# Use an official base image
FROM ubuntu:20.04
# Set the working directory
WORKDIR /app
# Set environment variables to avoid interaction during installation
ENV DEBIAN_FRONTEND=noninteractive
# Install necessary packages
RUN apt-get update && apt-get install -y \
build-essential \
cmake \
git \
libncurses5-dev \
zlib1g-dev \
vim
# Clone WHAM and its submodules
RUN git clone --recursive https://github.com/zeeev/wham.git /wham
# Modify bamtools_resolve.cpp
RUN cd /wham/src/bamtools/src/toolkit && \
sed -i 's/make_pair/pair/g' bamtools_resolve.cpp
# Change the working directory to /wham
WORKDIR /wham
# Execute make
RUN make
# Add /wham/bin to the PATH
ENV PATH=/wham/bin:$PATH
# Reset environment variable
ENV DEBIAN_FRONTEND=dialog
# Set the command to run the app
CMD ["bash"]