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Dockerfile
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FROM ubuntu:22.04 AS build
# Install build dependencies
RUN apt-get update && apt-get install -y \
build-essential \
git \
wget \
ca-certificates \
tar \
gzip \
autoconf \
libhts-dev \
&& rm -rf /var/lib/apt/lists/* \
mkdir /app
# Clone the repository
WORKDIR /app
RUN wget https://github.com/andersen-lab/ivar/archive/refs/tags/v1.4.3.tar.gz \
&& tar xvzf v1.4.3.tar.gz
# Build the project
WORKDIR /app/ivar-1.4.3/
RUN ./autogen.sh \
&& ./configure \
&& make
# Clone the repository
WORKDIR /app
RUN git clone https://github.com/nexomis/loose_ends.git
# Build the project
WORKDIR /app/loose_ends
RUN make
# Stage 2: Final
FROM ubuntu:22.04
# Install runtime dependencies
RUN export DEBIAN_FRONTEND=noninteractive \
&& apt-get update \
&& apt-get -y install --no-install-recommends \
libstdc++6 \
libc6 \
libhts3 \
samtools \
&& rm -rf /var/lib/apt/lists/*
# Copy the built executable from the build stage
COPY --from=build /app/loose_ends/loose_ends /usr/local/bin/loose_ends
COPY --from=build /app/ivar-1.4.3/src/ivar /usr/local/bin/ivar