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Dockerfile
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FROM kbase/kbase:sdkbase.latest
MAINTAINER KBase Developer
# -----------------------------------------
# In this section, you can install any system dependencies required
# to run your App. For instance, you could place an apt-get update or
# install line here, a git checkout to download code, or run any other
# installation scripts.
RUN apt-get update
# # Update setuptools and pip
# RUN pip install --upgrade pip setuptools
# # Here we install a python coverage tool and an
# # https library that is out of date in the base image.
# RUN pip install coverage
# # update security libraries in the base image
# RUN pip install cffi --upgrade \
# && pip install pyopenssl --upgrade \
# && pip install ndg-httpsclient --upgrade \
# && pip install pyasn1 --upgrade \
# && pip install requests --upgrade \
# && pip install 'requests[security]' --upgrade
# Install the KMC k-mer counter
RUN wget https://github.com/refresh-bio/KMC/releases/download/v3.1.0/KMC3.1.0.linux.tar.gz \
&& tar -xzf KMC3.1.0.linux.tar.gz \
&& cp kmc /bin \
&& cp kmc_dump /bin
# -----------------------------------------
COPY ./ /kb/module
RUN mkdir -p /kb/module/work
RUN chmod -R a+rw /kb/module
WORKDIR /kb/module
# Remove compile because it resetted the code
RUN make build build-startup-script build-executable-script build-test-script
ENTRYPOINT [ "./scripts/entrypoint.sh" ]
CMD [ ]