-
Notifications
You must be signed in to change notification settings - Fork 0
/
Dockerfile
63 lines (49 loc) · 1.86 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
FROM continuumio/miniconda3 AS build
COPY mexpose.yml .
RUN conda install -n base conda-libmamba-solver && \
conda config --set solver libmamba && \
conda env create -f mexpose.yml
# Install conda-pack:
RUN conda install -c conda-forge conda-pack
RUN conda-pack -n mexpose -o /tmp/env.tar && \
mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
rm /tmp/env.tar
RUN /venv/bin/conda-unpack
# Runtime-stage
FROM ubuntu:22.04 AS runtime
# Set environment variables
ENV DEBIAN_FRONTEND=noninteractive
ENV DISPLAY=:0
ENV XAUTHORITY=/root/.Xauthority
# Copy /venv from the previous stage:
COPY --from=build /venv /venv
# Install packages
RUN apt-get update && \
apt-get install -y \
software-properties-common \
libmysqlclient-dev \
openjdk-8-jdk \
pip \
curl \
unzip \
git \
subversion
# Add Firefox PPA and install Firefox
RUN add-apt-repository ppa:mozillateam/ppa -y && \
printf 'Package: * \nPin: release o=LP-PPA-mozillateam \nPin-Priority: 1001 \n' | tee /etc/apt/preferences.d/mozilla-firefox && \
apt-get install -y firefox && \
apt-get autoremove -y && \
rm -rf /var/lib/apt/lists/*
# Download and install Fiji
RUN curl -L https://downloads.micron.ox.ac.uk/fiji_update/mirrors/fiji-latest/fiji-linux64.zip -o /tmp/fiji-linux64.zip && \
unzip /tmp/fiji-linux64.zip -d /home && \
rm /tmp/fiji-linux64.zip
# Pull MeXpose github repository and IMC-Plugins
RUN cd /home && \
git clone https://github.com/KoellenspergerLab/MeXpose.git && \
svn export https://github.com/BodenmillerGroup/ImcPluginsCP/trunk/plugins
# Update .bashrc
RUN echo "source /home/MeXpose/aliases.sh" >> /root/.bashrc && \
echo "source /home/MeXpose/fiji_macro_launch.sh" >> /root/.bashrc && \
echo "source /venv/bin/activate" >> /root/.bashrc
CMD ["/bin/bash", "-i"]