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Dockerfile
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Dockerfile
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# syntax=docker/dockerfile:1.3
# ====================================================================================
# NOTE this docker uses `--network=none` option for RUN directives, you need to either
# - activate BuildKit with `export DOCKER_BUILDKIT=1`
# - run this using buildx
# ====================================================================================
# NOTE the following must match the ENTRYPOINT
ARG install_path=/opt/V-dock
ARG vpipe_path=${install_path}/V-pipe
ARG envs_path=${install_path}/conda_envs
ARG test_data=/test-data
ARG virus_download_list
# HACK Snakemake v8 has breaking changes
ARG snaketag=v7.32.4
###
### Stage 0: download conda environments
###
FROM snakemake/snakemake:${snaketag} AS create-envs
ARG install_path
ARG vpipe_path
ARG envs_path
ARG test_data
# hadolint ignore=DL3008
RUN apt-get update && apt-get install -y --no-install-recommends \
jdupes
# TODO: only move workflow files
#COPY . ${vpipe_path}
WORKDIR ${vpipe_path}/
COPY LICENSE.md ./LICENSE.md
COPY workflow ./workflow
COPY resources ./resources
COPY config ./config
COPY utils ./utils
COPY init_project.sh ./init_project.sh
COPY tests/data ${test_data}
WORKDIR /work
# configuration: activate all steps
RUN mkdir config \
&& printf 'output:\n snv: true\n local: true\n global: true\n visualization: true\n diversity: true\n QA: true\n upload: true\nupload:\n orig_cram: true\n' > config/config.yaml \
&& printf 'output:\n trim_primers: true\n' > config/config-trim.yaml \
&& printf '{ }\n' > config/config-empty.yaml
# TODO harmonize list with CI tests and Docker tests
# hadolint ignore=SC2162,SC2034,SC2086
RUN for virus in ${virus_download_list:-$(ls ${test_data}/)}; do printf '\n\n\e[36;1mvirus: %s\e[0m\n' "${virus}" \
&& ln -sf "${test_data}/${virus}/" ./samples \
&& extra=config/config-extra.yaml \
&& if test -e samples/samples.tsv; then cp -f samples/samples.tsv config/samples.tsv \
&& while read s b l p o; do test -z "${p}" && continue; extra="config/config-trim.yaml ${extra}"; printf '\e[36m(with primers trimming)\e[0m\n'; break; done < config/samples.tsv; fi \
&& if test -e samples/config-extra.yaml; then cp -f samples/config-extra.yaml config/config-extra.yaml; printf '\e[36m(with extra config)\e[0m\n'; cat config/config-extra.yaml; else cp -f config/config-empty.yaml config/config-extra.yaml; fi \
&& printf 'config files: %s\n' "${extra}" \
&& PYTHONUNBUFFERED=1 snakemake -s ${vpipe_path}/workflow/Snakefile -j 1 --conda-create-envs-only --use-conda --conda-prefix ${envs_path} --configfile ${extra} --config "general={virus_base_config: ${virus}}" \
&& rm -f samples config/samples.tsv config/config-extra.yaml \
; done \
&& jdupes -Lr ${envs_path}/
###
### Stage 1: base layer with V-pipe and environments
###
FROM snakemake/snakemake:${snaketag} AS vpipe-tests-base
ARG install_path
# NOTE rsync only used with local scratch
# hadolint ignore=DL3008
RUN apt-get update && apt-get install -y --no-install-recommends \
rsync \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# NOTE V-pipe/envs/*.yaml and conda_prefix/* must be in sync so that env checksums match
COPY --from=create-envs ${install_path} ${install_path}
###
### Test 1: test the base layer with hiv
###
FROM vpipe-tests-base AS test_hiv
ARG install_path
ARG vpipe_path
ARG envs_path
ARG test_data
ENV virus=hiv
WORKDIR /work
# NOTE output must be last
RUN mkdir config \
&& printf 'upload:\n orig_cram: true\noutput:\n snv: true\n local: true\n global: false\n visualization: true\n diversity: true\n QA: true\n upload: true\n' > config/config.yaml \
&& printf '{ }\n' > config/config-empty.yaml
COPY --from=create-envs ${test_data}/${virus} ./samples
# hadolint ignore=SC2162,SC2034
RUN if test -e samples/samples.tsv; then cp -f samples/samples.tsv config/samples.tsv \
&& while read s b l p o; do test -z "${p}" && continue; printf ' trim_primers: true\n' >> config/config.yaml && printf '\n\n\e[36m(with primers trimming)\e[0m\n'; break; done < config/samples.tsv; fi
RUN if test -e samples/config-extra.yaml; then cp -f samples/config-extra.yaml config/config-extra.yaml; else cp config/config-empty.yaml config/config-extra.yaml; fi
# NOTE see top comment if `--network=none` breaks build process
RUN --network=none \
PYTHONUNBUFFERED=1 snakemake -s ${vpipe_path}/workflow/Snakefile -j 4 --use-conda --conda-prefix ${envs_path} --configfile config/config-extra.yaml --config "general={virus_base_config: ${virus}}" \
&& echo "$(date --iso-8601=sec ; grep -E 'failed|for error' .snakemake/log/*.snakemake.log)" > ${install_path}/${virus}.teststamp
###
### Test 2: test the base layer with sars-cov-2
###
FROM vpipe-tests-base AS test_sars-cov-2
ARG install_path
ARG vpipe_path
ARG envs_path
ARG test_data
ENV virus=sars-cov-2
WORKDIR /work
# NOTE output must be last
RUN mkdir config \
&& printf 'upload:\n orig_cram: true\noutput:\n snv: true\n local: true\n global: false\n visualization: true\n diversity: true\n QA: true\n upload: true\n' > config/config.yaml \
&& printf '{ }\n' > config/config-empty.yaml
COPY --from=create-envs ${test_data}/${virus} ./samples
# hadolint ignore=SC2162,SC2034
RUN if test -e samples/samples.tsv; then cp -f samples/samples.tsv config/samples.tsv \
&& while read s b l p o; do test -z "${p}" && continue; printf ' trim_primers: true\n' >> config/config.yaml && printf '\n\n\e[36m(with primers trimming)\e[0m\n'; break; done < config/samples.tsv; fi
RUN if test -e samples/config-extra.yaml; then cp -f samples/config-extra.yaml config/config-extra.yaml; else cp config/config-empty.yaml config/config-extra.yaml; fi
# NOTE see top comment if `--network=none` breaks build process
RUN --network=none \
PYTHONUNBUFFERED=1 snakemake -s ${vpipe_path}/workflow/Snakefile -j 4 --use-conda --conda-prefix ${envs_path} --configfile config/config-extra.yaml --config "general={virus_base_config: ${virus}}" \
&& echo "$(date --iso-8601=sec ; grep -E 'failed|for error' .snakemake/log/*.snakemake.log)" > ${install_path}/${virus}.teststamp
###
### Final base: gather tests
###
FROM vpipe-tests-base as vpipe-final-base
ARG install_path
# NOTE individual test can be forced using the following on github actions
COPY --from=test_hiv ${install_path}/hiv.teststamp ${install_path}
COPY --from=test_sars-cov-2 ${install_path}/sars-cov-2.teststamp ${install_path}
###
### Final stage: setup image ready to run
###
# =============================================
# NOTE this will *skip* tests on GitHub actions
#FROM vpipe-test-base
#ARG install_path
#ARG vpipe_path
#ARG envs_path
# ---------------------------------------------
# HACK this will *force* tests on GitHub actions
FROM snakemake/snakemake:${snaketag}
ARG install_path
ARG vpipe_path
ARG envs_path
# hadolint ignore=DL3008
RUN apt-get update && apt-get install -y --no-install-recommends \
rsync \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
COPY --from=vpipe-final-base ${install_path} ${install_path}
# =============================================
LABEL maintainer="V-pipe Dev Team <v-pipe@bsse.ethz.ch>"
VOLUME /work
WORKDIR /work
# NOTE current docker versions do not offer a way to bake the content of an ARG into an ENTRYPOINT
ENTRYPOINT [ \
"snakemake", \
"-s", "/opt/V-dock/V-pipe/workflow/Snakefile", \
"--use-conda", \
"--conda-prefix", "/opt/V-dock/conda_envs" \
]