-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
59 lines (49 loc) · 1.44 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
# Dockerfile for ASHS (fast-ashs) version
FROM pyushkevich/itksnap:v3.8.2
ENV FLYWHEEL=/flywheel/v0
ENV FLYWHEEL_INPUT=${FLYWHEEL}/input
ENV FLYWHEEL_OUTPUT=${FLYWHEEL}/output
ENV PATH=${FLYWHEEL}:${FLYWHEEL}/flywheel/bin:$PATH
ENV PYTHONPATH=/usr/local/lib/python3.9/site-packages:${FLYWHEEL}/flywheel/lib
# Descriptor fields
LABEL version="fastashs-1.0.0"
LABEL maintainer="[email protected]"
LABEL description="ASHS base image"
# Make sure we have git, curl and other basics
RUN apt-get update
RUN apt-get install -y \
autoconf \
bc \
build-essential \
curl \
git \
jq \
imagemagick \
libtool \
parallel \
python3 \
time \
unzip \
vim \
wget
RUN wget -O /tmp/fw-linux.zip https://storage.googleapis.com/flywheel-dist/cli/19.0.5/fw-linux_amd64-19.0.5.zip
RUN (cd /tmp; unzip fw-linux.zip; cp linux_amd64/fw /usr/local/bin/)
# Set the working directory for the ASHS app
WORKDIR ${FLYWHEEL}
RUN pip3 install flywheel-sdk flywheel-gear-toolkit globre pytz pyjq tzlocal
# Copy the current scriptlet
COPY docker-ashs-base /app/
COPY ashsPrepT1T2Inputs \
ashsFwResultsHandler \
copyFile2Output \
config.json \
genMetadataFile \
manifest.json \
run \
runall \
trim_neck.sh \
txt2json \
${FLYWHEEL}/
RUN chmod 755 ashsFwResultsHandler run runall trim_neck.sh txt2json
COPY AshsAtlasesConfig.json /app/AshsAtlasesConfig.json
COPY testdata ${FLYWHEEL}/testdata