Dockerfile
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FROM alpine:latest
COPY . /RNANet
WORKDIR /
RUN apk update && apk add --no-cache \
curl \
freetype-dev \
gcc g++ \
linux-headers \
lapack-dev \
make \
musl-dev \
openblas-dev \
python3 python3-dev py3-pip py3-six py3-wheel \
py3-matplotlib py3-requests py3-scipy py3-setproctitle py3-sqlalchemy py3-tqdm \
sqlite \
\
&& python3 -m pip install biopython pandas psutil pymysql && \
\
wget -q -O /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub && \
wget https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.32-r0/glibc-2.32-r0.apk && \
apk add glibc-2.32-r0.apk && \
rm glibc-2.32-r0.apk && \
\
mkdir /3D && mkdir /sequences && \
\
mv /RNANet/scripts/x3dna-dssr /usr/local/bin/x3dna-dssr && chmod +x /usr/local/bin/x3dna-dssr && \
\
curl -SL http://eddylab.org/infernal/infernal-1.1.4.tar.gz | tar xz && cd infernal-1.1.4 && \
./configure && make -j 16 && make install && cd easel && make install && cd / && \
\
curl -SL https://github.com/epruesse/SINA/releases/download/v1.7.1/sina-1.7.1-linux.tar.gz | tar xz && mv sina-1.7.1-linux /sina && \
ln -s /sina/bin/sina /usr/local/bin/sina && \
\
rm -rf /infernal-1.1.4 && \
\
apk del openblas-dev gcc g++ gfortran binutils \
curl \
linux-headers \
make \
musl-dev \
py3-pip py3-wheel \
freetype-dev zlib-dev
RUN addgroup -S appgroup -g 1000 && \
adduser -S appuser -u 1000 -G appgroup && \
chown -R appuser:appgroup /3D && \
chown -R appuser:appgroup /sequences && \
mkdir /runDir && \
chown -R appuser:appgroup /runDir && \
chown -R appuser:appgroup /RNANet
USER appuser
VOLUME ["/3D", "/sequences", "/runDir"]
WORKDIR /runDir
ENTRYPOINT ["/RNANet/RNAnet.py", "--3d-folder", "/3D", "--seq-folder", "/sequences" ]