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Dockerfile
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FROM kbase/sdkpython:3.8.0
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 && apt-get -y upgrade \
&& apt-get install -y --no-install-recommends \
git \
wget \
g++ \
ca-certificates \
&& rm -rf /var/lib/apt/lists/*
RUN rm /bin/sh && ln -s /bin/bash /bin/sh
RUN conda create -n py39 python=3.9 \
&& source activate py39 \
&& conda install nose jinja2 \
&& pip3 install jsonrpcbase numpy pandas biopython \
&& pip3 install coverage
WORKDIR /tmp
# Install necessary packages
RUN apt-get update && apt-get install -y wget gnupg2 curl software-properties-common
# Add the antiSMASH repository and GPG key
# Note: Replace the URLs with the correct ones if they have changed or if specific versions for Ubuntu 18.04 are available
RUN wget -O /etc/apt/sources.list.d/antismash.list https://dl.secondarymetabolites.org/antismash-stretch.list && \
curl -fsSL https://dl.secondarymetabolites.org/antismash.asc | apt-key add -
RUN apt-get update && \
apt-get -y install hmmer2 hmmer diamond-aligner fasttree prodigal ncbi-blast+ muscle glimmerhmm
#RUN wget --quiet https://github.com/bbuchfink/diamond/releases/download/v2.0.9/diamond-linux64.tar.gz && \
# tar -zxf diamond-linux64.tar.gz diamond && \
# mv diamond /usr/bin/diamond && \
# diamond version
RUN wget https://dl.secondarymetabolites.org/releases/7.0.0/antismash-7.0.0.tar.gz \
&& tar -zxf antismash-7.0.0.tar.gz
RUN source activate py39 && pip install ./antismash-7.0.0
RUN source activate py39 && download-antismash-databases && antismash --check-prereqs
#RUN wget https://dl.secondarymetabolites.org/antismash-stretch.list -O /etc/apt/sources.list.d/antismash.list
#RUN wget -q -O- https://dl.secondarymetabolites.org/antismash.asc | sudo apt-key add -
#RUN apt-get update
#RUN apt-get install -y hmmer2 hmmer fasttree prodigal ncbi-blast+ muscle glimmerhmm
#RUN wget --quiet https://github.com/bbuchfink/diamond/releases/download/v2.0.9/diamond-linux64.tar.gz && \
# tar -zxf diamond-linux64.tar.gz diamond && \
# mv diamond /usr/bin/diamond && \
# diamond version
#WORKDIR /tmp
#RUN wget https://dl.secondarymetabolites.org/releases/6.0.0/antismash-6.0.0.tar.gz && tar -zxf antismash-6.0.0.tar.gz
#RUN sed -i 's/biopython >=1.78/biopython==1.76/' antismash-6.0.0/setup.py
#RUN sed -i 's/jinja2/jinja2==3.0.0/' antismash-6.0.0/setup.py
#RUN source activate py39 && pip install ./antismash-6.0.0
#RUN source activate py39 && download-antismash-databases
RUN pip install pandas
#===========
COPY . /kb/module
RUN mkdir -p /kb/module/work
RUN chmod -R a+rw /kb/module
WORKDIR /kb/module
RUN make all
ENTRYPOINT [ "./scripts/entrypoint.sh" ]
CMD [ ]