-
Notifications
You must be signed in to change notification settings - Fork 7
/
Dockerfile
73 lines (55 loc) · 2.61 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
FROM jupyter/datascience-notebook:lab-2.2.9
USER root
# Install a few dependencies for iCommands, text editing, and monitoring instances
RUN apt-get update && apt-get install -y lsb-release wget apt-transport-https curl supervisor nginx gnupg2 libfuse2 nano htop gcc less nodejs software-properties-common apt-utils glances
RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" > /etc/apt/sources.list.d/renci-irods.list && \
apt-get update && \
wget -q -c \
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb && \
apt install -y \
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
./python-requests_2.18.4-2ubuntu0.1_all.deb \
./libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb && \
rm -rf \
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
./python-requests_2.18.4-2ubuntu0.1_all.deb \
./libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb && \
apt install -y irods-icommands && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# Install Go
RUN wget -q -c https://dl.google.com/go/go1.17.6.linux-amd64.tar.gz -O - | sudo tar -xz -C /usr/local
ENV PATH=$PATH:/usr/local/go/bin
# Install CyberDuck CLI
RUN echo -e "deb https://s3.amazonaws.com/repo.deb.cyberduck.io stable main" | tee /etc/apt/sources.list.d/cyberduck.list > /dev/null && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys FE7097963FEFBE72 && \
apt-get update && \
apt-get install duck
# Install Github widget
RUN jupyter labextension install @jupyterlab/github
# Install and configure jupyter lab.
COPY jupyter_notebook_config.json /opt/conda/etc/jupyter/jupyter_notebook_config.json
# Add the jovyan user to UID 1000
RUN groupadd jovyan && usermod -aG jovyan jovyan && usermod -d /home/jovyan -u 1000 jovyan
RUN apt-get update && apt-get install -y sudo
RUN echo 'ALL ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
# Rebuild the Jupyter Lab with new tools
RUN jupyter lab build
# purge older nodejs
RUN apt purge nodejs -y
USER jovyan
WORKDIR /home/jovyan
# install iRODS plugin
RUN conda install -c conda-forge nodejs -y
RUN pip install jupyterlab_irods
USER root
RUN jupyter serverextension enable --py jupyterlab_irods
RUN jupyter labextension install ijab
USER jovyan
EXPOSE 8888
COPY entry.sh /bin
RUN mkdir -p /home/jovyan/.irods
ENTRYPOINT ["bash", "/bin/entry.sh"]