pante.Dockerfile

ARG IMAGE
ARG BEDTOOLS_IMAGE
ARG DECIPHER_IMAGE
ARG EAHELITRON_IMAGE
ARG GENOMETOOLS_IMAGE
ARG GFFPAL_IMAGE
ARG HMMER3_IMAGE
ARG INFERNAL_IMAGE
ARG MITEFINDER_IMAGE
ARG MMSEQS_IMAGE
ARG PYTHON3_IMAGE
ARG OCCULTERCUT_IMAGE
ARG REPEATMASKER_IMAGE
ARG RMBLAST_IMAGE
ARG TRNASCAN_IMAGE
ARG VSEARCH_IMAGE

FROM "${BEDTOOLS_IMAGE}" as bedtools_builder
FROM "${DECIPHER_IMAGE}" as decipher_builder
FROM "${EAHELITRON_IMAGE}" as eahelitron_builder
FROM "${GENOMETOOLS_IMAGE}" as genometools_builder
FROM "${GFFPAL_IMAGE}" as gffpal_builder
FROM "${HMMER3_IMAGE}" as hmmer3_builder
FROM "${INFERNAL_IMAGE}" as infernal_builder
FROM "${MITEFINDER_IMAGE}" as mitefinder_builder
FROM "${MMSEQS_IMAGE}" as mmseqs_builder
FROM "${OCCULTERCUT_IMAGE}" as occultercut_builder
FROM "${PYTHON3_IMAGE}" as python3_builder
FROM "${REPEATMASKER_IMAGE}" as repeatmasker_builder
FROM "${RMBLAST_IMAGE}" as rmblast_builder
FROM "${TRNASCAN_IMAGE}" as trnascan_builder
FROM "${VSEARCH_IMAGE}" as vsearch_builder

FROM "${IMAGE}"

ARG BEDTOOLS_VERSION
ARG BEDTOOLS_PREFIX_ARG
ENV BEDTOOLS_PREFIX="${BEDTOOLS_PREFIX_ARG}"

LABEL bedtools.version="${BEDTOOLS_VERSION}"

ENV PATH "${BEDTOOLS_PREFIX}/bin:${PATH}"

COPY --from=bedtools_builder "${BEDTOOLS_PREFIX}" "${BEDTOOLS_PREFIX}"
COPY --from=bedtools_builder "${APT_REQUIREMENTS_FILE}" /build/apt/bedtools.txt


ARG DECIPHER_VERSION
ARG DECIPHER_PREFIX_ARG
ENV DECIPHER_PREFIX="${DECIPHER_PREFIX_ARG}"
LABEL decipher.version="${DECIPHER_VERSION}"

ENV R_LIBS_USER="${DECIPHER_PREFIX}:${R_LIBS_USER:-}"

COPY --from=decipher_builder "${DECIPHER_PREFIX}" "${DECIPHER_PREFIX}"
COPY --from=decipher_builder "${APT_REQUIREMENTS_FILE}" /build/apt/decipher.txt

ARG EAHELITRON_COMMIT
ARG EAHELITRON_PREFIX_ARG
ENV EAHELITRON_PREFIX="${EAHELITRON_PREFIX_ARG}"
LABEL eahelitron.version="${EAHELITRON_COMMIT}"

ENV PATH="${EAHELITRON_PREFIX}/bin:${PATH}"

COPY --from=eahelitron_builder "${EAHELITRON_PREFIX}" "${EAHELITRON_PREFIX}"
COPY --from=eahelitron_builder "${APT_REQUIREMENTS_FILE}" /build/apt/eahelitron.txt

ARG GENOMETOOLS_VERSION
ARG GENOMETOOLS_PREFIX_ARG
ENV GENOMETOOLS_PREFIX="${GENOMETOOLS_PREFIX_ARG}"

LABEL genometools.version="${GENOMETOOLS_VERSION}"

ENV PATH="${GENOMETOOLS_PREFIX}/bin:${PATH}"
ENV INCLUDE="${GENOMETOOLS_PREFIX}/include:${INCLUDE}"
ENV CPATH="${GENOMETOOLS_PREFIX}/include:${CPATH}"
ENV LIBRARY_PATH="${GENOMETOOLS_PREFIX}/lib:${LIBRARY_PATH}"
ENV LD_LIBRARY_PATH="${GENOMETOOLS_PREFIX}/lib:${LD_LIBRARY_PATH}"
ENV LD_RUN_PATH="${GENOMETOOLS_PREFIX}/lib:${LD_RUN_PATH}"

COPY --from=genometools_builder "${GENOMETOOLS_PREFIX}" "${GENOMETOOLS_PREFIX}"
COPY --from=genometools_builder "${APT_REQUIREMENTS_FILE}" /build/apt/genometools.txt


ARG GFFPAL_COMMIT
ARG GFFPAL_PREFIX_ARG
ENV GFFPAL_PREFIX="${GFFPAL_PREFIX_ARG}"
LABEL gffpal.version="${GFFPAL_COMMIT}"

ENV PATH "${GFFPAL_PREFIX}/bin:${PATH}"
ENV PYTHONPATH "${GFFPAL_PREFIX}/lib/python3.7/site-packages:${PYTHONPATH}"

COPY --from=gffpal_builder "${GFFPAL_PREFIX}" "${GFFPAL_PREFIX}"
COPY --from=gffpal_builder "${APT_REQUIREMENTS_FILE}" /build/apt/gffpal.txt


ARG HMMER3_VERSION
ARG HMMER3_PREFIX_ARG
ENV HMMER3_PREFIX="${HMMER3_PREFIX_ARG}"

ENV PATH="${HMMER3_PREFIX}/bin:${PATH}"

LABEL hmmer3.version="${HMMER3_VERSION}"

COPY --from=hmmer3_builder "${HMMER3_PREFIX}" "${HMMER3_PREFIX}"
COPY --from=hmmer3_builder "${APT_REQUIREMENTS_FILE}" /build/apt/hmmer3.txt


ARG INFERNAL_VERSION
ARG INFERNAL_PREFIX_ARG
ENV INFERNAL_PREFIX="${INFERNAL_PREFIX_ARG}"
LABEL infernal.version="${INFERNAL_VERSION}"

ENV PATH="${INFERNAL_PREFIX}/bin:${PATH}"

COPY --from=infernal_builder "${INFERNAL_PREFIX}" "${INFERNAL_PREFIX}"
COPY --from=infernal_builder "${APT_REQUIREMENTS_FILE}" /build/apt/infernal.txt


ARG MITEFINDER_COMMIT
ARG MITEFINDER_PREFIX_ARG
ENV MITEFINDER_PREFIX="${MITEFINDER_PREFIX_ARG}"

ENV MITEFINDER_PROFILE="${MITEFINDER_PREFIX}/profile/pattern_scoring.txt"
ENV PATH="${MITEFINDER_PREFIX}/bin:${PATH}"

LABEL mitefinder.version = "${MITEFINDER_COMMIT}"

COPY --from=mitefinder_builder "${MITEFINDER_PREFIX}" "${MITEFINDER_PREFIX}"
COPY --from=mitefinder_builder "${APT_REQUIREMENTS_FILE}" /build/apt/mitefinder.txt


ARG MMSEQS_TAG
ARG MMSEQS_PREFIX_ARG
ENV MMSEQS_PREFIX="${MMSEQS_PREFIX_ARG}"
LABEL mmseqs.version="${MMSEQS_TAG}"

ENV PATH="${MMSEQS_PREFIX}/bin:${PATH}"

COPY --from=mmseqs_builder "${MMSEQS_PREFIX}" "${MMSEQS_PREFIX}"
COPY --from=mmseqs_builder "${APT_REQUIREMENTS_FILE}" /build/apt/mmseqs.txt


ARG OCCULTERCUT_VERSION
ARG OCCULTERCUT_PREFIX_ARG
ENV OCCULTERCUT_PREFIX="${OCCULTERCUT_PREFIX_ARG}"
LABEL occultercut.version="${OCCULTERCUT_VERSION}"

ENV PATH="${OCCULTERCUT_PREFIX}/bin:${PATH}"

COPY --from=occultercut_builder "${OCCULTERCUT_PREFIX}" "${OCCULTERCUT_PREFIX}"
COPY --from=occultercut_builder "${APT_REQUIREMENTS_FILE}" /build/apt/occultercut.txt


COPY --from=python3_builder "${APT_REQUIREMENTS_FILE}" /build/apt/python3.txt


ARG TRF_VERSION
ARG TRF_PREFIX_ARG
ENV TRF_PREFIX="${TRF_PREFIX_ARG}"
LABEL trf.version="${TRF_VERSION}"

COPY --from=repeatmasker_builder "${TRF_PREFIX}" "${TRF_PREFIX}"
ENV PATH="${TRF_PREFIX}/bin:${PATH}"

ARG NSEG_PREFIX_ARG
ENV NSEG_PREFIX="${NSEG_PREFIX_ARG}"
ENV PATH="${NSEG_PREFIX}/bin:${PATH}"
LABEL nseg.version="${NSEG_VERSION}"

COPY --from=repeatmasker_builder "${NSEG_PREFIX}" "${NSEG_PREFIX}"

ARG REPEATSCOUT_VERSION
ARG REPEATSCOUT_PREFIX_ARG
ENV REPEATSCOUT_PREFIX="${REPEATSCOUT_PREFIX_ARG}"
LABEL repeatscout.version="${REPEATSCOUT_VERSION}"

ENV PATH="${REPEATSCOUT_PREFIX}/bin:${PATH}"

COPY --from=repeatmasker_builder "${REPEATSCOUT_PREFIX}" "${REPEATSCOUT_PREFIX}"


ARG RECON_VERSION
ARG RECON_PREFIX_ARG
ENV RECON_PREFIX="${RECON_PREFIX_ARG}"
LABEL recon.version="${RECON_VERSION}"

ENV PATH="${RECON_PREFIX}/bin:${RECON_PREFIX}/scripts:${PATH}"

COPY --from=repeatmasker_builder "${RECON_PREFIX}" "${RECON_PREFIX}"


ARG RMASK_VERSION
ARG RMASK_URL
ARG RMASK_PREFIX_ARG
ENV RMASK_PREFIX="${RMASK_PREFIX_ARG}"
LABEL repeatmasker.version="${RMASK_VERSION}"

ARG RM_LIB_ARG="/data/rmlib"
ENV RM_LIB="${RM_LIB_ARG}"

COPY --from=repeatmasker_builder "${RMASK_PREFIX}" "${RMASK_PREFIX}"

ARG RMOD_VERSION
ARG RMOD_URL
ARG RMOD_PREFIX_ARG
ENV RMOD_PREFIX="${RMOD_PREFIX_ARG}"
LABEL repeatmodeler.version="${RMOD_VERSION}"

COPY --from=repeatmasker_builder "${RMOD_PREFIX}" "${RMOD_PREFIX}"

COPY --from=repeatmasker_builder "${APT_REQUIREMENTS_FILE}" /build/apt/repeatmasker.txt
ENV PATH="${RMASK_PREFIX}:${RMASK_PREFIX}/util:${RMOD_PREFIX}:${RMOD_PREFIX}/util:${PATH}"


ARG RMBLAST_VERSION
ARG RMBLAST_PREFIX_ARG
ENV RMBLAST_PREFIX="${RMBLAST_PREFIX_ARG}"

ENV PATH="${RMBLAST_PREFIX}/bin:${PATH}"
ENV CPATH="${RMBLAST_PREFIX}/include"
ENV LIBRARY_PATH="${RMBLAST_PREFIX}/lib:${LIBRARY_PATH}"
ENV LD_LIBRARY_PATH="${RMBLAST_PREFIX}/lib:${LD_LIBRARY_PATH}"

LABEL rmblast.version="${RMBLAST_VERSION}"

COPY --from=rmblast_builder "${RMBLAST_PREFIX}" "${RMBLAST_PREFIX}"
COPY --from=rmblast_builder "${APT_REQUIREMENTS_FILE}" /build/apt/rmblast.txt


ARG TRNASCAN_VERSION
ARG TRNASCAN_PREFIX_ARG
ENV TRNASCAN_PREFIX="${TRNASCAN_PREFIX_ARG}"
LABEL trnascan.version="${TRNASCAN_VERSION}"

ENV PATH="${TRNASCAN_PREFIX}/bin:${PATH}"
ENV INCLUDE="${TRNASCAN_PREFIX}/include:${INCLUDE}"
ENV CPATH="${TRNASCAN_PREFIX}/include:${CPATH}"
ENV LIBRARY_PATH="${TRNASCAN_PREFIX}/lib:${LIBRARY_PATH}"
ENV LD_LIBRARY_PATH="${TRNASCAN_PREFIX}/lib:${LD_LIBRARY_PATH}"
ENV LD_RUN_PATH="${TRNASCAN_PREFIX}/lib:${LD_RUN_PATH}"

COPY --from=trnascan_builder "${TRNASCAN_PREFIX}" "${TRNASCAN_PREFIX}"
COPY --from=trnascan_builder "${APT_REQUIREMENTS_FILE}" /build/apt/trnascan.txt


ARG VSEARCH_VERSION
ARG VSEARCH_PREFIX_ARG
ENV VSEARCH_PREFIX="${VSEARCH_PREFIX_ARG}"

ENV PATH="${VSEARCH_PREFIX}/bin:${PATH}"

LABEL vsearch.version="${VSEARCH_VERSION}"

COPY --from=vsearch_builder "${VSEARCH_PREFIX}" "${VSEARCH_PREFIX}"
COPY --from=vsearch_builder "${APT_REQUIREMENTS_FILE}" /build/apt/vsearch.txt


RUN  set -eu \
  && DEBIAN_FRONTEND=noninteractive \
  && . /build/base.sh \
  && apt-get update \
  && apt_install_from_file /build/apt/*.txt \
  && rm -rf /var/lib/apt/lists/* \
  && cat /build/apt/*.txt >> "${APT_REQUIREMENTS_FILE}"