forked from openworm/tests
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
96 lines (81 loc) · 3.09 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
FROM jupyter/scipy-notebook
USER root
RUN apt-get update
RUN apt-get install -y default-jre
USER jovyan
WORKDIR /home/jovyan/work
RUN mkdir openworm
ENV OPENWORM_HOME /home/jovyan/work/openworm
# SciUnit
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/scidash/sciunit/tarball/dev -O out.tar.gz
RUN mkdir sciunit
RUN tar -xvzf out.tar.gz --strip-components=1 -C sciunit
WORKDIR sciunit
RUN pip install -e . --process-dependency-links
# NeuronUnit
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/scidash/neuronunit/tarball/dev -O out.tar.gz
RUN mkdir neuronunit
RUN tar -xvzf out.tar.gz --strip-components=1 -C neuronunit
WORKDIR neuronunit
RUN pip install -e . --process-dependency-links
# ChannelWorm
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/openworm/ChannelWorm/tarball/sciunit -O out.tar.gz
RUN mkdir ChannelWorm
RUN tar -xvzf out.tar.gz --strip-components=1 -C ChannelWorm
WORKDIR ChannelWorm
RUN pip install -e . --process-dependency-links
# CElegansNeuroML
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/openworm/CElegansNeuroML/tarball/sciunit -O out.tar.gz
RUN mkdir CElegansNeuroML
RUN tar -xvzf out.tar.gz --strip-components=1 -C CElegansNeuroML
WORKDIR CElegansNeuroML
RUN pip install -e . --process-dependency-links
# open-worm-analysis-toolbox
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/rgerkin/open-worm-analysis-toolbox/tarball/sciunit -O out.tar.gz
RUN mkdir open-worm-analysis-toolbox
RUN tar -xvzf out.tar.gz --strip-components=1 -C open-worm-analysis-toolbox
WORKDIR open-worm-analysis-toolbox
RUN pip install -e . --process-dependency-links
# One level deeper
WORKDIR open_worm_analysis_toolbox
RUN cp user_config_example.txt user_config.py
WORKDIR $OPENWORM_HOME/open-worm-analysis-toolbox
RUN mkdir example_data
WORKDIR example_data
#RUN wget "https://drive.google.com/uc?export=download&id=0B7to9gBdZEyGWVAzUlYwbk1ad0E" -O example_contour_and_skeleton_info.mat
#RUN wget "https://drive.google.com/uc?export=download&id=0B7to9gBdZEyGX2tFQ1JyRzdUYUE" -O example_video_feature_file.mat
#RUN wget "https://drive.google.com/uc?export=download&id=0B7to9gBdZEyGakg5U3loVUktRm8" -O example_video_norm_worm.mat
# cache bust
RUN ls
# wcon
WORKDIR $OPENWORM_HOME
RUN wget http://github.com/rgerkin/tracker-commons/tarball/master -O out.tar.gz
RUN mkdir tracker-commons
RUN tar -xvzf out.tar.gz --strip-components=1 -C tracker-commons
WORKDIR tracker-commons/src/Python
RUN pip install -e . --process-dependency-links
RUN pip install -U nbconvert IPython
# This tests package
WORKDIR $OPENWORM_HOME
#VOLUME $OPENWORM_HOME/tests
#RUN git clone http://github.com/openworm/tests
WORKDIR tests
COPY --chown=jovyan:users . $OPENWORM_HOME/tests
USER root
RUN chown jovyan:users $OPENWORM_HOME/tests
USER jovyan
#USER root
#RUN chown -R jovyan .
#USER jovyan
RUN pip install -e . --process-dependency-links
#RUN pip install -e .[channels,cells] --process-dependency-links
#RUN python -m unittest -b owtests
#ENTRYPOINT /bin/bash
#WORKDIR $HOME/work
ENTRYPOINT start-notebook.sh --NotebookApp.token=''
RUN cp $OPENWORM_HOME/tracker-commons/wcon_schema.json $OPENWORM_HOME/tracker-commons/src/Python/wcon/wcon_schema.json