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Update Pipeline structure

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Patrick Jentsch
2022-01-18 12:58:42 +01:00
parent 3c9a800886
commit cdb4f1889c
5 changed files with 175 additions and 180 deletions
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@ -9,38 +9,32 @@ ENV LANG=C.UTF-8
RUN apt-get update \
&& apt-get install --no-install-recommends --yes \
wget
imagemagick \
procps \
wget \
&& mv /etc/ImageMagick-6/policy.xml /etc/ImageMagick-6/policy.xml.bak
# Install the NLP pipeline and it's dependencies #
# Install the File setup pipeline and it's dependencies #
## Install pyFlow ##
ENV PYFLOW_VERSION=1.1.20
RUN wget --no-check-certificate --quiet \
"https://github.com/Illumina/pyflow/releases/download/v${PYFLOW_VERSION}/pyflow-${PYFLOW_VERSION}.tar.gz" \
&& tar -xzf "pyflow-${PYFLOW_VERSION}.tar.gz" \
&& cd "pyflow-${PYFLOW_VERSION}" \
&& apt-get install --no-install-recommends --yes \
python2.7 \
&& python2.7 setup.py build install \
&& cd .. \
&& rm -r "pyflow-${PYFLOW_VERSION}" "pyflow-${PYFLOW_VERSION}.tar.gz"
&& tar -xzf "pyflow-${PYFLOW_VERSION}.tar.gz" \
&& cd "pyflow-${PYFLOW_VERSION}" \
&& apt-get install --no-install-recommends --yes \
python2.7 \
&& python2.7 setup.py build install \
&& cd - > /dev/null \
&& rm -r "pyflow-${PYFLOW_VERSION}" "pyflow-${PYFLOW_VERSION}.tar.gz"
## Further dependencies ##
RUN apt-get install --no-install-recommends --yes \
imagemagick \
procps \
python3.7 \
zip \
&& mv /etc/ImageMagick-6/policy.xml /etc/ImageMagick-6/policy.xml.bak
RUN rm -r /var/lib/apt/lists/*
## Install Pipeline ##
COPY file-setup /usr/local/bin
RUN rm -r /var/lib/apt/lists/*
ENTRYPOINT ["file-setup"]
CMD ["--help"]