zeeev / wham

Structural variant detection and association testing

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

if the dirty build doesn't work on ubuntu, due to gcc issues, this docker approach worked for me

sasidharPasupuleti opened this issue · comments

# 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"]

above dockerfile works as solution