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lines changed Original file line number Diff line number Diff line change @@ -49,7 +49,7 @@ RUN conda env update -n base -f envs/hamronization_workflow.yaml
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RUN snakemake --configfile test/test_config.yaml --use-conda --conda-cleanup-pkgs cache --jobs 1 --conda-create-envs-only
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# make Snakemake install the the non-conda binary deps (but not the databases)
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- RUN snakemake --configfile test/test_config.yaml --use-conda --conda-cleanup-pkgs cache --jobs 1 bindeps/resistomeanalyzer/ resistome bindeps/rarefactionanalyzer/ rarefaction bindeps/snpfinder /snpfinder
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+ RUN snakemake --configfile test/test_config.yaml --use-conda --conda-cleanup-pkgs cache --jobs 1 bindeps/resistome bindeps/rarefaction bindeps/snpfinder
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# this maiden run pulls all databases in, thus finalising the self-contained image
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RUN snakemake --configfile test/test_config.yaml --use-conda --conda-cleanup-pkgs cache --jobs 1 results/hamronized_report.tsv && \
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