Dockerfile.snptest

# SPDX-License-Identifier: GPL-2.0
ARG BASE
FROM $BASE

# build-args
ARG BASE
ARG RUN_CMD
ARG BUILD_REPO

WORKDIR /runtime

ARG SNPTEST_URL="https://www.well.ox.ac.uk/~gav/resources/"
ARG SNPTEST_VER="snptest_v2.5.6"
ARG SNPTEST_ARCH="CentOS_Linux7.9.2009-x86_64_static"
ARG SNPTEST_TAR=${SNPTEST_VER}_${SNPTEST_ARCH}.tgz
ARG SNPTEST_DIR="/opt/bin"

RUN wget ${SNPTEST_URL}/${SNPTEST_TAR} && mkdir -p ${SNPTEST_DIR} && \
        tar xvf $SNPTEST_TAR --strip-components=1 -C ${SNPTEST_DIR} && \
        ln -s "${SNPTEST_DIR}/${SNPTEST_VER}" \
		"${SNPTEST_DIR}/${RUN_CMD}" && rm $SNPTEST_TAR
ENV PATH=${SNPTEST_DIR}:${PATH}

ARG TEST="/test.sh"
COPY --chmod=0555 src/test/$RUN_CMD.sh ${TEST}

ARG ENTRY="/entrypoint.sh"
RUN echo "#!/bin/bash" > ${ENTRY} && echo "$RUN_CMD \$@" >> ${ENTRY} && \
	chmod ugo+rx ${ENTRY}
ENTRYPOINT [ "/entrypoint.sh" ]

LABEL org.opencontainers.image.base.name="${BASE}"
LABEL org.opencontainers.image.description="SNPtest from https://www.well.ox.ac.uk/~gav/resources/"
LABEL org.opencontainers.image.url="${BUILD_REPO}"