zeeev / wham

Structural variant detection and association testing
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if the dirty build doesn't work on ubuntu, due to gcc issues, this docker approach worked for me #63

Closed sasidharPasupuleti closed 11 months ago

sasidharPasupuleti commented 11 months ago
# 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"]
sasidharPasupuleti commented 11 months ago

above dockerfile works as solution