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.

To view or modify the configuration:

Locate rpconfig.json in src/rolypoly/.
Open the file with a text editor.
Modify the settings as needed.
Save the file.

Example configuration:

{
        "ROLYPOLY_DATA": "/clusterfs/jgi/scratch/science/metagen/neri/projects/rolypoly/data/"
}

Note: It's recommended to use the get-data command to set up the initial configuration and download necessary resources.

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 value in rpconfig.json.

Use string values ("True" / "False"):

{
    "ROLYPOLY_DATA": "/path/to/rolypoly_data",
    "ROLYPOLY_REMIND_CITATIONS": "False"
}

Notes:

"False" disables citation reminder output to the console.
"True" enables citation reminder output.
For normal CLI use, rpconfig.json is the source of truth because RolyPoly reads it at startup and exports these values into the process environment.

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/ -ll 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

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}}'

Tip: keep JSON keys aligned to the command's documented step names.