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FROM python:3.9-bullseye
## Install sudo
RUN apt-get update && \
apt-get install -y sudo
## Set timezone
RUN echo America/New_York | sudo tee /etc/timezone && \
sudo dpkg-reconfigure --frontend noninteractive tzdata
ENV DEBIAN_FRONTEND noninteractive
## Install base dependencies
RUN sudo apt-get update && \
sudo apt-get dist-upgrade -y && \
sudo apt-get -y autoremove && \
sudo apt-get install -y \
build-essential \
software-properties-common \
libcurl4-openssl-dev \
git \
make \
cmake \
gcc-9 \
g++-9
## Clone GitHub repo
RUN mkdir -p /app
WORKDIR /app
RUN git clone https://github.com/bailey-lab/SeekDeep
WORKDIR /app/SeekDeep
## Run SeekDeep Setup
RUN ./setup.py --libs cmake:3.7.2 --symlinkBin
RUN echo "" >> ~/.profile && echo "#Add SeekDeep bin to your path" >> ~/.profile && echo "export PATH=\"$(pwd)/bin:\$PATH\"" >> ~/.profile
RUN . ~/.profile
RUN ./setup.py --addBashCompletion
RUN ./install.sh 7
RUN export PATH=/app/SeekDeep/bin/:$PATH && \
ln -s /app/SeekDeep/bin/SeekDeep /usr/bin/
## Add other tools
RUN ./setup.py --symlinkBin --overWrite
RUN sudo apt install -y \
bowtie2 \
muscle \
samtools
## Expose Ports
EXPOSE 9881
# 8000 22 3389