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docker: refactor manylinux Dockerfile #137

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docker: refactor manylinux Dockerfile #137

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docker: refactor manylinux Dockerfile
radusuciu Feb 2, 2024
35a2f0b
docker: install more packages from yum in manylinux image
radusuciu Feb 6, 2024
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56 changes: 35 additions & 21 deletions dockerfiles/pyopenms/manylinux/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,38 +1,52 @@
FROM quay.io/pypa/manylinux2014_x86_64

#defaults, can be overwritten from outside
ARG OPENMS_BRANCH="master"
ARG CONTRIB_BUILD_DIR="/contrib-build"
ARG OPENMS_VERSION="latest"

# make source files from context available in docker
COPY . /contrib

RUN yum install -y wget
RUN yum install -y xz qt5-qtbase-devel
RUN yum install -y qt5-qtbase-devel qt5-qtsvg qt5-qtsvg-devel python-devel
# RUN yum install -y libsvm-devel glpk-devel libzip-devel zlib-devel xerces-c-devel bzip2-devel sqlite-devel hdf5-devel
RUN yum install -y libtool
RUN yum install -y \
# build system dependencies
wget \
xz \
libtool \
cmake3 \
# OpenMS and PyOpenMS build dependencies
libsvm-devel \
glpk-devel \
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Avoid, if it works with coinor

libzip-devel \
zlib-devel \
xerces-c-devel \
bzip2-devel \
hdf5-devel \
qt5-qtbase-devel \
qt5-qtsvg-devel \
eigen3-devel \
python-devel
# TODO: do we need sqlite-devel?
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Yes. It is probably a dependency of something

# TODO: can we install boost from yum?
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Yes probably

# TODO: is coin-or-CoinUtils-devel useful?
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Yes but probably a dependency of other CoinOR libs

# TODO: do we need KissFFT? It's not installed in the regular contrib Dockerfile
Comment on lines +26 to +29
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@jpfeuffer I think we don't need KissFFT right?

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I think not


RUN yum install -y cmake3
RUN ln -s /usr/bin/cmake3 /usr/bin/cmake

# builds contrib for the current checked out branch
# during cleanup: removes archives
RUN mkdir contrib-build
RUN ls -l
WORKDIR /contrib-build
RUN ls -l
RUN cmake -DBUILD_TYPE=ALL ../contrib && rm -rf archives src

WORKDIR ${CONTRIB_BUILD_DIR}
RUN cmake -DBUILD_TYPE="BOOST;COINOR;KISSFFT;OPENMP" ../contrib && rm -rf archives src
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this currently doesn't work because our IT is down (again)

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On Linux you probably don't need contrib.
I guess even centos7 has everything we need.

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that would simplify things a lot

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I was too quick. Should have known that CoinOR is basically available nowhere..

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yes, IIRC this was one of the blockers of using yum for everything


WORKDIR /

# Metadata
LABEL base.image="manylinux2014_x86_64"
LABEL version="1.0"
LABEL version="${OPENMS_VERSION}"
LABEL software="OpenMS (dependencies for manylinux2014)"
LABEL software.version="$OPENMS_VERSION"
LABEL description="C++ libraries and tools for MS/MS data analysis"
LABEL website="http://www.openms.org/"
LABEL documentation="http://www.openms.org/"
LABEL license="http://www.openms.org/"
LABEL software.version="$OPENMS_VERSION-manylinux2014"
LABEL description="Base image to build OpenMS: C++ libraries and tools for MS/MS data analysis"
LABEL website="https://www.openms.org/"
LABEL documentation="https://www.openms.org/"
LABEL license="https://www.openms.org/"
LABEL tags="Proteomics"

# to link to repo on github container registry
LABEL org.opencontainers.image.source https://github.com/OpenMS/contrib