Dockerfile

ARG GFASTATS_VER=1.3.7

FROM ubuntu:jammy as app

ARG GFASTATS_VER

LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="gfastats"
LABEL software.version=${GFASTATS_VER}
LABEL description="The swiss army knife for genome assembly."
LABEL website="https://github.com/vgl-hub/gfastats"
LABEL license="https://github.com/vgl-hub/gfastats/blob/main/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="eriny@utah.gov"

RUN apt-get update && apt-get install -y --no-install-recommends \
  ca-certificates \
  procps \
  wget \
  make \
  g++ \
  zlib1g-dev \
  unzip && \
  apt-get autoclean && rm -rf /var/lib/apt/lists/*

WORKDIR /usr/local/bin

RUN wget -q https://github.com/vgl-hub/gfastats/releases/download/v${GFASTATS_VER}/gfastats.v${GFASTATS_VER}-linux.zip && \
  unzip gfastats.v${GFASTATS_VER}-linux.zip && \
  rm gfastats.v${GFASTATS_VER}-linux.zip && \
  chmod +x gfastats

ENV PATH="$PATH" \
  LC_ALL=C

CMD gfastats --help

WORKDIR /data

FROM app as test

ARG GFASTATS_VER

WORKDIR /test

RUN gfastats --help && gfastats --version

RUN wget -q https://github.com/vgl-hub/gfastats/archive/refs/tags/v${GFASTATS_VER}.tar.gz && \
  tar -xvf v${GFASTATS_VER}.tar.gz

RUN gfastats gfastats-${GFASTATS_VER}/testFiles/random1.fasta -o gfa && \
  gfastats gfastats-${GFASTATS_VER}/testFiles/random2.gfa2 && \
  gfastats gfastats-${GFASTATS_VER}/testFiles/random1.fasta -k gfastats-${GFASTATS_VER}/testFiles/random1.instructions.sak -o gfa && \
  gfastats --tabular --seq-report gfastats-${GFASTATS_VER}/testFiles/random6.circular.gfa