Configuration¶

RolyPoly uses a configuration file (rpconfig.json) to store settings such as the data directory. This file is automatically updated when using rolypoly get-data. You can view or edit it manually if needed, it's located in the src/rolypoly/ directory.

Example configuration:

    {
    "ROLYPOLY_DATA": "/home/neri/projects/rolypoly/data/",
    "ROLYPOLY_TEST_DIR": "$RP_DIR/testing_folder/",
    "ROLYPOLY_REMIND_CITATIONS": "False"
    }

Environment variables should work. Note: I recommend using the get-data command to set up the initial configuration and download necessary resources. there's a fallback, if that path is missing, it checks a path relative to the rolypoly code directory.

Recommended setup command:

rolypoly get-data --rolypoly-data /path/to/rolypoly_data

Useful Tidbits¶

Silence citation reminders¶

RolyPoly citation reminder printing is controlled by the ROLYPOLY_REMIND_CITATIONS

{
    "ROLYPOLY_REMIND_CITATIONS": "False"
}

Notes: - "False" disables citation reminder output to the console. - "True" enables citation reminder output.

Enable debug logging for troubleshooting¶

Most commands expose a hidden log-level flag used heavily in tests and debugging.

Examples:

rolypoly filter-reads -i reads.fq -o out/ -ll DEBUG
rolypoly marker-search -i contigs.fasta -o marker_out/ -log-level DEBUG

Tip: if a command supports --log-file, set it explicitly so debug output is persisted in a predictable location.

Keep temporary/intermediate files¶

Many commands create temporary intermediates and remove them by default.

Use --keep-tmp when available to preserve those files for inspection:

rolypoly assemble -id filtered_reads/ -o assembly_out/ --keep-tmp
rolypoly filter-contigs -i contigs.fasta -d host.fasta --keep-tmp

Force a specific temp directory¶

Some commands allow overriding temp paths (for example, --temp-dir or --tmpdir). This is useful on HPC systems when you want local scratch I/O.

Examples:

rolypoly marker-search -i contigs.fasta -o marker_out/ --temp-dir /tmp/rp_marker_tmp
rolypoly mask-dna -i host.fasta -o host_masked.fasta --tmpdir /tmp/rp_mask_tmp

Overwrite existing output files¶

If the output path provided to a command exists, the commands may behave weird. to delete the existing output, use --overwrite .

skip-existing¶

If the output path provided to a command exists, some intermediary steps may be skipped if the output files appear to exist. This is useful for resuming a pipeline after an interruption. Note, it may require setting the same temp directory as before, and this is INCOMPATIBLE with --overwrite.

Override step parameters safely¶

Several pipeline-style commands support JSON overrides for internal tool parameters. This is useful for tuning without editing source code.

Example:

rolypoly filter-reads \
    -i reads.fq \
    -o filtered/ \
    --override-parameters '{"dedupe": {"passes": 2}, "trim_adapters": {"minlen": 55}}'