forked from poldracklab/fitlins
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
238 lines (218 loc) · 7.61 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
# Generated by Neurodocker v0.3.2.
#
# 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
#
# Timestamp: 2018-03-08 22:26:14
FROM neurodebian@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c
ARG DEBIAN_FRONTEND=noninteractive
#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
ENV LANG="en_US.UTF-8" \
LC_ALL="C.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
apt-utils bzip2 ca-certificates curl locales unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& localedef --force --inputfile=en_US --charmap=UTF-8 C.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 +x' >> $ND_ENTRYPOINT \
&& echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
LABEL maintainer="Christopher J. Markiewicz"
ARG PYTHON_VERSION_MAJOR="3"
ARG PYTHON_VERSION_MINOR="6"
ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
ENV MKL_NUM_THREADS="1" \
OMP_NUM_THREADS="1"
# Create new user: neuro
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro
#------------------
# Install Miniconda
#------------------
ENV CONDA_DIR=/opt/conda \
PATH=/opt/conda/bin:$PATH
RUN echo "Downloading Miniconda installer ..." \
&& miniconda_installer=/tmp/miniconda.sh \
&& curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& /bin/bash $miniconda_installer -b -p $CONDA_DIR \
&& rm -f $miniconda_installer \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& conda update -n base conda \
&& conda clean -tipsy && sync
#-------------------------
# Create conda environment
#-------------------------
RUN conda create -y -q --name neuro python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \
icu=58.1 \
mkl=2018.0.1 \
mkl-service \
git=2.9.3 \
&& sync && conda clean -tipsy && sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
#-------------------------
# Update conda environment
#-------------------------
RUN conda install -y -q --name neuro numpy=1.14.1 \
scipy=1.0.0 \
scikit-learn=0.19.1 \
matplotlib=2.1.2 \
seaborn=0.8.1 \
pandas=0.22.0 \
nipype=1.0.1 \
patsy \
&& sync && conda clean -tipsy && sync
COPY [".", "/src/fitlins"]
USER root
# User-defined instruction
RUN mkdir /work && chown -R neuro /src /work
USER neuro
#-------------------------
# Update conda environment
#-------------------------
RUN /bin/bash -c "source activate neuro \
&& pip install -q --no-cache-dir -r /src/fitlins/requirements.txt" \
&& sync
#-------------------------
# Update conda environment
#-------------------------
RUN /bin/bash -c "source activate neuro \
&& pip install -q --no-cache-dir -e /src/fitlins[all]" \
&& sync
WORKDIR /work
ENTRYPOINT ["/neurodocker/startup.sh", "fitlins"]
LABEL org.label-schema.build-date="$BUILD_DATE" \
org.label-schema.name="FitLins" \
org.label-schema.description="FitLins - Fit Linear Models to BIDS datasets" \
org.label-schema.url="https://github.com/poldracklab/fitlins" \
org.label-schema.vcs-ref="$VCS_REF" \
org.label-schema.vcs-url="https://github.com/poldracklab/fitlins" \
org.label-schema.version="$VERSION" \
org.label-schema.schema-version="1.0"
#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "check_urls": false, \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c" \
\n ], \
\n [ \
\n "label", \
\n { \
\n "maintainer": "Christopher J. Markiewicz" \
\n } \
\n ], \
\n [ \
\n "arg", \
\n { \
\n "PYTHON_VERSION_MAJOR": "3", \
\n "PYTHON_VERSION_MINOR": "6", \
\n "BUILD_DATE": "", \
\n "VCS_REF": "", \
\n "VERSION": "" \
\n } \
\n ], \
\n [ \
\n "env", \
\n { \
\n "MKL_NUM_THREADS": "1", \
\n "OMP_NUM_THREADS": "1" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "activate": true, \
\n "conda_install": "python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} icu=58.1 mkl=2018.0.1 mkl-service git=2.9.3" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "conda_install": "numpy=1.14.1 scipy=1.0.0 scikit-learn=0.19.1 matplotlib=2.1.2 seaborn=0.8.1 pandas=0.22.0 nipype=1.0.1 patsy" \
\n } \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/src/fitlins" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "run", \
\n "mkdir /work && chown -R neuro /src /work" \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "pip_opts": "-r", \
\n "pip_install": "/src/fitlins/requirements.txt" \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "env_name": "neuro", \
\n "pip_opts": "-e", \
\n "pip_install": "/src/fitlins[all]" \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/work" \
\n ], \
\n [ \
\n "entrypoint", \
\n "/neurodocker/startup.sh fitlins" \
\n ], \
\n [ \
\n "label", \
\n { \
\n "org.label-schema.build-date": "$BUILD_DATE", \
\n "org.label-schema.name": "FitLins", \
\n "org.label-schema.description": "FitLins - Fit Linear Models to BIDS datasets", \
\n "org.label-schema.url": "https://github.com/poldracklab/fitlins", \
\n "org.label-schema.vcs-ref": "$VCS_REF", \
\n "org.label-schema.vcs-url": "https://github.com/poldracklab/fitlins", \
\n "org.label-schema.version": "$VERSION", \
\n "org.label-schema.schema-version": "1.0" \
\n } \
\n ] \
\n ], \
\n "generation_timestamp": "2018-03-08 22:26:14", \
\n "neurodocker_version": "0.3.2" \
\n}' > /neurodocker/neurodocker_specs.json