,24 @@ RUN echo '{ \
149141 \n [ \
150142 \n "miniconda", \
151143 \n { \
152- \n "env_name": "neuro", \
153- \n "conda_install": "python=2 traits=4.6.0", \
154- \n "activate": true, \
155- \n "pip_install": "https://github.com/moloney/dcmstack/tarball/master /src/heudiconv[all]" \
144+ \n "use_env": "base", \
145+ \n "conda_install": [ \
146+ \n "python=3.6", \
147+ \n "traits>=4.6.0", \
148+ \n "scipy", \
149+ \n "numpy", \
150+ \n "pandas", \
151+ \n "nomkl" \
152+ \n ], \
153+ \n "pip_install": [ \
154+ \n "/src/heudiconv[all]" \
155+ \n ], \
156+ \n "pip_opts": "--editable" \
156157 \n } \
157158 \n ], \
158159 \n [ \
159160 \n "entrypoint", \
160- \n "/neurodocker/startup.sh heudiconv" \
161+ \n "heudiconv" \
161162 \n ] \
162- \n ], \
163- \n "generation_timestamp": "2018-06-29 18:14:08", \
164- \n "neurodocker_version": "0.3.2" \
163+ \n ] \
165164 \n }' > /neurodocker/neurodocker_specs.json
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