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Dockerfile
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FROM ubuntu:bionic
MAINTAINER Benjamin Viart and Claudio lorenzi
ENV TZ=Europe/Paris
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
less \
locales \
wget \
make build-essential gcc gawk \
ca-certificates \
python3-pip \
python3.7 \
python3-setuptools \
r-base r-base-core \
pymol \
&& rm -rf /var/lib/apt/lists/* && \
pip3 install --upgrade pip && \
pip3 install pdb-tools numpy==1.18.5 scipy==1.4.1 scikit-learn==0.24.1 \
pandas==1.1.3 pymoo==0.4.2.1 biopython==1.76 matplotlib==3.3.0 \
tensorflow==2.3.0 keras==2.4.3
## Includes a change of the makefile required for the installation ( https://sourceforge.net/p/fpocket/mailman/message/28785185/ )
RUN wget https://netix.dl.sourceforge.net/project/fpocket/fpocket2.tar.gz && \
tar -xzf fpocket2.tar.gz && \
cd ./fpocket2/ && \
awk '{ gsub(/\$\(LINKER\) \$\(LFLAGS\) \$\^ \-o \$@/, "$(LINKER) $^ -o $@ $(LFLAGS)"); print }' ./makefile > ./makefile.tmp && \
cat ./makefile.tmp && \
mv ./makefile.tmp ./makefile && \
make && \
make test && \
make install
RUN mkdir /stride && cd /stride && wget http://webclu.bio.wzw.tum.de/stride/stride.tar.gz && \
tar -zxf stride.tar.gz && make && mv ./stride /usr/bin/
COPY ./pickpocket /PickPocket/pickpocket
COPY ./data /PickPocket/data
RUN ln -s /PickPocket/pickpocket/pickPocket.py /usr/bin/pickPocket
WORKDIR /PickPocket
ENTRYPOINT ["pickPocket"]