generated from Neubias-WG5/W_Template
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathDockerfile
54 lines (46 loc) · 2.72 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
FROM python:3.7-stretch
# ------------------------------------------------------------------------------
# Install Cytomine python client
RUN git clone https://github.com/cytomine-uliege/Cytomine-python-client.git && \
cd /Cytomine-python-client && git checkout tags/v2.7.3 && pip install . && \
rm -r /Cytomine-python-client
# ------------------------------------------------------------------------------
# Install BIAFLOWS utilities (annotation exporter, compute metrics, helpers,...)
RUN apt-get update && apt-get install libgeos-dev -y && apt-get clean
RUN git clone https://github.com/Neubias-WG5/biaflows-utilities.git && \
cd /biaflows-utilities/ && git checkout tags/v0.9.2 && pip install .
# install utilities binaries
RUN chmod +x /biaflows-utilities/bin/*
RUN cp /biaflows-utilities/bin/* /usr/bin/ && \
rm -r /biaflows-utilities
# ------------------------------------------------------------------------------
RUN pip install imageio
RUN pip install cellpose==0.6.1
RUN pip install numpy==1.19.4
RUN mkdir /root/.cellpose && \
mkdir /root/.cellpose/models && \
cd /root/.cellpose/models && \
wget http://www.cellpose.org/models/nuclei_0 && \
wget http://www.cellpose.org/models/nuclei_1 && \
wget http://www.cellpose.org/models/nuclei_2 && \
wget http://www.cellpose.org/models/nuclei_3 && \
wget http://www.cellpose.org/models/size_nuclei_0.npy && \
wget --no-check-certificate https://www.cellpose.org/models/cyto_0 && \
wget --no-check-certificate https://www.cellpose.org/models/cyto_1 && \
wget --no-check-certificate https://www.cellpose.org/models/cyto_2 && \
wget --no-check-certificate https://www.cellpose.org/models/cyto_3 && \
wget --no-check-certificate https://www.cellpose.org/models/size_cyto_0.npy && \
wget --no-check-certificate https://www.cellpose.org/models/cytotorch_0 && \
wget --no-check-certificate https://www.cellpose.org/models/cytotorch_1 && \
wget --no-check-certificate https://www.cellpose.org/models/cytotorch_2 && \
wget --no-check-certificate https://www.cellpose.org/models/cytotorch_3 && \
wget --no-check-certificate https://www.cellpose.org/models/size_cytotorch_0.npy && \
wget --no-check-certificate https://www.cellpose.org/models/nucleitorch_0 && \
wget --no-check-certificate https://www.cellpose.org/models/nucleitorch_1 && \
wget --no-check-certificate https://www.cellpose.org/models/nucleitorch_2 && \
wget --no-check-certificate https://www.cellpose.org/models/nucleitorch_3 && \
wget --no-check-certificate https://www.cellpose.org/models/size_nucleitorch_0.npy
ADD wrapper.py /app/wrapper.py
# for running the wrapper locally
ADD descriptor.json /app/descriptor.json
ENTRYPOINT ["python3.7","/app/wrapper.py"]