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> Note: This command should be run in the directory containing the GL_RefAnnotTable-A_1.1.0 folder downloaded in [step 2](#2-download-the-workflow-files). Depending on your network speed, this may take approximately 20 minutes.
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Once complete, an apptainer folder containing the Apptainer images will be created. Export this folder as an Apptainer configuration environment variable:
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Once complete, an apptainer folder containing the Apptainer image will be created. Export this folder as an Apptainer configuration environment variable:
- Specify the target organism using a positional command line argument. `Mus musculus` is used in the example above.
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- To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments. The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
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- No input files are required. Specify the target organism using a positional command line argument. `Mus musculus` is used in the example above. To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments. The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
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- Optional: a reference table CSV can be supplied as a second positional argument instead of using the default [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
- No input files are required. Specify the target organism using a positional command line argument. `Mus musculus` is used in the example above. To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments. The correct argument for each organism can also be found in the 'species' column of [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
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- No input files are required. Specify the target organism using a positional command line argument. `Mus musculus` is used in the example above. To see a list of all available organisms, run `Rscript GL-DPPD-7110-A_build-genome-annots-tab.R` without positional arguments. The correct argument for each organism can also be found in the 'species' column of the [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
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- Optional: a reference table CSV can be supplied as a second positional argument instead of using the default [GL-DPPD-7110-A_annotations.csv](../../Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv)
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