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Fix generated CWL/JSON files

Merged Fix generated CWL/JSON files
RAP-423_DockerRequirement into master
Merged Marcel Loose requested to merge RAP-423_DockerRequirement into master
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FROM ubuntu:20.04 as builder
 
 
# This Dockerfile builds a Docker image for the Rapthor pipeline
 
# and all its dependencies.
 
 
ARG PORTABLE=TRUE
 
 
# Install all build-time dependencies
 
RUN export DEBIAN_FRONTEND=noninteractive && \
 
apt-get update && \
 
apt-get install -y \
 
bison \
 
build-essential \
 
casacore-data \
 
casacore-dev \
 
casacore-tools \
 
cmake \
 
flex \
 
gfortran \
 
git \
 
libarmadillo-dev \
 
libboost-date-time-dev \
 
libboost-filesystem-dev \
 
libboost-numpy-dev \
 
libboost-program-options-dev \
 
libboost-python-dev \
 
libboost-system-dev \
 
libboost-test-dev \
 
libcfitsio-dev \
 
libfftw3-dev \
 
libgsl-dev \
 
libgtkmm-3.0-dev \
 
libhdf5-serial-dev \
 
liblua5.3-dev \
 
libpng-dev \
 
ninja-build \
 
pybind11-dev \
 
python3-dev \
 
wcslib-dev \
 
wget
 
 
# Prepare the environment for installing the Rapthor source dependencies.
 
RUN mkdir /src
 
RUN git config --global alias.shallow-clone "!git clone --depth 1 --recurse-submodules --shallow-submodules"
 
WORKDIR /src
 
 
# Install IDG
 
# A shallow clone of IDG breaks its version number. This is an issue for DP3
 
# since it has a minimal version requirement.
 
RUN git clone https://git.astron.nl/RD/idg.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DBUILD_WITH_PYTHON=OFF \
 
-DBUILD_TESTING=OFF \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/idg \
 
-B/src/idg/build \
 
-G Ninja
 
RUN ninja -C /src/idg/build install
 
 
# Install EveryBeam
 
RUN git shallow-clone https://git.astron.nl/RD/EveryBeam.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DBUILD_WITH_PYTHON=ON \
 
-DBUILD_TESTING=OFF \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/EveryBeam \
 
-B/src/EveryBeam/build \
 
-G Ninja
 
RUN ninja -C /src/EveryBeam/build install
 
 
# Install Dysco
 
RUN git shallow-clone https://github.com/aroffringa/dysco.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/dysco \
 
-B/src/dysco/build \
 
-G Ninja
 
RUN ninja -C /src/dysco/build install
 
 
# Install AOFlagger
 
RUN git shallow-clone https://gitlab.com/aroffringa/aoflagger.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/aoflagger \
 
-B/src/aoflagger/build \
 
-G Ninja
 
RUN ninja -C /src/aoflagger/build install
 
 
# Install WSClean
 
RUN git shallow-clone https://gitlab.com/aroffringa/wsclean.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DBUILD_TESTING=OFF \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/wsclean \
 
-B/src/wsclean/build \
 
-G Ninja
 
RUN ninja -C /src/wsclean/build install
 
 
# Install DP3
 
RUN git shallow-clone https://git.astron.nl/RD/DP3.git
 
RUN cmake \
 
-DCMAKE_BUILD_TYPE:STRING=Release \
 
-DBUILD_TESTING=OFF \
 
-DPORTABLE=${PORTABLE} \
 
-H/src/DP3 \
 
-B/src/DP3/build \
 
-G Ninja
 
RUN ninja -C /src/DP3/build install
 
 
# Generate file with one-liner package version descriptions
 
RUN mkdir -p /usr/local/share/rapthor; \
 
for p in $(find /src -type d -name .git | sort); \
 
do \
 
d=$(dirname $p); b=$(basename $d); cd $d; l=$(git log -1 --oneline); \
 
echo "$b: $l"; \
 
done \
 
> /usr/local/share/rapthor/sw-versions.txt
 
 
# Do not use `pip` from the Debian repository, but fetch it from PyPA.
 
# This way, we are sure that the latest versions of `pip`, `setuptools`, and
 
# `wheel` are installed in /usr/local, the only directory we're going to copy
 
# over to the next build stage.
 
RUN wget https://bootstrap.pypa.io/get-pip.py && \
 
python3 get-pip.py
 
 
# Install all Python dependencies for Rapthor
 
COPY ./requirements.txt .
 
RUN python3 -m pip install -r requirements.txt
 
 
#---------------------------------------------------------------------------
 
# The image will now be rebuilt without adding the sources, in order to
 
# reduce the size of the image.
 
#---------------------------------------------------------------------------
 
FROM ubuntu:20.04 as runner
 
 
COPY --from=builder /usr/local /usr/local
 
 
# Only install run-time required packages
 
RUN export DEBIAN_FRONTEND=noninteractive && \
 
apt-get update && \
 
apt-get install -y \
 
casacore-tools \
 
libarmadillo9 \
 
libatkmm-1.6-1v5 \
 
libboost-date-time1.71.0 \
 
libboost-filesystem1.71.0 \
 
libboost-program-options1.71.0 \
 
libcairomm-1.0-1v5 \
 
libcasa-casa4 \
 
libcasa-fits4 \
 
libcasa-measures4 \
 
libcasa-ms4 \
 
libcasa-scimath4 \
 
libcasa-tables4 \
 
libcfitsio8 \
 
libfftw3-double3 \
 
libfftw3-single3 \
 
libglibmm-2.4-1v5 \
 
libgomp1 \
 
libgsl23 \
 
libgtkmm-3.0-1v5 \
 
libhdf5-103 \
 
libhdf5-cpp-103 \
 
liblapack3 \
 
liblua5.3-0 \
 
libpangomm-1.4-1v5 \
 
libpng16-16 \
 
libpython3.8 \
 
libsigc++-2.0-0v5 \
 
libstdc++6 \
 
nodejs \
 
python3 \
 
python3-distutils \
 
wget
 
 
RUN rm -rf /var/lib/apt/lists/*
 
 
# Install WSRT Measures (extra casacore data). We purposely do this in the
 
# `runner` stage and not in the `builder` stage, because otherwise the
 
# previous `apt-get install` would clobber the files we had installed in
 
# in the `builder` stage (as `casacore-data` is installed as a dependency).
 
# Note: The file on the ftp site is updated daily. When warnings regarding
 
# leap seconds appear, ignore them or regenerate the docker image.
 
RUN wget -q -O /WSRT_Measures.ztar \
 
ftp://ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar && \
 
cd /var/lib/casacore/data && \
 
tar xfz /WSRT_Measures.ztar && \
 
rm /WSRT_Measures.ztar
 
 
# Try to run the compiled tools to make sure they run without
 
# a problem (e.g. no missing libraries).
 
RUN aoflagger --version && \
 
DP3 --version && \
 
wsclean --version
 
 
# Install current version of Rapthor
 
COPY . /tmp/rapthor
 
RUN python3 -m pip install --upgrade --no-cache-dir /tmp/rapthor
 
RUN rm -rf /tmp/*